diff --git a/README.txt b/README.txt index 0067857c..b440d7e2 100644 --- a/README.txt +++ b/README.txt @@ -5,7 +5,7 @@ $Rev$ This file is part of Simulation Core Library, a Java-based library for efficient numerical simulation of biological models. - Copyright (C) 2007-2013 jointly by the following organizations: + Copyright (C) 2007-2012 jointly by the following organizations: 1. University of Tuebingen, Germany 2. Keio University, Japan 3. 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doc/api/version_1.1/org/simulator/sedml/package-use.html diff --git a/doc/web/version_1.1/overview-frame.html b/doc/api/version_1.1/overview-frame.html similarity index 100% rename from doc/web/version_1.1/overview-frame.html rename to doc/api/version_1.1/overview-frame.html diff --git a/doc/web/version_1.1/overview-summary.html b/doc/api/version_1.1/overview-summary.html similarity index 100% rename from doc/web/version_1.1/overview-summary.html rename to doc/api/version_1.1/overview-summary.html diff --git a/doc/web/version_1.1/overview-tree.html b/doc/api/version_1.1/overview-tree.html similarity index 100% rename from doc/web/version_1.1/overview-tree.html rename to doc/api/version_1.1/overview-tree.html diff --git a/doc/web/version_1.1/package-list b/doc/api/version_1.1/package-list similarity index 100% rename from doc/web/version_1.1/package-list rename to doc/api/version_1.1/package-list diff --git a/doc/web/version_1.1/resources/inherit.gif b/doc/api/version_1.1/resources/inherit.gif similarity index 100% rename from doc/web/version_1.1/resources/inherit.gif rename to doc/api/version_1.1/resources/inherit.gif diff --git a/doc/web/version_1.1/serialized-form.html b/doc/api/version_1.1/serialized-form.html similarity index 100% rename from doc/web/version_1.1/serialized-form.html rename to doc/api/version_1.1/serialized-form.html diff --git a/doc/web/version_1.1/stylesheet.css b/doc/api/version_1.1/stylesheet.css similarity index 100% rename from doc/web/version_1.1/stylesheet.css rename to doc/api/version_1.1/stylesheet.css diff --git a/doc/web/version_1.2/allclasses-frame.html b/doc/api/version_1.2/allclasses-frame.html similarity index 98% rename from doc/web/version_1.2/allclasses-frame.html rename to doc/api/version_1.2/allclasses-frame.html index 0cbcad0a..94cb5ae4 100644 --- a/doc/web/version_1.2/allclasses-frame.html +++ b/doc/api/version_1.2/allclasses-frame.html @@ -2,12 +2,12 @@ - + All Classes - + diff --git a/doc/web/version_1.2/allclasses-noframe.html b/doc/api/version_1.2/allclasses-noframe.html similarity index 98% rename from doc/web/version_1.2/allclasses-noframe.html rename to doc/api/version_1.2/allclasses-noframe.html index 7cf58677..eb072989 100644 --- a/doc/web/version_1.2/allclasses-noframe.html +++ b/doc/api/version_1.2/allclasses-noframe.html @@ -2,12 +2,12 @@ - + All Classes - + diff --git a/doc/web/version_1.2/constant-values.html b/doc/api/version_1.2/constant-values.html similarity index 99% rename from doc/web/version_1.2/constant-values.html rename to doc/api/version_1.2/constant-values.html index cdacdb82..e90f87f3 100644 --- a/doc/web/version_1.2/constant-values.html +++ b/doc/api/version_1.2/constant-values.html @@ -2,12 +2,12 @@ - + Constant Field Values - + @@ -433,7 +433,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/deprecated-list.html b/doc/api/version_1.2/deprecated-list.html similarity index 97% rename from doc/web/version_1.2/deprecated-list.html rename to doc/api/version_1.2/deprecated-list.html index 22d27d47..aed81eb4 100644 --- a/doc/web/version_1.2/deprecated-list.html +++ b/doc/api/version_1.2/deprecated-list.html @@ -2,12 +2,12 @@ - + Deprecated List - + @@ -111,7 +111,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/help-doc.html b/doc/api/version_1.2/help-doc.html similarity index 98% rename from doc/web/version_1.2/help-doc.html rename to doc/api/version_1.2/help-doc.html index 86e907fe..aaf015fd 100644 --- a/doc/web/version_1.2/help-doc.html +++ b/doc/api/version_1.2/help-doc.html @@ -2,12 +2,12 @@ - + API Help - + @@ -188,7 +188,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-1.html b/doc/api/version_1.2/index-files/index-1.html similarity index 99% rename from doc/web/version_1.2/index-files/index-1.html rename to doc/api/version_1.2/index-files/index-1.html index a554632c..86fd46ff 100644 --- a/doc/web/version_1.2/index-files/index-1.html +++ b/doc/api/version_1.2/index-files/index-1.html @@ -2,12 +2,12 @@ - + A-Index - + @@ -302,7 +302,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-10.html b/doc/api/version_1.2/index-files/index-10.html similarity index 98% rename from doc/web/version_1.2/index-files/index-10.html rename to doc/api/version_1.2/index-files/index-10.html index 26dd119a..5f3c710f 100644 --- a/doc/web/version_1.2/index-files/index-10.html +++ b/doc/api/version_1.2/index-files/index-10.html @@ -2,12 +2,12 @@ - + K-Index - + @@ -116,7 +116,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-11.html b/doc/api/version_1.2/index-files/index-11.html similarity index 98% rename from doc/web/version_1.2/index-files/index-11.html rename to doc/api/version_1.2/index-files/index-11.html index 54987520..45ae93fa 100644 --- a/doc/web/version_1.2/index-files/index-11.html +++ b/doc/api/version_1.2/index-files/index-11.html @@ -2,12 +2,12 @@ - + L-Index - + @@ -167,7 +167,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-12.html b/doc/api/version_1.2/index-files/index-12.html similarity index 99% rename from doc/web/version_1.2/index-files/index-12.html rename to doc/api/version_1.2/index-files/index-12.html index f8b6bd9c..835b6b4a 100644 --- a/doc/web/version_1.2/index-files/index-12.html +++ b/doc/api/version_1.2/index-files/index-12.html @@ -2,12 +2,12 @@ - + M-Index - + @@ -200,7 +200,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-13.html b/doc/api/version_1.2/index-files/index-13.html similarity index 98% rename from doc/web/version_1.2/index-files/index-13.html rename to doc/api/version_1.2/index-files/index-13.html index 2eea8202..22ff29fe 100644 --- a/doc/web/version_1.2/index-files/index-13.html +++ b/doc/api/version_1.2/index-files/index-13.html @@ -2,12 +2,12 @@ - + N-Index - + @@ -140,7 +140,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-14.html b/doc/api/version_1.2/index-files/index-14.html similarity index 98% rename from doc/web/version_1.2/index-files/index-14.html rename to doc/api/version_1.2/index-files/index-14.html index 4c347920..b58c51f8 100644 --- a/doc/web/version_1.2/index-files/index-14.html +++ b/doc/api/version_1.2/index-files/index-14.html @@ -2,12 +2,12 @@ - + O-Index - + @@ -112,7 +112,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-15.html b/doc/api/version_1.2/index-files/index-15.html similarity index 99% rename from doc/web/version_1.2/index-files/index-15.html rename to doc/api/version_1.2/index-files/index-15.html index b78f8b19..fa82c32f 100644 --- a/doc/web/version_1.2/index-files/index-15.html +++ b/doc/api/version_1.2/index-files/index-15.html @@ -2,12 +2,12 @@ - + P-Index - + @@ -187,7 +187,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-16.html b/doc/api/version_1.2/index-files/index-16.html similarity index 98% rename from doc/web/version_1.2/index-files/index-16.html rename to doc/api/version_1.2/index-files/index-16.html index 1ecbe1b2..c0e3b7d0 100644 --- a/doc/web/version_1.2/index-files/index-16.html +++ b/doc/api/version_1.2/index-files/index-16.html @@ -2,12 +2,12 @@ - + Q-Index - + @@ -116,7 +116,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-17.html b/doc/api/version_1.2/index-files/index-17.html similarity index 99% rename from doc/web/version_1.2/index-files/index-17.html rename to doc/api/version_1.2/index-files/index-17.html index 2d80a204..23e360ed 100644 --- a/doc/web/version_1.2/index-files/index-17.html +++ b/doc/api/version_1.2/index-files/index-17.html @@ -2,12 +2,12 @@ - + R-Index - + @@ -251,7 +251,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-18.html b/doc/api/version_1.2/index-files/index-18.html similarity index 99% rename from doc/web/version_1.2/index-files/index-18.html rename to doc/api/version_1.2/index-files/index-18.html index b5e7b53d..52c295f3 100644 --- a/doc/web/version_1.2/index-files/index-18.html +++ b/doc/api/version_1.2/index-files/index-18.html @@ -2,12 +2,12 @@ - + S-Index - + @@ -405,7 +405,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-19.html b/doc/api/version_1.2/index-files/index-19.html similarity index 99% rename from doc/web/version_1.2/index-files/index-19.html rename to doc/api/version_1.2/index-files/index-19.html index 26849123..5ab36494 100644 --- a/doc/web/version_1.2/index-files/index-19.html +++ b/doc/api/version_1.2/index-files/index-19.html @@ -2,12 +2,12 @@ - + T-Index - + @@ -190,7 +190,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-2.html b/doc/api/version_1.2/index-files/index-2.html similarity index 97% rename from doc/web/version_1.2/index-files/index-2.html rename to doc/api/version_1.2/index-files/index-2.html index 78dfba13..91eaa66a 100644 --- a/doc/web/version_1.2/index-files/index-2.html +++ b/doc/api/version_1.2/index-files/index-2.html @@ -2,12 +2,12 @@ - + B-Index - + @@ -114,7 +114,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-20.html b/doc/api/version_1.2/index-files/index-20.html similarity index 98% rename from doc/web/version_1.2/index-files/index-20.html rename to doc/api/version_1.2/index-files/index-20.html index e7c4e0ec..f22bb05e 100644 --- a/doc/web/version_1.2/index-files/index-20.html +++ b/doc/api/version_1.2/index-files/index-20.html @@ -2,12 +2,12 @@ - + U-Index - + @@ -120,7 +120,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-21.html b/doc/api/version_1.2/index-files/index-21.html similarity index 98% rename from doc/web/version_1.2/index-files/index-21.html rename to doc/api/version_1.2/index-files/index-21.html index f5935b28..eb4a9996 100644 --- a/doc/web/version_1.2/index-files/index-21.html +++ b/doc/api/version_1.2/index-files/index-21.html @@ -2,12 +2,12 @@ - + V-Index - + @@ -148,7 +148,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-22.html b/doc/api/version_1.2/index-files/index-22.html similarity index 97% rename from doc/web/version_1.2/index-files/index-22.html rename to doc/api/version_1.2/index-files/index-22.html index 7761d984..60ce80aa 100644 --- a/doc/web/version_1.2/index-files/index-22.html +++ b/doc/api/version_1.2/index-files/index-22.html @@ -2,12 +2,12 @@ - + X-Index - + @@ -110,7 +110,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-23.html b/doc/api/version_1.2/index-files/index-23.html similarity index 97% rename from doc/web/version_1.2/index-files/index-23.html rename to doc/api/version_1.2/index-files/index-23.html index 5e63574e..9ed2ec53 100644 --- a/doc/web/version_1.2/index-files/index-23.html +++ b/doc/api/version_1.2/index-files/index-23.html @@ -2,12 +2,12 @@ - + Y-Index - + @@ -111,7 +111,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-24.html b/doc/api/version_1.2/index-files/index-24.html similarity index 97% rename from doc/web/version_1.2/index-files/index-24.html rename to doc/api/version_1.2/index-files/index-24.html index bb70df56..4c5602a8 100644 --- a/doc/web/version_1.2/index-files/index-24.html +++ b/doc/api/version_1.2/index-files/index-24.html @@ -2,12 +2,12 @@ - + Z-Index - + @@ -110,7 +110,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-3.html b/doc/api/version_1.2/index-files/index-3.html similarity index 99% rename from doc/web/version_1.2/index-files/index-3.html rename to doc/api/version_1.2/index-files/index-3.html index d5faf866..1e171319 100644 --- a/doc/web/version_1.2/index-files/index-3.html +++ b/doc/api/version_1.2/index-files/index-3.html @@ -2,12 +2,12 @@ - + C-Index - + @@ -431,7 +431,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-4.html b/doc/api/version_1.2/index-files/index-4.html similarity index 99% rename from doc/web/version_1.2/index-files/index-4.html rename to doc/api/version_1.2/index-files/index-4.html index e455b4b2..1fc6fa2f 100644 --- a/doc/web/version_1.2/index-files/index-4.html +++ b/doc/api/version_1.2/index-files/index-4.html @@ -2,12 +2,12 @@ - + D-Index - + @@ -190,7 +190,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-5.html b/doc/api/version_1.2/index-files/index-5.html similarity index 98% rename from doc/web/version_1.2/index-files/index-5.html rename to doc/api/version_1.2/index-files/index-5.html index e9cdd1c3..a5fe0075 100644 --- a/doc/web/version_1.2/index-files/index-5.html +++ b/doc/api/version_1.2/index-files/index-5.html @@ -2,12 +2,12 @@ - + E-Index - + @@ -172,7 +172,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-6.html b/doc/api/version_1.2/index-files/index-6.html similarity index 99% rename from doc/web/version_1.2/index-files/index-6.html rename to doc/api/version_1.2/index-files/index-6.html index 007d3f3d..258e0724 100644 --- a/doc/web/version_1.2/index-files/index-6.html +++ b/doc/api/version_1.2/index-files/index-6.html @@ -2,12 +2,12 @@ - + F-Index - + @@ -173,7 +173,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-7.html b/doc/api/version_1.2/index-files/index-7.html similarity index 99% rename from doc/web/version_1.2/index-files/index-7.html rename to doc/api/version_1.2/index-files/index-7.html index bb30581e..a0b53ee0 100644 --- a/doc/web/version_1.2/index-files/index-7.html +++ b/doc/api/version_1.2/index-files/index-7.html @@ -2,12 +2,12 @@ - + G-Index - + @@ -583,7 +583,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-8.html b/doc/api/version_1.2/index-files/index-8.html similarity index 98% rename from doc/web/version_1.2/index-files/index-8.html rename to doc/api/version_1.2/index-files/index-8.html index 5e4b83f4..ef26cee7 100644 --- a/doc/web/version_1.2/index-files/index-8.html +++ b/doc/api/version_1.2/index-files/index-8.html @@ -2,12 +2,12 @@ - + H-Index - + @@ -153,7 +153,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index-files/index-9.html b/doc/api/version_1.2/index-files/index-9.html similarity index 99% rename from doc/web/version_1.2/index-files/index-9.html rename to doc/api/version_1.2/index-files/index-9.html index 5f6418c9..84e77316 100644 --- a/doc/web/version_1.2/index-files/index-9.html +++ b/doc/api/version_1.2/index-files/index-9.html @@ -2,12 +2,12 @@ - + I-Index - + @@ -216,7 +216,7 @@ -Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/index.html b/doc/api/version_1.2/index.html similarity index 95% rename from doc/web/version_1.2/index.html rename to doc/api/version_1.2/index.html index 54245a7e..df90886d 100644 --- a/doc/web/version_1.2/index.html +++ b/doc/api/version_1.2/index.html @@ -2,7 +2,7 @@ - + Generated Documentation (Untitled) diff --git a/doc/web/version_1.2/javadoc-style.css b/doc/api/version_1.2/javadoc-style.css similarity index 100% rename from doc/web/version_1.2/javadoc-style.css rename to doc/api/version_1.2/javadoc-style.css diff --git a/doc/web/version_1.2/org/simulator/About.html b/doc/api/version_1.2/org/simulator/About.html similarity index 98% rename from doc/web/version_1.2/org/simulator/About.html rename to doc/api/version_1.2/org/simulator/About.html index f696283e..8d50ccf9 100644 --- a/doc/web/version_1.2/org/simulator/About.html +++ b/doc/api/version_1.2/org/simulator/About.html @@ -2,12 +2,12 @@ - + About - + @@ -223,7 +223,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/SBMLTestSuiteRunner.html b/doc/api/version_1.2/org/simulator/SBMLTestSuiteRunner.html similarity index 99% rename from doc/web/version_1.2/org/simulator/SBMLTestSuiteRunner.html rename to doc/api/version_1.2/org/simulator/SBMLTestSuiteRunner.html index 712c072a..da8ec200 100644 --- a/doc/web/version_1.2/org/simulator/SBMLTestSuiteRunner.html +++ b/doc/api/version_1.2/org/simulator/SBMLTestSuiteRunner.html @@ -2,12 +2,12 @@ - + SBMLTestSuiteRunner - + @@ -454,7 +454,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/SBMLTestSuiteWrapper.html b/doc/api/version_1.2/org/simulator/SBMLTestSuiteWrapper.html similarity index 98% rename from doc/web/version_1.2/org/simulator/SBMLTestSuiteWrapper.html rename to doc/api/version_1.2/org/simulator/SBMLTestSuiteWrapper.html index ad76e55e..90b8e0b2 100644 --- a/doc/web/version_1.2/org/simulator/SBMLTestSuiteWrapper.html +++ b/doc/api/version_1.2/org/simulator/SBMLTestSuiteWrapper.html @@ -2,12 +2,12 @@ - + SBMLTestSuiteWrapper - + @@ -103,7 +103,7 @@

Version:
-
$Rev: 337 $
+
$Rev: 333 $
Author:
Roland Keller
@@ -262,7 +262,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/SimulatorTest.html b/doc/api/version_1.2/org/simulator/SimulatorTest.html similarity index 98% rename from doc/web/version_1.2/org/simulator/SimulatorTest.html rename to doc/api/version_1.2/org/simulator/SimulatorTest.html index 708e331f..d55583dc 100644 --- a/doc/web/version_1.2/org/simulator/SimulatorTest.html +++ b/doc/api/version_1.2/org/simulator/SimulatorTest.html @@ -2,12 +2,12 @@ - + SimulatorTest - + @@ -236,7 +236,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/TestBiomodels.html b/doc/api/version_1.2/org/simulator/TestBiomodels.html similarity index 99% rename from doc/web/version_1.2/org/simulator/TestBiomodels.html rename to doc/api/version_1.2/org/simulator/TestBiomodels.html index 7dbfc6a3..989d6a10 100644 --- a/doc/web/version_1.2/org/simulator/TestBiomodels.html +++ b/doc/api/version_1.2/org/simulator/TestBiomodels.html @@ -2,12 +2,12 @@ - + TestBiomodels - + @@ -268,7 +268,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/class-use/About.html b/doc/api/version_1.2/org/simulator/class-use/About.html similarity index 97% rename from doc/web/version_1.2/org/simulator/class-use/About.html rename to doc/api/version_1.2/org/simulator/class-use/About.html index cb807b55..070473e2 100644 --- a/doc/web/version_1.2/org/simulator/class-use/About.html +++ b/doc/api/version_1.2/org/simulator/class-use/About.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.About - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/class-use/SBMLTestSuiteRunner.html b/doc/api/version_1.2/org/simulator/class-use/SBMLTestSuiteRunner.html similarity index 97% rename from doc/web/version_1.2/org/simulator/class-use/SBMLTestSuiteRunner.html rename to doc/api/version_1.2/org/simulator/class-use/SBMLTestSuiteRunner.html index bd9f6f47..0d47dedc 100644 --- a/doc/web/version_1.2/org/simulator/class-use/SBMLTestSuiteRunner.html +++ b/doc/api/version_1.2/org/simulator/class-use/SBMLTestSuiteRunner.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.SBMLTestSuiteRunner - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/class-use/SBMLTestSuiteWrapper.html b/doc/api/version_1.2/org/simulator/class-use/SBMLTestSuiteWrapper.html similarity index 97% rename from doc/web/version_1.2/org/simulator/class-use/SBMLTestSuiteWrapper.html rename to doc/api/version_1.2/org/simulator/class-use/SBMLTestSuiteWrapper.html index 9568b362..9a178d36 100644 --- a/doc/web/version_1.2/org/simulator/class-use/SBMLTestSuiteWrapper.html +++ b/doc/api/version_1.2/org/simulator/class-use/SBMLTestSuiteWrapper.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.SBMLTestSuiteWrapper - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/class-use/SimulatorTest.html b/doc/api/version_1.2/org/simulator/class-use/SimulatorTest.html similarity index 97% rename from doc/web/version_1.2/org/simulator/class-use/SimulatorTest.html rename to doc/api/version_1.2/org/simulator/class-use/SimulatorTest.html index 88e0237e..fbda0d42 100644 --- a/doc/web/version_1.2/org/simulator/class-use/SimulatorTest.html +++ b/doc/api/version_1.2/org/simulator/class-use/SimulatorTest.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.SimulatorTest - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/class-use/TestBiomodels.html b/doc/api/version_1.2/org/simulator/class-use/TestBiomodels.html similarity index 97% rename from doc/web/version_1.2/org/simulator/class-use/TestBiomodels.html rename to doc/api/version_1.2/org/simulator/class-use/TestBiomodels.html index f39fb887..28f69573 100644 --- a/doc/web/version_1.2/org/simulator/class-use/TestBiomodels.html +++ b/doc/api/version_1.2/org/simulator/class-use/TestBiomodels.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.TestBiomodels - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/io/CSVImporter.html b/doc/api/version_1.2/org/simulator/io/CSVImporter.html similarity index 98% rename from doc/web/version_1.2/org/simulator/io/CSVImporter.html rename to doc/api/version_1.2/org/simulator/io/CSVImporter.html index 979ce062..93f1d9f5 100644 --- a/doc/web/version_1.2/org/simulator/io/CSVImporter.html +++ b/doc/api/version_1.2/org/simulator/io/CSVImporter.html @@ -2,12 +2,12 @@ - + CSVImporter - + @@ -229,7 +229,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/io/class-use/CSVImporter.html b/doc/api/version_1.2/org/simulator/io/class-use/CSVImporter.html similarity index 97% rename from doc/web/version_1.2/org/simulator/io/class-use/CSVImporter.html rename to doc/api/version_1.2/org/simulator/io/class-use/CSVImporter.html index b4afcec0..3d79fafb 100644 --- a/doc/web/version_1.2/org/simulator/io/class-use/CSVImporter.html +++ b/doc/api/version_1.2/org/simulator/io/class-use/CSVImporter.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.io.CSVImporter - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/io/package-frame.html b/doc/api/version_1.2/org/simulator/io/package-frame.html similarity index 86% rename from doc/web/version_1.2/org/simulator/io/package-frame.html rename to doc/api/version_1.2/org/simulator/io/package-frame.html index ffd18b87..a86c0935 100644 --- a/doc/web/version_1.2/org/simulator/io/package-frame.html +++ b/doc/api/version_1.2/org/simulator/io/package-frame.html @@ -2,12 +2,12 @@ - + org.simulator.io - + diff --git a/doc/web/version_1.2/org/simulator/io/package-summary.html b/doc/api/version_1.2/org/simulator/io/package-summary.html similarity index 97% rename from doc/web/version_1.2/org/simulator/io/package-summary.html rename to doc/api/version_1.2/org/simulator/io/package-summary.html index cbb99ded..f3c5c8f1 100644 --- a/doc/web/version_1.2/org/simulator/io/package-summary.html +++ b/doc/api/version_1.2/org/simulator/io/package-summary.html @@ -2,12 +2,12 @@ - + org.simulator.io - + @@ -139,7 +139,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/io/package-tree.html b/doc/api/version_1.2/org/simulator/io/package-tree.html similarity index 97% rename from doc/web/version_1.2/org/simulator/io/package-tree.html rename to doc/api/version_1.2/org/simulator/io/package-tree.html index e679cad7..9a1b4738 100644 --- a/doc/web/version_1.2/org/simulator/io/package-tree.html +++ b/doc/api/version_1.2/org/simulator/io/package-tree.html @@ -2,12 +2,12 @@ - + org.simulator.io Class Hierarchy - + @@ -118,7 +118,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/io/package-use.html b/doc/api/version_1.2/org/simulator/io/package-use.html similarity index 97% rename from doc/web/version_1.2/org/simulator/io/package-use.html rename to doc/api/version_1.2/org/simulator/io/package-use.html index 9236a7ba..01561a43 100644 --- a/doc/web/version_1.2/org/simulator/io/package-use.html +++ b/doc/api/version_1.2/org/simulator/io/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.simulator.io - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/ArithmeticMean.html b/doc/api/version_1.2/org/simulator/math/ArithmeticMean.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/ArithmeticMean.html rename to doc/api/version_1.2/org/simulator/math/ArithmeticMean.html index 28401094..88ce88ca 100644 --- a/doc/web/version_1.2/org/simulator/math/ArithmeticMean.html +++ b/doc/api/version_1.2/org/simulator/math/ArithmeticMean.html @@ -2,12 +2,12 @@ - + ArithmeticMean - + @@ -243,7 +243,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/DistanceSum.html b/doc/api/version_1.2/org/simulator/math/DistanceSum.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/DistanceSum.html rename to doc/api/version_1.2/org/simulator/math/DistanceSum.html index b76880eb..7dfad245 100644 --- a/doc/web/version_1.2/org/simulator/math/DistanceSum.html +++ b/doc/api/version_1.2/org/simulator/math/DistanceSum.html @@ -2,12 +2,12 @@ - + DistanceSum - + @@ -241,7 +241,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/EuclideanDistance.html b/doc/api/version_1.2/org/simulator/math/EuclideanDistance.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/EuclideanDistance.html rename to doc/api/version_1.2/org/simulator/math/EuclideanDistance.html index 5aac2aba..10b7987c 100644 --- a/doc/web/version_1.2/org/simulator/math/EuclideanDistance.html +++ b/doc/api/version_1.2/org/simulator/math/EuclideanDistance.html @@ -2,12 +2,12 @@ - + EuclideanDistance - + @@ -281,7 +281,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/ManhattanDistance.html b/doc/api/version_1.2/org/simulator/math/ManhattanDistance.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/ManhattanDistance.html rename to doc/api/version_1.2/org/simulator/math/ManhattanDistance.html index e5066562..68bcf9e4 100644 --- a/doc/web/version_1.2/org/simulator/math/ManhattanDistance.html +++ b/doc/api/version_1.2/org/simulator/math/ManhattanDistance.html @@ -2,12 +2,12 @@ - + ManhattanDistance - + @@ -281,7 +281,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/Mathematics.html b/doc/api/version_1.2/org/simulator/math/Mathematics.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/Mathematics.html rename to doc/api/version_1.2/org/simulator/math/Mathematics.html index 0a20cc72..abcc5a3c 100644 --- a/doc/web/version_1.2/org/simulator/math/Mathematics.html +++ b/doc/api/version_1.2/org/simulator/math/Mathematics.html @@ -2,12 +2,12 @@ - + Mathematics - + @@ -487,7 +487,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/MatrixOperations.MatrixException.html b/doc/api/version_1.2/org/simulator/math/MatrixOperations.MatrixException.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/MatrixOperations.MatrixException.html rename to doc/api/version_1.2/org/simulator/math/MatrixOperations.MatrixException.html index f635932c..7943ca45 100644 --- a/doc/web/version_1.2/org/simulator/math/MatrixOperations.MatrixException.html +++ b/doc/api/version_1.2/org/simulator/math/MatrixOperations.MatrixException.html @@ -2,12 +2,12 @@ - + MatrixOperations.MatrixException - + @@ -227,7 +227,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/MatrixOperations.html b/doc/api/version_1.2/org/simulator/math/MatrixOperations.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/MatrixOperations.html rename to doc/api/version_1.2/org/simulator/math/MatrixOperations.html index c3e4c3bd..67d65d28 100644 --- a/doc/web/version_1.2/org/simulator/math/MatrixOperations.html +++ b/doc/api/version_1.2/org/simulator/math/MatrixOperations.html @@ -2,12 +2,12 @@ - + MatrixOperations - + @@ -598,7 +598,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/MeanFunction.html b/doc/api/version_1.2/org/simulator/math/MeanFunction.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/MeanFunction.html rename to doc/api/version_1.2/org/simulator/math/MeanFunction.html index 75c2abcc..dcf11f40 100644 --- a/doc/web/version_1.2/org/simulator/math/MeanFunction.html +++ b/doc/api/version_1.2/org/simulator/math/MeanFunction.html @@ -2,12 +2,12 @@ - + MeanFunction - + @@ -285,7 +285,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/N_Metric.html b/doc/api/version_1.2/org/simulator/math/N_Metric.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/N_Metric.html rename to doc/api/version_1.2/org/simulator/math/N_Metric.html index fd2c6195..b5fd2a24 100644 --- a/doc/web/version_1.2/org/simulator/math/N_Metric.html +++ b/doc/api/version_1.2/org/simulator/math/N_Metric.html @@ -2,12 +2,12 @@ - + N_Metric - + @@ -376,7 +376,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/PearsonCorrelation.html b/doc/api/version_1.2/org/simulator/math/PearsonCorrelation.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/PearsonCorrelation.html rename to doc/api/version_1.2/org/simulator/math/PearsonCorrelation.html index a4f25b3e..bec4cc9f 100644 --- a/doc/web/version_1.2/org/simulator/math/PearsonCorrelation.html +++ b/doc/api/version_1.2/org/simulator/math/PearsonCorrelation.html @@ -2,12 +2,12 @@ - + PearsonCorrelation - + @@ -292,7 +292,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/QualityMeasure.html b/doc/api/version_1.2/org/simulator/math/QualityMeasure.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/QualityMeasure.html rename to doc/api/version_1.2/org/simulator/math/QualityMeasure.html index 78241cf7..873dd336 100644 --- a/doc/web/version_1.2/org/simulator/math/QualityMeasure.html +++ b/doc/api/version_1.2/org/simulator/math/QualityMeasure.html @@ -2,12 +2,12 @@ - + QualityMeasure - + @@ -562,7 +562,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/RNG.html b/doc/api/version_1.2/org/simulator/math/RNG.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/RNG.html rename to doc/api/version_1.2/org/simulator/math/RNG.html index 7aa68ed8..1d23cecf 100644 --- a/doc/web/version_1.2/org/simulator/math/RNG.html +++ b/doc/api/version_1.2/org/simulator/math/RNG.html @@ -2,12 +2,12 @@ - + RNG - + @@ -228,7 +228,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/RelativeEuclideanDistance.html b/doc/api/version_1.2/org/simulator/math/RelativeEuclideanDistance.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/RelativeEuclideanDistance.html rename to doc/api/version_1.2/org/simulator/math/RelativeEuclideanDistance.html index d46a8496..6b2eb46a 100644 --- a/doc/web/version_1.2/org/simulator/math/RelativeEuclideanDistance.html +++ b/doc/api/version_1.2/org/simulator/math/RelativeEuclideanDistance.html @@ -2,12 +2,12 @@ - + RelativeEuclideanDistance - + @@ -281,7 +281,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/RelativeManhattanDistance.html b/doc/api/version_1.2/org/simulator/math/RelativeManhattanDistance.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/RelativeManhattanDistance.html rename to doc/api/version_1.2/org/simulator/math/RelativeManhattanDistance.html index 47d7d753..522b2baa 100644 --- a/doc/web/version_1.2/org/simulator/math/RelativeManhattanDistance.html +++ b/doc/api/version_1.2/org/simulator/math/RelativeManhattanDistance.html @@ -2,12 +2,12 @@ - + RelativeManhattanDistance - + @@ -281,7 +281,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/RelativeSquaredError.html b/doc/api/version_1.2/org/simulator/math/RelativeSquaredError.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/RelativeSquaredError.html rename to doc/api/version_1.2/org/simulator/math/RelativeSquaredError.html index e9f26313..d5a66b8a 100644 --- a/doc/web/version_1.2/org/simulator/math/RelativeSquaredError.html +++ b/doc/api/version_1.2/org/simulator/math/RelativeSquaredError.html @@ -2,12 +2,12 @@ - + RelativeSquaredError - + @@ -251,7 +251,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/Relative_N_Metric.html b/doc/api/version_1.2/org/simulator/math/Relative_N_Metric.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/Relative_N_Metric.html rename to doc/api/version_1.2/org/simulator/math/Relative_N_Metric.html index 015cd3fe..1832b6d6 100644 --- a/doc/web/version_1.2/org/simulator/math/Relative_N_Metric.html +++ b/doc/api/version_1.2/org/simulator/math/Relative_N_Metric.html @@ -2,12 +2,12 @@ - + Relative_N_Metric - + @@ -388,7 +388,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/ArithmeticMean.html b/doc/api/version_1.2/org/simulator/math/class-use/ArithmeticMean.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/ArithmeticMean.html rename to doc/api/version_1.2/org/simulator/math/class-use/ArithmeticMean.html index 51336de5..7a0f9a17 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/ArithmeticMean.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/ArithmeticMean.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.ArithmeticMean - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/DistanceSum.html b/doc/api/version_1.2/org/simulator/math/class-use/DistanceSum.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/DistanceSum.html rename to doc/api/version_1.2/org/simulator/math/class-use/DistanceSum.html index d6182c24..8d2cd357 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/DistanceSum.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/DistanceSum.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.DistanceSum - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/EuclideanDistance.html b/doc/api/version_1.2/org/simulator/math/class-use/EuclideanDistance.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/EuclideanDistance.html rename to doc/api/version_1.2/org/simulator/math/class-use/EuclideanDistance.html index 22f88474..3d9a1064 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/EuclideanDistance.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/EuclideanDistance.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.EuclideanDistance - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/ManhattanDistance.html b/doc/api/version_1.2/org/simulator/math/class-use/ManhattanDistance.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/ManhattanDistance.html rename to doc/api/version_1.2/org/simulator/math/class-use/ManhattanDistance.html index 8adcb538..dea7aba0 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/ManhattanDistance.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/ManhattanDistance.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.ManhattanDistance - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/Mathematics.html b/doc/api/version_1.2/org/simulator/math/class-use/Mathematics.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/Mathematics.html rename to doc/api/version_1.2/org/simulator/math/class-use/Mathematics.html index cfbdedec..add9fed0 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/Mathematics.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/Mathematics.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.Mathematics - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/MatrixOperations.MatrixException.html b/doc/api/version_1.2/org/simulator/math/class-use/MatrixOperations.MatrixException.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/class-use/MatrixOperations.MatrixException.html rename to doc/api/version_1.2/org/simulator/math/class-use/MatrixOperations.MatrixException.html index 283b5532..e3e1b020 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/MatrixOperations.MatrixException.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/MatrixOperations.MatrixException.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.MatrixOperations.MatrixException - + @@ -161,7 +161,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/MatrixOperations.html b/doc/api/version_1.2/org/simulator/math/class-use/MatrixOperations.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/MatrixOperations.html rename to doc/api/version_1.2/org/simulator/math/class-use/MatrixOperations.html index 3247f465..1a7669cf 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/MatrixOperations.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/MatrixOperations.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.MatrixOperations - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/MeanFunction.html b/doc/api/version_1.2/org/simulator/math/class-use/MeanFunction.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/class-use/MeanFunction.html rename to doc/api/version_1.2/org/simulator/math/class-use/MeanFunction.html index 045c2c52..783e798f 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/MeanFunction.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/MeanFunction.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.MeanFunction - + @@ -216,7 +216,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/N_Metric.html b/doc/api/version_1.2/org/simulator/math/class-use/N_Metric.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/class-use/N_Metric.html rename to doc/api/version_1.2/org/simulator/math/class-use/N_Metric.html index e0464552..1a76be13 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/N_Metric.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/N_Metric.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.N_Metric - + @@ -192,7 +192,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/PearsonCorrelation.html b/doc/api/version_1.2/org/simulator/math/class-use/PearsonCorrelation.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/PearsonCorrelation.html rename to doc/api/version_1.2/org/simulator/math/class-use/PearsonCorrelation.html index 3aad8896..c1ce904f 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/PearsonCorrelation.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/PearsonCorrelation.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.PearsonCorrelation - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/QualityMeasure.html b/doc/api/version_1.2/org/simulator/math/class-use/QualityMeasure.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/class-use/QualityMeasure.html rename to doc/api/version_1.2/org/simulator/math/class-use/QualityMeasure.html index 7c6db9b1..15c8ddb2 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/QualityMeasure.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/QualityMeasure.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.QualityMeasure - + @@ -202,7 +202,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/RNG.html b/doc/api/version_1.2/org/simulator/math/class-use/RNG.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/RNG.html rename to doc/api/version_1.2/org/simulator/math/class-use/RNG.html index f3156982..b8e91388 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/RNG.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/RNG.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.RNG - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/RelativeEuclideanDistance.html b/doc/api/version_1.2/org/simulator/math/class-use/RelativeEuclideanDistance.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/RelativeEuclideanDistance.html rename to doc/api/version_1.2/org/simulator/math/class-use/RelativeEuclideanDistance.html index 54e4a2e4..f69863e7 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/RelativeEuclideanDistance.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/RelativeEuclideanDistance.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.RelativeEuclideanDistance - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/RelativeManhattanDistance.html b/doc/api/version_1.2/org/simulator/math/class-use/RelativeManhattanDistance.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/RelativeManhattanDistance.html rename to doc/api/version_1.2/org/simulator/math/class-use/RelativeManhattanDistance.html index afdf4237..26a893c9 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/RelativeManhattanDistance.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/RelativeManhattanDistance.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.RelativeManhattanDistance - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/RelativeSquaredError.html b/doc/api/version_1.2/org/simulator/math/class-use/RelativeSquaredError.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/class-use/RelativeSquaredError.html rename to doc/api/version_1.2/org/simulator/math/class-use/RelativeSquaredError.html index d8e6bb7b..9a9d8939 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/RelativeSquaredError.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/RelativeSquaredError.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.RelativeSquaredError - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/class-use/Relative_N_Metric.html b/doc/api/version_1.2/org/simulator/math/class-use/Relative_N_Metric.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/class-use/Relative_N_Metric.html rename to doc/api/version_1.2/org/simulator/math/class-use/Relative_N_Metric.html index 05e11cd2..9830ffac 100644 --- a/doc/web/version_1.2/org/simulator/math/class-use/Relative_N_Metric.html +++ b/doc/api/version_1.2/org/simulator/math/class-use/Relative_N_Metric.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.Relative_N_Metric - + @@ -153,7 +153,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/AbstractDESSolver.html b/doc/api/version_1.2/org/simulator/math/odes/AbstractDESSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/AbstractDESSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/AbstractDESSolver.html index d7bb115c..2712aae7 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/AbstractDESSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/AbstractDESSolver.html @@ -2,12 +2,12 @@ - + AbstractDESSolver - + @@ -115,7 +115,7 @@

Since:
0.9
Version:
-
$Rev: 338 $
+
$Rev: 332 $
Author:
Alexander Dörr, Andreas Dräger, Roland Keller, Hannes Planatscher, Philip Stevens, Max Zwießele
See Also:
Serialized Form @@ -1299,7 +1299,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/AdamsBashforthSolver.html b/doc/api/version_1.2/org/simulator/math/odes/AdamsBashforthSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/AdamsBashforthSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/AdamsBashforthSolver.html index 29d50998..792cd15c 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/AdamsBashforthSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/AdamsBashforthSolver.html @@ -2,12 +2,12 @@ - + AdamsBashforthSolver - + @@ -428,7 +428,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/AdamsMoultonSolver.html b/doc/api/version_1.2/org/simulator/math/odes/AdamsMoultonSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/AdamsMoultonSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/AdamsMoultonSolver.html index 6cd988db..55379c12 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/AdamsMoultonSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/AdamsMoultonSolver.html @@ -2,12 +2,12 @@ - + AdamsMoultonSolver - + @@ -426,7 +426,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/AdaptiveStepsizeIntegrator.html b/doc/api/version_1.2/org/simulator/math/odes/AdaptiveStepsizeIntegrator.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/AdaptiveStepsizeIntegrator.html rename to doc/api/version_1.2/org/simulator/math/odes/AdaptiveStepsizeIntegrator.html index 51a2e8ef..16b7d6e8 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/AdaptiveStepsizeIntegrator.html +++ b/doc/api/version_1.2/org/simulator/math/odes/AdaptiveStepsizeIntegrator.html @@ -2,12 +2,12 @@ - + AdaptiveStepsizeIntegrator - + @@ -426,7 +426,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/DESSolver.html b/doc/api/version_1.2/org/simulator/math/odes/DESSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/DESSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/DESSolver.html index a2a51362..6a2b6f44 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/DESSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/DESSolver.html @@ -2,12 +2,12 @@ - + DESSolver - + @@ -576,7 +576,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/DESystem.html b/doc/api/version_1.2/org/simulator/math/odes/DESystem.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/DESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/DESystem.html index 53253dc0..7510ef94 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/DESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/DESystem.html @@ -2,12 +2,12 @@ - + DESystem - + @@ -259,7 +259,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/DelayValueHolder.html b/doc/api/version_1.2/org/simulator/math/odes/DelayValueHolder.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/DelayValueHolder.html rename to doc/api/version_1.2/org/simulator/math/odes/DelayValueHolder.html index 352bae09..ccde1845 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/DelayValueHolder.html +++ b/doc/api/version_1.2/org/simulator/math/odes/DelayValueHolder.html @@ -2,12 +2,12 @@ - + DelayValueHolder - + @@ -196,7 +196,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/DelayedDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/DelayedDESystem.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/DelayedDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/DelayedDESystem.html index 663b4851..eb61f248 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/DelayedDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/DelayedDESystem.html @@ -2,12 +2,12 @@ - + DelayedDESystem - + @@ -203,7 +203,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/DormandPrince54Solver.html b/doc/api/version_1.2/org/simulator/math/odes/DormandPrince54Solver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/DormandPrince54Solver.html rename to doc/api/version_1.2/org/simulator/math/odes/DormandPrince54Solver.html index a911bdff..c65a82f9 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/DormandPrince54Solver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/DormandPrince54Solver.html @@ -2,12 +2,12 @@ - + DormandPrince54Solver - + @@ -428,7 +428,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/DormandPrince853Solver.html b/doc/api/version_1.2/org/simulator/math/odes/DormandPrince853Solver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/DormandPrince853Solver.html rename to doc/api/version_1.2/org/simulator/math/odes/DormandPrince853Solver.html index ec565999..59ee45c9 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/DormandPrince853Solver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/DormandPrince853Solver.html @@ -2,12 +2,12 @@ - + DormandPrince853Solver - + @@ -428,7 +428,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/EulerMethod.html b/doc/api/version_1.2/org/simulator/math/odes/EulerMethod.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/EulerMethod.html rename to doc/api/version_1.2/org/simulator/math/odes/EulerMethod.html index 69972ef4..93362866 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/EulerMethod.html +++ b/doc/api/version_1.2/org/simulator/math/odes/EulerMethod.html @@ -2,12 +2,12 @@ - + EulerMethod - + @@ -429,7 +429,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/EventDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/EventDESystem.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/EventDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/EventDESystem.html index a07e97ee..4bd5c4fe 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/EventDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/EventDESystem.html @@ -2,12 +2,12 @@ - + EventDESystem - + @@ -324,7 +324,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/EventInProgress.html b/doc/api/version_1.2/org/simulator/math/odes/EventInProgress.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/EventInProgress.html rename to doc/api/version_1.2/org/simulator/math/odes/EventInProgress.html index 903d9e40..abe86792 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/EventInProgress.html +++ b/doc/api/version_1.2/org/simulator/math/odes/EventInProgress.html @@ -2,12 +2,12 @@ - + EventInProgress - + @@ -737,7 +737,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/FastProcessDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/FastProcessDESystem.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/FastProcessDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/FastProcessDESystem.html index 1ed0f473..d00d013c 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/FastProcessDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/FastProcessDESystem.html @@ -2,12 +2,12 @@ - + FastProcessDESystem - + @@ -227,7 +227,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/FirstOrderSolver.html b/doc/api/version_1.2/org/simulator/math/odes/FirstOrderSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/FirstOrderSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/FirstOrderSolver.html index 59baf17e..6d459b13 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/FirstOrderSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/FirstOrderSolver.html @@ -2,12 +2,12 @@ - + FirstOrderSolver - + @@ -502,7 +502,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/GraggBulirschStoerSolver.html b/doc/api/version_1.2/org/simulator/math/odes/GraggBulirschStoerSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/GraggBulirschStoerSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/GraggBulirschStoerSolver.html index 0fb5d282..9c159e01 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/GraggBulirschStoerSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/GraggBulirschStoerSolver.html @@ -2,12 +2,12 @@ - + GraggBulirschStoerSolver - + @@ -428,7 +428,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/HighamHall54Solver.html b/doc/api/version_1.2/org/simulator/math/odes/HighamHall54Solver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/HighamHall54Solver.html rename to doc/api/version_1.2/org/simulator/math/odes/HighamHall54Solver.html index 74d4a02c..47dd88fb 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/HighamHall54Solver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/HighamHall54Solver.html @@ -2,12 +2,12 @@ - + HighamHall54Solver - + @@ -428,7 +428,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/MultiTable.Block.Column.html b/doc/api/version_1.2/org/simulator/math/odes/MultiTable.Block.Column.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/MultiTable.Block.Column.html rename to doc/api/version_1.2/org/simulator/math/odes/MultiTable.Block.Column.html index 8a59e1a0..470a3309 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/MultiTable.Block.Column.html +++ b/doc/api/version_1.2/org/simulator/math/odes/MultiTable.Block.Column.html @@ -2,12 +2,12 @@ - + MultiTable.Block.Column - + @@ -368,7 +368,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/MultiTable.Block.html b/doc/api/version_1.2/org/simulator/math/odes/MultiTable.Block.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/MultiTable.Block.html rename to doc/api/version_1.2/org/simulator/math/odes/MultiTable.Block.html index 8de23abf..6cdc64be 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/MultiTable.Block.html +++ b/doc/api/version_1.2/org/simulator/math/odes/MultiTable.Block.html @@ -2,12 +2,12 @@ - + MultiTable.Block - + @@ -691,7 +691,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/MultiTable.html b/doc/api/version_1.2/org/simulator/math/odes/MultiTable.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/MultiTable.html rename to doc/api/version_1.2/org/simulator/math/odes/MultiTable.html index 05a28863..8e843f87 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/MultiTable.html +++ b/doc/api/version_1.2/org/simulator/math/odes/MultiTable.html @@ -2,12 +2,12 @@ - + MultiTable - + @@ -977,7 +977,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/ParameterizedDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/ParameterizedDESystem.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/ParameterizedDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/ParameterizedDESystem.html index 2ab3e227..7234a45f 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/ParameterizedDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/ParameterizedDESystem.html @@ -2,12 +2,12 @@ - + ParameterizedDESystem - + @@ -309,7 +309,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/RichDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/RichDESystem.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/RichDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/RichDESystem.html index eb36e968..1cd628cc 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/RichDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/RichDESystem.html @@ -2,12 +2,12 @@ - + RichDESystem - + @@ -282,7 +282,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/RosenbrockSolver.html b/doc/api/version_1.2/org/simulator/math/odes/RosenbrockSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/RosenbrockSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/RosenbrockSolver.html index a6f3379a..983f8333 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/RosenbrockSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/RosenbrockSolver.html @@ -2,12 +2,12 @@ - + RosenbrockSolver - + @@ -1280,7 +1280,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/RungeKutta_EventSolver.html b/doc/api/version_1.2/org/simulator/math/odes/RungeKutta_EventSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/RungeKutta_EventSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/RungeKutta_EventSolver.html index 76150f07..515f0c6a 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/RungeKutta_EventSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/RungeKutta_EventSolver.html @@ -2,12 +2,12 @@ - + RungeKutta_EventSolver - + @@ -478,7 +478,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/AbstractDESSolver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/AbstractDESSolver.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/AbstractDESSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/AbstractDESSolver.html index 0928d408..ea950095 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/AbstractDESSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/AbstractDESSolver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.AbstractDESSolver - + @@ -333,7 +333,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/AdamsBashforthSolver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/AdamsBashforthSolver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/AdamsBashforthSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/AdamsBashforthSolver.html index 30f2387b..6764f078 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/AdamsBashforthSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/AdamsBashforthSolver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.AdamsBashforthSolver - + @@ -159,7 +159,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/AdamsMoultonSolver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/AdamsMoultonSolver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/AdamsMoultonSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/AdamsMoultonSolver.html index d9a437c1..322b2fc5 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/AdamsMoultonSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/AdamsMoultonSolver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.AdamsMoultonSolver - + @@ -159,7 +159,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/AdaptiveStepsizeIntegrator.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/AdaptiveStepsizeIntegrator.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/AdaptiveStepsizeIntegrator.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/AdaptiveStepsizeIntegrator.html index a5436fbc..9ebed9c8 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/AdaptiveStepsizeIntegrator.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/AdaptiveStepsizeIntegrator.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.AdaptiveStepsizeIntegrator - + @@ -216,7 +216,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/DESSolver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/DESSolver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/DESSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/DESSolver.html index cfd3bce7..f77eff04 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/DESSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/DESSolver.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.math.odes.DESSolver - + @@ -250,7 +250,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/DESystem.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/DESystem.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/DESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/DESystem.html index 74ff58b8..7103d31b 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/DESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/DESystem.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.math.odes.DESystem - + @@ -439,7 +439,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/DelayValueHolder.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/DelayValueHolder.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/DelayValueHolder.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/DelayValueHolder.html index 7b67b44f..b6e0202d 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/DelayValueHolder.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/DelayValueHolder.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.math.odes.DelayValueHolder - + @@ -316,7 +316,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/DelayedDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/DelayedDESystem.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/DelayedDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/DelayedDESystem.html index 335a350f..4937f01f 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/DelayedDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/DelayedDESystem.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.math.odes.DelayedDESystem - + @@ -148,7 +148,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/DormandPrince54Solver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/DormandPrince54Solver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/DormandPrince54Solver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/DormandPrince54Solver.html index 9eeeedb3..c745fe85 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/DormandPrince54Solver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/DormandPrince54Solver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.DormandPrince54Solver - + @@ -159,7 +159,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/DormandPrince853Solver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/DormandPrince853Solver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/DormandPrince853Solver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/DormandPrince853Solver.html index 0f30b676..0cf49037 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/DormandPrince853Solver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/DormandPrince853Solver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.DormandPrince853Solver - + @@ -159,7 +159,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/EulerMethod.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/EulerMethod.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/EulerMethod.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/EulerMethod.html index b11d87ab..d6c99b80 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/EulerMethod.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/EulerMethod.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.EulerMethod - + @@ -159,7 +159,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/EventDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/EventDESystem.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/EventDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/EventDESystem.html index 4ca5821e..3bb69ea8 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/EventDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/EventDESystem.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.math.odes.EventDESystem - + @@ -190,7 +190,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/EventInProgress.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/EventInProgress.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/EventInProgress.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/EventInProgress.html index d8782a34..d02f90d0 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/EventInProgress.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/EventInProgress.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.EventInProgress - + @@ -207,7 +207,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/FastProcessDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/FastProcessDESystem.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/FastProcessDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/FastProcessDESystem.html index 65a07a93..92a8d566 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/FastProcessDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/FastProcessDESystem.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.math.odes.FastProcessDESystem - + @@ -179,7 +179,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/FirstOrderSolver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/FirstOrderSolver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/FirstOrderSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/FirstOrderSolver.html index d4359d05..e91964a4 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/FirstOrderSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/FirstOrderSolver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.FirstOrderSolver - + @@ -215,7 +215,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/GraggBulirschStoerSolver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/GraggBulirschStoerSolver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/GraggBulirschStoerSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/GraggBulirschStoerSolver.html index fe0d2ef0..9692848c 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/GraggBulirschStoerSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/GraggBulirschStoerSolver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.GraggBulirschStoerSolver - + @@ -159,7 +159,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/HighamHall54Solver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/HighamHall54Solver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/HighamHall54Solver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/HighamHall54Solver.html index 31f0deb9..6addf018 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/HighamHall54Solver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/HighamHall54Solver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.HighamHall54Solver - + @@ -159,7 +159,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.Column.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.Column.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.Column.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.Column.html index f7fabebc..ed7f6c09 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.Column.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.Column.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.MultiTable.Block.Column - + @@ -170,7 +170,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.html index a38c99bd..aaf821e1 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.Block.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.MultiTable.Block - + @@ -214,7 +214,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.html index be37b682..a98f788b 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/MultiTable.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/MultiTable.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.MultiTable - + @@ -450,7 +450,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/ParameterizedDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/ParameterizedDESystem.html similarity index 97% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/ParameterizedDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/ParameterizedDESystem.html index fd22e0d5..36952202 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/ParameterizedDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/ParameterizedDESystem.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.math.odes.ParameterizedDESystem - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/RichDESystem.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/RichDESystem.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/RichDESystem.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/RichDESystem.html index c971dc0a..0c521625 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/RichDESystem.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/RichDESystem.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.math.odes.RichDESystem - + @@ -148,7 +148,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/RosenbrockSolver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/RosenbrockSolver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/RosenbrockSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/RosenbrockSolver.html index d72a635a..3e57f624 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/RosenbrockSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/RosenbrockSolver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.RosenbrockSolver - + @@ -143,7 +143,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/class-use/RungeKutta_EventSolver.html b/doc/api/version_1.2/org/simulator/math/odes/class-use/RungeKutta_EventSolver.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/class-use/RungeKutta_EventSolver.html rename to doc/api/version_1.2/org/simulator/math/odes/class-use/RungeKutta_EventSolver.html index 88fc50f7..779b3058 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/class-use/RungeKutta_EventSolver.html +++ b/doc/api/version_1.2/org/simulator/math/odes/class-use/RungeKutta_EventSolver.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.math.odes.RungeKutta_EventSolver - + @@ -159,7 +159,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/package-frame.html b/doc/api/version_1.2/org/simulator/math/odes/package-frame.html similarity index 96% rename from doc/web/version_1.2/org/simulator/math/odes/package-frame.html rename to doc/api/version_1.2/org/simulator/math/odes/package-frame.html index db94b1c4..fcda5348 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/package-frame.html +++ b/doc/api/version_1.2/org/simulator/math/odes/package-frame.html @@ -2,12 +2,12 @@ - + org.simulator.math.odes - + diff --git a/doc/web/version_1.2/org/simulator/math/odes/package-summary.html b/doc/api/version_1.2/org/simulator/math/odes/package-summary.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/package-summary.html rename to doc/api/version_1.2/org/simulator/math/odes/package-summary.html index 775e5b17..b71c45eb 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/package-summary.html +++ b/doc/api/version_1.2/org/simulator/math/odes/package-summary.html @@ -2,12 +2,12 @@ - + org.simulator.math.odes - + @@ -242,7 +242,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/package-tree.html b/doc/api/version_1.2/org/simulator/math/odes/package-tree.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/odes/package-tree.html rename to doc/api/version_1.2/org/simulator/math/odes/package-tree.html index a77bb3ab..634f22d0 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/package-tree.html +++ b/doc/api/version_1.2/org/simulator/math/odes/package-tree.html @@ -2,12 +2,12 @@ - + org.simulator.math.odes Class Hierarchy - + @@ -149,7 +149,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/odes/package-use.html b/doc/api/version_1.2/org/simulator/math/odes/package-use.html similarity index 99% rename from doc/web/version_1.2/org/simulator/math/odes/package-use.html rename to doc/api/version_1.2/org/simulator/math/odes/package-use.html index 4d4cbfc4..20b5503e 100644 --- a/doc/web/version_1.2/org/simulator/math/odes/package-use.html +++ b/doc/api/version_1.2/org/simulator/math/odes/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.simulator.math.odes - + @@ -432,7 +432,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/package-frame.html b/doc/api/version_1.2/org/simulator/math/package-frame.html similarity index 95% rename from doc/web/version_1.2/org/simulator/math/package-frame.html rename to doc/api/version_1.2/org/simulator/math/package-frame.html index a560f16b..2e4a8675 100644 --- a/doc/web/version_1.2/org/simulator/math/package-frame.html +++ b/doc/api/version_1.2/org/simulator/math/package-frame.html @@ -2,12 +2,12 @@ - + org.simulator.math - + diff --git a/doc/web/version_1.2/org/simulator/math/package-summary.html b/doc/api/version_1.2/org/simulator/math/package-summary.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/package-summary.html rename to doc/api/version_1.2/org/simulator/math/package-summary.html index 7af0787c..bfd94426 100644 --- a/doc/web/version_1.2/org/simulator/math/package-summary.html +++ b/doc/api/version_1.2/org/simulator/math/package-summary.html @@ -2,12 +2,12 @@ - + org.simulator.math - + @@ -212,7 +212,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/package-tree.html b/doc/api/version_1.2/org/simulator/math/package-tree.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/package-tree.html rename to doc/api/version_1.2/org/simulator/math/package-tree.html index 7ae51ada..f09b4414 100644 --- a/doc/web/version_1.2/org/simulator/math/package-tree.html +++ b/doc/api/version_1.2/org/simulator/math/package-tree.html @@ -2,12 +2,12 @@ - + org.simulator.math Class Hierarchy - + @@ -133,7 +133,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/math/package-use.html b/doc/api/version_1.2/org/simulator/math/package-use.html similarity index 98% rename from doc/web/version_1.2/org/simulator/math/package-use.html rename to doc/api/version_1.2/org/simulator/math/package-use.html index f0706895..0749dde0 100644 --- a/doc/web/version_1.2/org/simulator/math/package-use.html +++ b/doc/api/version_1.2/org/simulator/math/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.simulator.math - + @@ -160,7 +160,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/package-frame.html b/doc/api/version_1.2/org/simulator/package-frame.html similarity index 92% rename from doc/web/version_1.2/org/simulator/package-frame.html rename to doc/api/version_1.2/org/simulator/package-frame.html index cc4ea624..9d7d5369 100644 --- a/doc/web/version_1.2/org/simulator/package-frame.html +++ b/doc/api/version_1.2/org/simulator/package-frame.html @@ -2,12 +2,12 @@ - + org.simulator - + diff --git a/doc/web/version_1.2/org/simulator/package-summary.html b/doc/api/version_1.2/org/simulator/package-summary.html similarity index 98% rename from doc/web/version_1.2/org/simulator/package-summary.html rename to doc/api/version_1.2/org/simulator/package-summary.html index ff441174..f90cb8b7 100644 --- a/doc/web/version_1.2/org/simulator/package-summary.html +++ b/doc/api/version_1.2/org/simulator/package-summary.html @@ -2,12 +2,12 @@ - + org.simulator - + @@ -169,7 +169,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/package-tree.html b/doc/api/version_1.2/org/simulator/package-tree.html similarity index 97% rename from doc/web/version_1.2/org/simulator/package-tree.html rename to doc/api/version_1.2/org/simulator/package-tree.html index c28c083e..a2699666 100644 --- a/doc/web/version_1.2/org/simulator/package-tree.html +++ b/doc/api/version_1.2/org/simulator/package-tree.html @@ -2,12 +2,12 @@ - + org.simulator Class Hierarchy - + @@ -128,7 +128,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/package-use.html b/doc/api/version_1.2/org/simulator/package-use.html similarity index 97% rename from doc/web/version_1.2/org/simulator/package-use.html rename to doc/api/version_1.2/org/simulator/package-use.html index 0aa445bb..3600ee01 100644 --- a/doc/web/version_1.2/org/simulator/package-use.html +++ b/doc/api/version_1.2/org/simulator/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.simulator - + @@ -136,7 +136,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/AlgebraicRuleConverter.html b/doc/api/version_1.2/org/simulator/sbml/AlgebraicRuleConverter.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/AlgebraicRuleConverter.html rename to doc/api/version_1.2/org/simulator/sbml/AlgebraicRuleConverter.html index e52e7b8d..9a5b9e6c 100644 --- a/doc/web/version_1.2/org/simulator/sbml/AlgebraicRuleConverter.html +++ b/doc/api/version_1.2/org/simulator/sbml/AlgebraicRuleConverter.html @@ -2,12 +2,12 @@ - + AlgebraicRuleConverter - + @@ -235,7 +235,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/SBMLEventInProgress.html b/doc/api/version_1.2/org/simulator/sbml/SBMLEventInProgress.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/SBMLEventInProgress.html rename to doc/api/version_1.2/org/simulator/sbml/SBMLEventInProgress.html index 72b89dee..2e453d14 100644 --- a/doc/web/version_1.2/org/simulator/sbml/SBMLEventInProgress.html +++ b/doc/api/version_1.2/org/simulator/sbml/SBMLEventInProgress.html @@ -2,12 +2,12 @@ - + SBMLEventInProgress - + @@ -767,7 +767,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/SBMLEventInProgressWithDelay.html b/doc/api/version_1.2/org/simulator/sbml/SBMLEventInProgressWithDelay.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/SBMLEventInProgressWithDelay.html rename to doc/api/version_1.2/org/simulator/sbml/SBMLEventInProgressWithDelay.html index 88c07db1..f9839eca 100644 --- a/doc/web/version_1.2/org/simulator/sbml/SBMLEventInProgressWithDelay.html +++ b/doc/api/version_1.2/org/simulator/sbml/SBMLEventInProgressWithDelay.html @@ -2,12 +2,12 @@ - + SBMLEventInProgressWithDelay - + @@ -391,7 +391,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/SBMLValueHolder.html b/doc/api/version_1.2/org/simulator/sbml/SBMLValueHolder.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/SBMLValueHolder.html rename to doc/api/version_1.2/org/simulator/sbml/SBMLValueHolder.html index 3de2e46e..24c6c9fa 100644 --- a/doc/web/version_1.2/org/simulator/sbml/SBMLValueHolder.html +++ b/doc/api/version_1.2/org/simulator/sbml/SBMLValueHolder.html @@ -2,12 +2,12 @@ - + SBMLValueHolder - + @@ -378,7 +378,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/SBMLinterpreter.html b/doc/api/version_1.2/org/simulator/sbml/SBMLinterpreter.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/SBMLinterpreter.html rename to doc/api/version_1.2/org/simulator/sbml/SBMLinterpreter.html index 7c0fc857..8ba793e4 100644 --- a/doc/web/version_1.2/org/simulator/sbml/SBMLinterpreter.html +++ b/doc/api/version_1.2/org/simulator/sbml/SBMLinterpreter.html @@ -2,12 +2,12 @@ - + SBMLinterpreter - + @@ -1569,7 +1569,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/ASTNodeInterpreter.html b/doc/api/version_1.2/org/simulator/sbml/astnode/ASTNodeInterpreter.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/ASTNodeInterpreter.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/ASTNodeInterpreter.html index f34ab4f7..6eca282b 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/ASTNodeInterpreter.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/ASTNodeInterpreter.html @@ -2,12 +2,12 @@ - + ASTNodeInterpreter - + @@ -1811,7 +1811,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/ASTNodeValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/ASTNodeValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/ASTNodeValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/ASTNodeValue.html index 97771582..74f1f8dd 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/ASTNodeValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/ASTNodeValue.html @@ -2,12 +2,12 @@ - + ASTNodeValue - + @@ -922,7 +922,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/AssignmentRuleValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/AssignmentRuleValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/AssignmentRuleValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/AssignmentRuleValue.html index 901ae3ed..13ef8fcc 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/AssignmentRuleValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/AssignmentRuleValue.html @@ -2,12 +2,12 @@ - + AssignmentRuleValue - + @@ -332,7 +332,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/CompartmentOrParameterValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/CompartmentOrParameterValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/CompartmentOrParameterValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/CompartmentOrParameterValue.html index bb5562c2..eafa4afa 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/CompartmentOrParameterValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/CompartmentOrParameterValue.html @@ -2,12 +2,12 @@ - + CompartmentOrParameterValue - + @@ -356,7 +356,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/DivideValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/DivideValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/DivideValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/DivideValue.html index 36d15d6d..7ad700f9 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/DivideValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/DivideValue.html @@ -2,12 +2,12 @@ - + DivideValue - + @@ -259,7 +259,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/FunctionValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/FunctionValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/FunctionValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/FunctionValue.html index 8d32f05f..83a893c7 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/FunctionValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/FunctionValue.html @@ -2,12 +2,12 @@ - + FunctionValue - + @@ -461,7 +461,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/IntegerValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/IntegerValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/IntegerValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/IntegerValue.html index 7d25b499..a2b35475 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/IntegerValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/IntegerValue.html @@ -2,12 +2,12 @@ - + IntegerValue - + @@ -282,7 +282,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/LocalParameterValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/LocalParameterValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/LocalParameterValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/LocalParameterValue.html index 66858837..3071bd7c 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/LocalParameterValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/LocalParameterValue.html @@ -2,12 +2,12 @@ - + LocalParameterValue - + @@ -293,7 +293,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/MinusValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/MinusValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/MinusValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/MinusValue.html index 32818750..3fb7f1c6 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/MinusValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/MinusValue.html @@ -2,12 +2,12 @@ - + MinusValue - + @@ -259,7 +259,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/NamedValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/NamedValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/NamedValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/NamedValue.html index 051497cd..41ccb073 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/NamedValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/NamedValue.html @@ -2,12 +2,12 @@ - + NamedValue - + @@ -261,7 +261,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/PlusValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/PlusValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/PlusValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/PlusValue.html index ab63d4d7..b1cf65a9 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/PlusValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/PlusValue.html @@ -2,12 +2,12 @@ - + PlusValue - + @@ -259,7 +259,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/PowerValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/PowerValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/PowerValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/PowerValue.html index 40fb94b0..d8aafefc 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/PowerValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/PowerValue.html @@ -2,12 +2,12 @@ - + PowerValue - + @@ -259,7 +259,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/RateRuleValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/RateRuleValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/RateRuleValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/RateRuleValue.html index 8d16d0a0..2495672a 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/RateRuleValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/RateRuleValue.html @@ -2,12 +2,12 @@ - + RateRuleValue - + @@ -311,7 +311,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/ReactionValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/ReactionValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/ReactionValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/ReactionValue.html index b3a3b259..8f8e59ee 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/ReactionValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/ReactionValue.html @@ -2,12 +2,12 @@ - + ReactionValue - + @@ -312,7 +312,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/RootFunctionValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/RootFunctionValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/RootFunctionValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/RootFunctionValue.html index 5f92b51c..82e66591 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/RootFunctionValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/RootFunctionValue.html @@ -2,12 +2,12 @@ - + RootFunctionValue - + @@ -259,7 +259,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/RuleValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/RuleValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/RuleValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/RuleValue.html index 444b3563..276d40bd 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/RuleValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/RuleValue.html @@ -2,12 +2,12 @@ - + RuleValue - + @@ -521,7 +521,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/SpeciesReferenceValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/SpeciesReferenceValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/SpeciesReferenceValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/SpeciesReferenceValue.html index 5c6e5661..921f54f0 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/SpeciesReferenceValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/SpeciesReferenceValue.html @@ -2,12 +2,12 @@ - + SpeciesReferenceValue - + @@ -265,7 +265,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/SpeciesValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/SpeciesValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/SpeciesValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/SpeciesValue.html index 1323c828..abf54258 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/SpeciesValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/SpeciesValue.html @@ -2,12 +2,12 @@ - + SpeciesValue - + @@ -462,7 +462,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/StoichiometryValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/StoichiometryValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/StoichiometryValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/StoichiometryValue.html index 14a76935..35f5103f 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/StoichiometryValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/StoichiometryValue.html @@ -2,12 +2,12 @@ - + StoichiometryValue - + @@ -296,7 +296,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/TimesValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/TimesValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/TimesValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/TimesValue.html index f8c46739..ff6ebfa6 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/TimesValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/TimesValue.html @@ -2,12 +2,12 @@ - + TimesValue - + @@ -261,7 +261,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeInterpreter.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeInterpreter.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeInterpreter.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeInterpreter.html index 949799f1..40debd08 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeInterpreter.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeInterpreter.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.ASTNodeInterpreter - + @@ -274,7 +274,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeValue.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeValue.html index c9a3cea7..a76d4b11 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ASTNodeValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.ASTNodeValue - + @@ -1111,7 +1111,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/AssignmentRuleValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/AssignmentRuleValue.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/AssignmentRuleValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/AssignmentRuleValue.html index 1a99b93e..0c4104a0 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/AssignmentRuleValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/AssignmentRuleValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.AssignmentRuleValue - + @@ -177,7 +177,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/CompartmentOrParameterValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/CompartmentOrParameterValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/CompartmentOrParameterValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/CompartmentOrParameterValue.html index 53bb8379..69a7c23f 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/CompartmentOrParameterValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/CompartmentOrParameterValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.CompartmentOrParameterValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/DivideValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/DivideValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/DivideValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/DivideValue.html index 80d94431..17fc03c2 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/DivideValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/DivideValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.DivideValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/FunctionValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/FunctionValue.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/FunctionValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/FunctionValue.html index 56433a14..c925f81d 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/FunctionValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/FunctionValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.FunctionValue - + @@ -146,7 +146,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/IntegerValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/IntegerValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/IntegerValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/IntegerValue.html index 4018e6f9..52356dae 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/IntegerValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/IntegerValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.IntegerValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/LocalParameterValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/LocalParameterValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/LocalParameterValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/LocalParameterValue.html index 1689fcf0..e1ef1e12 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/LocalParameterValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/LocalParameterValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.LocalParameterValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/MinusValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/MinusValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/MinusValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/MinusValue.html index 14973fcd..87dcc178 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/MinusValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/MinusValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.MinusValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/NamedValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/NamedValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/NamedValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/NamedValue.html index 1896dd68..3b2812cd 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/NamedValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/NamedValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.NamedValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/PlusValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/PlusValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/PlusValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/PlusValue.html index e5736f58..77c18b39 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/PlusValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/PlusValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.PlusValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/PowerValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/PowerValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/PowerValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/PowerValue.html index 1f0194ba..5c4ccf60 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/PowerValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/PowerValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.PowerValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RateRuleValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RateRuleValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RateRuleValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RateRuleValue.html index 1c844d47..f261b4c4 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RateRuleValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RateRuleValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.RateRuleValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ReactionValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ReactionValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ReactionValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ReactionValue.html index 9c143e56..5330a5d6 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/ReactionValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/ReactionValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.ReactionValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RootFunctionValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RootFunctionValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RootFunctionValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RootFunctionValue.html index fd2e70fa..0dff8851 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RootFunctionValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RootFunctionValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.RootFunctionValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RuleValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RuleValue.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RuleValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RuleValue.html index 7e9fd104..6badf7d8 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/RuleValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/RuleValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.RuleValue - + @@ -154,7 +154,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesReferenceValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesReferenceValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesReferenceValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesReferenceValue.html index aef45eac..19b03850 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesReferenceValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesReferenceValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.SpeciesReferenceValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesValue.html index 725d0733..ee345d1d 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/SpeciesValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.SpeciesValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/StoichiometryValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/StoichiometryValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/StoichiometryValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/StoichiometryValue.html index 9ed4be35..c63c91a1 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/StoichiometryValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/StoichiometryValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.StoichiometryValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/TimesValue.html b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/TimesValue.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/astnode/class-use/TimesValue.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/class-use/TimesValue.html index 593fd2ad..9bf05692 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/class-use/TimesValue.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/class-use/TimesValue.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.astnode.TimesValue - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/package-frame.html b/doc/api/version_1.2/org/simulator/sbml/astnode/package-frame.html similarity index 96% rename from doc/web/version_1.2/org/simulator/sbml/astnode/package-frame.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/package-frame.html index 9e9fd913..288542f9 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/package-frame.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/package-frame.html @@ -2,12 +2,12 @@ - + org.simulator.sbml.astnode - + diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/package-summary.html b/doc/api/version_1.2/org/simulator/sbml/astnode/package-summary.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/astnode/package-summary.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/package-summary.html index 97f88bea..54a4a6de 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/package-summary.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/package-summary.html @@ -2,12 +2,12 @@ - + org.simulator.sbml.astnode - + @@ -218,7 +218,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/package-tree.html b/doc/api/version_1.2/org/simulator/sbml/astnode/package-tree.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/astnode/package-tree.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/package-tree.html index 0023a8da..9ec6d18f 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/package-tree.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/package-tree.html @@ -2,12 +2,12 @@ - + org.simulator.sbml.astnode Class Hierarchy - + @@ -122,7 +122,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/astnode/package-use.html b/doc/api/version_1.2/org/simulator/sbml/astnode/package-use.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/astnode/package-use.html rename to doc/api/version_1.2/org/simulator/sbml/astnode/package-use.html index eb6e8ee4..a06b327b 100644 --- a/doc/web/version_1.2/org/simulator/sbml/astnode/package-use.html +++ b/doc/api/version_1.2/org/simulator/sbml/astnode/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.simulator.sbml.astnode - + @@ -181,7 +181,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/class-use/AlgebraicRuleConverter.html b/doc/api/version_1.2/org/simulator/sbml/class-use/AlgebraicRuleConverter.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/class-use/AlgebraicRuleConverter.html rename to doc/api/version_1.2/org/simulator/sbml/class-use/AlgebraicRuleConverter.html index 952b4bc8..40261625 100644 --- a/doc/web/version_1.2/org/simulator/sbml/class-use/AlgebraicRuleConverter.html +++ b/doc/api/version_1.2/org/simulator/sbml/class-use/AlgebraicRuleConverter.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.AlgebraicRuleConverter - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgress.html b/doc/api/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgress.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgress.html rename to doc/api/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgress.html index 8b90979e..69e49247 100644 --- a/doc/web/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgress.html +++ b/doc/api/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgress.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.SBMLEventInProgress - + @@ -147,7 +147,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgressWithDelay.html b/doc/api/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgressWithDelay.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgressWithDelay.html rename to doc/api/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgressWithDelay.html index 4e17ac98..f63c9d9d 100644 --- a/doc/web/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgressWithDelay.html +++ b/doc/api/version_1.2/org/simulator/sbml/class-use/SBMLEventInProgressWithDelay.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.SBMLEventInProgressWithDelay - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/class-use/SBMLValueHolder.html b/doc/api/version_1.2/org/simulator/sbml/class-use/SBMLValueHolder.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sbml/class-use/SBMLValueHolder.html rename to doc/api/version_1.2/org/simulator/sbml/class-use/SBMLValueHolder.html index cf9dbcf9..a63f6e88 100644 --- a/doc/web/version_1.2/org/simulator/sbml/class-use/SBMLValueHolder.html +++ b/doc/api/version_1.2/org/simulator/sbml/class-use/SBMLValueHolder.html @@ -2,12 +2,12 @@ - + Uses of Interface org.simulator.sbml.SBMLValueHolder - + @@ -282,7 +282,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/class-use/SBMLinterpreter.html b/doc/api/version_1.2/org/simulator/sbml/class-use/SBMLinterpreter.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sbml/class-use/SBMLinterpreter.html rename to doc/api/version_1.2/org/simulator/sbml/class-use/SBMLinterpreter.html index 8215c32b..4fb065c8 100644 --- a/doc/web/version_1.2/org/simulator/sbml/class-use/SBMLinterpreter.html +++ b/doc/api/version_1.2/org/simulator/sbml/class-use/SBMLinterpreter.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sbml.SBMLinterpreter - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/package-frame.html b/doc/api/version_1.2/org/simulator/sbml/package-frame.html similarity index 92% rename from doc/web/version_1.2/org/simulator/sbml/package-frame.html rename to doc/api/version_1.2/org/simulator/sbml/package-frame.html index e7ec1bb4..f7814021 100644 --- a/doc/web/version_1.2/org/simulator/sbml/package-frame.html +++ b/doc/api/version_1.2/org/simulator/sbml/package-frame.html @@ -2,12 +2,12 @@ - + org.simulator.sbml - + diff --git a/doc/web/version_1.2/org/simulator/sbml/package-summary.html b/doc/api/version_1.2/org/simulator/sbml/package-summary.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/package-summary.html rename to doc/api/version_1.2/org/simulator/sbml/package-summary.html index 14150c9a..57b90012 100644 --- a/doc/web/version_1.2/org/simulator/sbml/package-summary.html +++ b/doc/api/version_1.2/org/simulator/sbml/package-summary.html @@ -2,12 +2,12 @@ - + org.simulator.sbml - + @@ -175,7 +175,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/package-tree.html b/doc/api/version_1.2/org/simulator/sbml/package-tree.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/package-tree.html rename to doc/api/version_1.2/org/simulator/sbml/package-tree.html index 85fa592c..37d91a51 100644 --- a/doc/web/version_1.2/org/simulator/sbml/package-tree.html +++ b/doc/api/version_1.2/org/simulator/sbml/package-tree.html @@ -2,12 +2,12 @@ - + org.simulator.sbml Class Hierarchy - + @@ -134,7 +134,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sbml/package-use.html b/doc/api/version_1.2/org/simulator/sbml/package-use.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sbml/package-use.html rename to doc/api/version_1.2/org/simulator/sbml/package-use.html index 4b9ed081..c4641898 100644 --- a/doc/web/version_1.2/org/simulator/sbml/package-use.html +++ b/doc/api/version_1.2/org/simulator/sbml/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.simulator.sbml - + @@ -167,7 +167,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/ExecutionException.html b/doc/api/version_1.2/org/simulator/sedml/ExecutionException.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sedml/ExecutionException.html rename to doc/api/version_1.2/org/simulator/sedml/ExecutionException.html index 4be4a24d..57e48dd2 100644 --- a/doc/web/version_1.2/org/simulator/sedml/ExecutionException.html +++ b/doc/api/version_1.2/org/simulator/sedml/ExecutionException.html @@ -2,12 +2,12 @@ - + ExecutionException - + @@ -210,7 +210,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/MultTableSEDMLWrapper.html b/doc/api/version_1.2/org/simulator/sedml/MultTableSEDMLWrapper.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sedml/MultTableSEDMLWrapper.html rename to doc/api/version_1.2/org/simulator/sedml/MultTableSEDMLWrapper.html index 346f11b3..dcf588d6 100644 --- a/doc/web/version_1.2/org/simulator/sedml/MultTableSEDMLWrapper.html +++ b/doc/api/version_1.2/org/simulator/sedml/MultTableSEDMLWrapper.html @@ -2,12 +2,12 @@ - + MultTableSEDMLWrapper - + @@ -414,7 +414,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/SEDMLExecutor.html b/doc/api/version_1.2/org/simulator/sedml/SEDMLExecutor.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sedml/SEDMLExecutor.html rename to doc/api/version_1.2/org/simulator/sedml/SEDMLExecutor.html index 82124c33..f4b477b5 100644 --- a/doc/web/version_1.2/org/simulator/sedml/SEDMLExecutor.html +++ b/doc/api/version_1.2/org/simulator/sedml/SEDMLExecutor.html @@ -2,12 +2,12 @@ - + SEDMLExecutor - + @@ -238,7 +238,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/SEDMLExecutorTest.html b/doc/api/version_1.2/org/simulator/sedml/SEDMLExecutorTest.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sedml/SEDMLExecutorTest.html rename to doc/api/version_1.2/org/simulator/sedml/SEDMLExecutorTest.html index 9df7ee63..aaae86dd 100644 --- a/doc/web/version_1.2/org/simulator/sedml/SEDMLExecutorTest.html +++ b/doc/api/version_1.2/org/simulator/sedml/SEDMLExecutorTest.html @@ -2,12 +2,12 @@ - + SEDMLExecutorTest - + @@ -295,7 +295,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/SEDMLWriter.html b/doc/api/version_1.2/org/simulator/sedml/SEDMLWriter.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sedml/SEDMLWriter.html rename to doc/api/version_1.2/org/simulator/sedml/SEDMLWriter.html index 82d14585..7bbe9adb 100644 --- a/doc/web/version_1.2/org/simulator/sedml/SEDMLWriter.html +++ b/doc/api/version_1.2/org/simulator/sedml/SEDMLWriter.html @@ -2,12 +2,12 @@ - + SEDMLWriter - + @@ -289,7 +289,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/SEDMLWriterTest.html b/doc/api/version_1.2/org/simulator/sedml/SEDMLWriterTest.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sedml/SEDMLWriterTest.html rename to doc/api/version_1.2/org/simulator/sedml/SEDMLWriterTest.html index 0b61d587..3744663e 100644 --- a/doc/web/version_1.2/org/simulator/sedml/SEDMLWriterTest.html +++ b/doc/api/version_1.2/org/simulator/sedml/SEDMLWriterTest.html @@ -2,12 +2,12 @@ - + SEDMLWriterTest - + @@ -278,7 +278,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/SedMLSBMLSimulatorExecutor.html b/doc/api/version_1.2/org/simulator/sedml/SedMLSBMLSimulatorExecutor.html similarity index 99% rename from doc/web/version_1.2/org/simulator/sedml/SedMLSBMLSimulatorExecutor.html rename to doc/api/version_1.2/org/simulator/sedml/SedMLSBMLSimulatorExecutor.html index 96a9b8bb..4c0ec1e6 100644 --- a/doc/web/version_1.2/org/simulator/sedml/SedMLSBMLSimulatorExecutor.html +++ b/doc/api/version_1.2/org/simulator/sedml/SedMLSBMLSimulatorExecutor.html @@ -2,12 +2,12 @@ - + SedMLSBMLSimulatorExecutor - + @@ -402,7 +402,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/class-use/ExecutionException.html b/doc/api/version_1.2/org/simulator/sedml/class-use/ExecutionException.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sedml/class-use/ExecutionException.html rename to doc/api/version_1.2/org/simulator/sedml/class-use/ExecutionException.html index acf75e0e..d01c4185 100644 --- a/doc/web/version_1.2/org/simulator/sedml/class-use/ExecutionException.html +++ b/doc/api/version_1.2/org/simulator/sedml/class-use/ExecutionException.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sedml.ExecutionException - + @@ -146,7 +146,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/class-use/MultTableSEDMLWrapper.html b/doc/api/version_1.2/org/simulator/sedml/class-use/MultTableSEDMLWrapper.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sedml/class-use/MultTableSEDMLWrapper.html rename to doc/api/version_1.2/org/simulator/sedml/class-use/MultTableSEDMLWrapper.html index 4cedfe93..3864d842 100644 --- a/doc/web/version_1.2/org/simulator/sedml/class-use/MultTableSEDMLWrapper.html +++ b/doc/api/version_1.2/org/simulator/sedml/class-use/MultTableSEDMLWrapper.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sedml.MultTableSEDMLWrapper - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLExecutor.html b/doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLExecutor.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLExecutor.html rename to doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLExecutor.html index 39762f19..704fe6aa 100644 --- a/doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLExecutor.html +++ b/doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLExecutor.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sedml.SEDMLExecutor - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLExecutorTest.html b/doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLExecutorTest.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLExecutorTest.html rename to doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLExecutorTest.html index 448fd0fe..e7767e74 100644 --- a/doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLExecutorTest.html +++ b/doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLExecutorTest.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sedml.SEDMLExecutorTest - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLWriter.html b/doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLWriter.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLWriter.html rename to doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLWriter.html index e32823cb..6fbd637d 100644 --- a/doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLWriter.html +++ b/doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLWriter.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sedml.SEDMLWriter - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLWriterTest.html b/doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLWriterTest.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLWriterTest.html rename to doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLWriterTest.html index d76a06ba..5e2fa927 100644 --- a/doc/web/version_1.2/org/simulator/sedml/class-use/SEDMLWriterTest.html +++ b/doc/api/version_1.2/org/simulator/sedml/class-use/SEDMLWriterTest.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sedml.SEDMLWriterTest - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/class-use/SedMLSBMLSimulatorExecutor.html b/doc/api/version_1.2/org/simulator/sedml/class-use/SedMLSBMLSimulatorExecutor.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sedml/class-use/SedMLSBMLSimulatorExecutor.html rename to doc/api/version_1.2/org/simulator/sedml/class-use/SedMLSBMLSimulatorExecutor.html index 5365f0ac..c72ab385 100644 --- a/doc/web/version_1.2/org/simulator/sedml/class-use/SedMLSBMLSimulatorExecutor.html +++ b/doc/api/version_1.2/org/simulator/sedml/class-use/SedMLSBMLSimulatorExecutor.html @@ -2,12 +2,12 @@ - + Uses of Class org.simulator.sedml.SedMLSBMLSimulatorExecutor - + @@ -109,7 +109,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/package-frame.html b/doc/api/version_1.2/org/simulator/sedml/package-frame.html similarity index 93% rename from doc/web/version_1.2/org/simulator/sedml/package-frame.html rename to doc/api/version_1.2/org/simulator/sedml/package-frame.html index 76b2ec00..e4b40851 100644 --- a/doc/web/version_1.2/org/simulator/sedml/package-frame.html +++ b/doc/api/version_1.2/org/simulator/sedml/package-frame.html @@ -2,12 +2,12 @@ - + org.simulator.sedml - + diff --git a/doc/web/version_1.2/org/simulator/sedml/package-summary.html b/doc/api/version_1.2/org/simulator/sedml/package-summary.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sedml/package-summary.html rename to doc/api/version_1.2/org/simulator/sedml/package-summary.html index 8733fe06..b1c107fa 100644 --- a/doc/web/version_1.2/org/simulator/sedml/package-summary.html +++ b/doc/api/version_1.2/org/simulator/sedml/package-summary.html @@ -2,12 +2,12 @@ - + org.simulator.sedml - + @@ -159,8 +159,6 @@

-
Author:
-
Richard Adams
@@ -186,7 +184,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/package-tree.html b/doc/api/version_1.2/org/simulator/sedml/package-tree.html similarity index 98% rename from doc/web/version_1.2/org/simulator/sedml/package-tree.html rename to doc/api/version_1.2/org/simulator/sedml/package-tree.html index 690d7914..167c5464 100644 --- a/doc/web/version_1.2/org/simulator/sedml/package-tree.html +++ b/doc/api/version_1.2/org/simulator/sedml/package-tree.html @@ -2,12 +2,12 @@ - + org.simulator.sedml Class Hierarchy - + @@ -128,7 +128,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/org/simulator/sedml/package-use.html b/doc/api/version_1.2/org/simulator/sedml/package-use.html similarity index 97% rename from doc/web/version_1.2/org/simulator/sedml/package-use.html rename to doc/api/version_1.2/org/simulator/sedml/package-use.html index 691915ed..8186920d 100644 --- a/doc/web/version_1.2/org/simulator/sedml/package-use.html +++ b/doc/api/version_1.2/org/simulator/sedml/package-use.html @@ -2,12 +2,12 @@ - + Uses of Package org.simulator.sedml - + @@ -135,7 +135,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/overview-frame.html b/doc/api/version_1.2/overview-frame.html similarity index 94% rename from doc/web/version_1.2/overview-frame.html rename to doc/api/version_1.2/overview-frame.html index 6912e718..86c69073 100644 --- a/doc/web/version_1.2/overview-frame.html +++ b/doc/api/version_1.2/overview-frame.html @@ -2,12 +2,12 @@ - + Overview List - + diff --git a/doc/web/version_1.2/overview-summary.html b/doc/api/version_1.2/overview-summary.html similarity index 98% rename from doc/web/version_1.2/overview-summary.html rename to doc/api/version_1.2/overview-summary.html index 8ccf2611..7ef79e9c 100644 --- a/doc/web/version_1.2/overview-summary.html +++ b/doc/api/version_1.2/overview-summary.html @@ -2,12 +2,12 @@ - + Overview - + @@ -326,7 +326,7 @@

Simulation of the models from BioModels database

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/overview-tree.html b/doc/api/version_1.2/overview-tree.html similarity index 99% rename from doc/web/version_1.2/overview-tree.html rename to doc/api/version_1.2/overview-tree.html index bcfd2f54..a6b4a47e 100644 --- a/doc/web/version_1.2/overview-tree.html +++ b/doc/api/version_1.2/overview-tree.html @@ -2,12 +2,12 @@ - + Class Hierarchy - + @@ -191,7 +191,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/web/version_1.2/package-list b/doc/api/version_1.2/package-list similarity index 100% rename from doc/web/version_1.2/package-list rename to doc/api/version_1.2/package-list diff --git a/doc/web/version_1.2/resources/inherit.gif b/doc/api/version_1.2/resources/inherit.gif similarity index 100% rename from doc/web/version_1.2/resources/inherit.gif rename to doc/api/version_1.2/resources/inherit.gif diff --git a/doc/web/version_1.2/serialized-form.html b/doc/api/version_1.2/serialized-form.html similarity index 99% rename from doc/web/version_1.2/serialized-form.html rename to doc/api/version_1.2/serialized-form.html index 34a0c434..8100d7e7 100644 --- a/doc/web/version_1.2/serialized-form.html +++ b/doc/api/version_1.2/serialized-form.html @@ -2,12 +2,12 @@ - + Serialized Form - + @@ -1896,7 +1896,7 @@

-Generated December 20 2012 +Generated December 13 2012 diff --git a/doc/publications/2012_BMC_SystBiol/Review/Point2PointList.rtf b/doc/publications/2012_BMC_SystBiol/Review/Point2PointList.rtf deleted file mode 100644 index 5aeebaee..00000000 --- a/doc/publications/2012_BMC_SystBiol/Review/Point2PointList.rtf +++ /dev/null @@ -1,795 +0,0 @@ -{\rtf1\adeflang1025\ansi\ansicpg1252\uc1\adeff0\deff0\stshfdbch31505\stshfloch31506\stshfhich31506\stshfbi0\deflang1031\deflangfe1031\themelang1031\themelangfe1041\themelangcs0{\fonttbl{\f0\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\f1\fbidi \fswiss\fcharset0\fprq2{\*\panose 020b0604020202020204}Arial;} -{\f2\fbidi \fmodern\fcharset0\fprq1{\*\panose 02070309020205020404}Courier New;}{\f3\fbidi \froman\fcharset2\fprq2{\*\panose 05050102010706020507}Symbol;}{\f10\fbidi \fnil\fcharset2\fprq2{\*\panose 05000000000000000000}Wingdings;} -{\f11\fbidi \fmodern\fcharset128\fprq1{\*\panose 02020609040205080304}MS 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\ltrch\fcs0 \insrsid4286719 \chftnsep -\par }}{\*\ftnsepc \ltrpar \pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid7416744 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 -\fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid4286719 \chftnsepc -\par }}{\*\aftnsep \ltrpar \pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid7416744 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 -\fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid4286719 \chftnsep -\par }}{\*\aftnsepc \ltrpar \pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid7416744 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 -\fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \insrsid4286719 \chftnsepc -\par }}\ltrpar \sectd \ltrsect\linex0\headery708\footery708\colsx708\endnhere\sectlinegrid360\sectdefaultcl\sectrsid2714031\sftnbj {\headerl \ltrpar \ltrrow\trowd \irow0\irowband0\lastrow \ltrrow\ts11\tsrowd\trgaph108\trbrdrv\brdrs\brdrw10 -\trftsWidth2\trwWidth5000\trftsWidthB3\trautofit1\trpaddl108\trpaddr108\trpaddfl3\trpaddft3\trpaddfb3\trpaddfr3\tblrsid802636\tbllkhdrrows\tbllkhdrcols\tbllknocolband\tblind-1152\tblindtype3 \clvertalt\clbrdrt\brdrtbl \clbrdrl\brdrtbl \clbrdrb\brdrtbl -\clbrdrr\brdrs\brdrw10 \cltxlrtb\clftsWidth3\clwWidth1152\clshdrawnil \cellx-108\clvertalt\clbrdrt\brdrtbl \clbrdrl\brdrs\brdrw10 \clbrdrb\brdrtbl \clbrdrr\brdrtbl \cltxlrtb\clNoWrap\clftsWidth1\clshdrawnil \cellx8022\pard\plain \ltrpar -\s19\qr \li0\ri0\widctlpar\intbl\tqc\tx4536\tqr\tx9072\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 -{\field{\*\fldinst {\rtlch\fcs1 \af0 \ltrch\fcs0 \fs16\insrsid7416744\charrsid7416744 \hich\af1\dbch\af31505\loch\f1 PAGE \\\hich\af1\dbch\af31505\loch\f1 * MERGEFORMAT}}{\fldrslt {\rtlch\fcs1 \af0 \ltrch\fcs0 -\fs16\lang1024\langfe1024\noproof\insrsid1194370 \hich\af1\dbch\af31505\loch\f1 4}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sftnbj {\rtlch\fcs1 \af0 \ltrch\fcs0 \b\fs16\insrsid7416744\charrsid7416744 \cell }\pard \ltrpar -\s19\qj \li0\ri0\widctlpar\intbl\tqc\tx4536\tqr\tx9072\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\pararsid7416744 {\rtlch\fcs1 \af0 \ltrch\fcs0 \fs16\insrsid7416744\charrsid7416744 \hich\af1\dbch\af31505\loch\f1 Point to point list\cell -}\pard\plain \ltrpar\ql \li0\ri0\widctlpar\intbl\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 -\af0 \ltrch\fcs0 \fs16\insrsid7416744\charrsid7416744 \trowd \irow0\irowband0\lastrow \ltrrow\ts11\tsrowd\trgaph108\trbrdrv\brdrs\brdrw10 -\trftsWidth2\trwWidth5000\trftsWidthB3\trautofit1\trpaddl108\trpaddr108\trpaddfl3\trpaddft3\trpaddfb3\trpaddfr3\tblrsid802636\tbllkhdrrows\tbllkhdrcols\tbllknocolband\tblind-1152\tblindtype3 \clvertalt\clbrdrt\brdrtbl \clbrdrl\brdrtbl \clbrdrb\brdrtbl -\clbrdrr\brdrs\brdrw10 \cltxlrtb\clftsWidth3\clwWidth1152\clshdrawnil \cellx-108\clvertalt\clbrdrt\brdrtbl \clbrdrl\brdrs\brdrw10 \clbrdrb\brdrtbl \clbrdrr\brdrtbl \cltxlrtb\clNoWrap\clftsWidth1\clshdrawnil \cellx8022\row }\pard\plain \ltrpar -\s19\qj \li0\ri0\widctlpar\tqc\tx4536\tqr\tx9072\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \fs16\insrsid7416744\charrsid7416744 -\par }}{\headerr \ltrpar \ltrrow\trowd \irow0\irowband0\lastrow \ltrrow\ts11\tsrowd\trgaph115\trbrdrb\brdrs\brdrw10\brdrcf22 -\trftsWidth2\trwWidth5000\trftsWidthB3\trautofit1\trpaddl115\trpaddr115\trpaddfl3\trpaddft3\trpaddfb3\trpaddfr3\tblrsid3155772\tbllkhdrrows\tbllkhdrcols\tbllknocolband\tblind0\tblindtype3 \clvertalt\clbrdrt\brdrtbl \clbrdrl\brdrtbl \clbrdrb\brdrnone -\clbrdrr\brdrs\brdrw10\brdrcf22 \cltxlrtb\clftsWidth2\clwWidth4813\clshdrawnil \cellx8833\clvertalt\clbrdrt\brdrtbl \clbrdrl\brdrs\brdrw10\brdrcf22 \clbrdrb\brdrnone \clbrdrr\brdrtbl \cltxlrtb\clftsWidth2\clwWidth187\clshdrawnil \cellx9181 -\pard\plain \ltrpar\qr \li0\ri0\widctlpar\intbl\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\pararsid7416744 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0\afs34 \ltrch\fcs0 \fs16\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid7416744 \hich\af1\dbch\af31505\loch\f1 The systems biology simulation core algorithm}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\b\fs16\cf21\lang1033\langfe1031\dbch\af0\langnp1033\insrsid7416744\charrsid16667774 \cell }\pard \ltrpar\qj \li0\ri0\widctlpar\intbl\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0 {\field{\*\fldinst {\rtlch\fcs1 \af0 \ltrch\fcs0 -\b\fs16\cf21\insrsid7416744\charrsid7416744 \hich\af1\dbch\af31505\loch\f1 PAGE \\* MERGEFORMAT}}{\fldrslt {\rtlch\fcs1 \af0 \ltrch\fcs0 \b\fs16\cf21\lang1024\langfe1024\noproof\insrsid13642216 \hich\af1\dbch\af31505\loch\f1 5}}}\sectd \ltrsect -\linex0\endnhere\sectdefaultcl\sftnbj {\rtlch\fcs1 \af0 \ltrch\fcs0 \fs16\cf21\dbch\af0\insrsid7416744\charrsid7416744 \cell }\pard \ltrpar\ql \li0\ri0\widctlpar\intbl\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0 {\rtlch\fcs1 \af0 \ltrch\fcs0 -\fs16\insrsid7416744\charrsid7416744 \trowd \irow0\irowband0\lastrow \ltrrow\ts11\tsrowd\trgaph115\trbrdrb\brdrs\brdrw10\brdrcf22 -\trftsWidth2\trwWidth5000\trftsWidthB3\trautofit1\trpaddl115\trpaddr115\trpaddfl3\trpaddft3\trpaddfb3\trpaddfr3\tblrsid3155772\tbllkhdrrows\tbllkhdrcols\tbllknocolband\tblind0\tblindtype3 \clvertalt\clbrdrt\brdrtbl \clbrdrl\brdrtbl \clbrdrb\brdrnone -\clbrdrr\brdrs\brdrw10\brdrcf22 \cltxlrtb\clftsWidth2\clwWidth4813\clshdrawnil \cellx8833\clvertalt\clbrdrt\brdrtbl \clbrdrl\brdrs\brdrw10\brdrcf22 \clbrdrb\brdrnone \clbrdrr\brdrtbl \cltxlrtb\clftsWidth2\clwWidth187\clshdrawnil \cellx9181\row -}\pard\plain \ltrpar\s19\qj \li0\ri0\widctlpar\tqc\tx4536\tqr\tx9072\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 -\fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \fs16\insrsid7416744\charrsid7416744 -\par }}{\*\pnseclvl1\pnucrm\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl2\pnucltr\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl3\pndec\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl4\pnlcltr\pnstart1\pnindent720\pnhang {\pntxta )}} -{\*\pnseclvl5\pndec\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl6\pnlcltr\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl7\pnlcrm\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl8 -\pnlcltr\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl9\pnlcrm\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}\pard\plain \ltrpar\s15\qj \li0\ri0\sa300\widctlpar\brdrb\brdrs\brdrw20\brsp80\brdrcf18 -\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314\contextualspace \rtlch\fcs1 \ab\af0\afs52\alang1025 \ltrch\fcs0 -\b\fs52\expnd1\expndtw5\cf19\lang1031\langfe1031\kerning28\loch\af1\hich\af1\dbch\af31501\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31501\loch\f1 -Point to point list -\par }\pard\plain \ltrpar\s1\qj \li0\ri0\sb480\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ab\af0\afs32\alang1025 \ltrch\fcs0 -\b\fs32\cf17\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31501\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31501\loch\f1 Reviewer number: 1 -\par }\pard\plain \ltrpar\qj \li0\ri0\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -I liked this article a lot! Its dual purpose of 'introducing this software library' and}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 'telling others how to interpret the tricky bits of SBML' are both good goals, and}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -they were integrated well in this paper. -\par }\pard\plain \ltrpar\qj \li0\ri0\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 -\par \hich\af1\dbch\af31505\loch\f1 Thanks. -\par -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 Major Compulsory Revisions: -\par \hich\af1\dbch\af31505\loch\f1 1. Explain the methodology behind the Biomodels database comparison. While I}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 know how the test\hich\af1\dbch\af31505\loch\f1 suite works, I am unclear how you tested models against the}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 Bi\hich\af1\dbch\af31505\loch\f1 o -\hich\af1\dbch\af31505\loch\f1 models database. I know in the past, the only way to compare simulators}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 against the biomodels db was to perform the same analysis on all of them and}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -display the results (Frank Bergmann did thi\hich\af1\dbch\af31505\loch\f1 s in 2008; your reference 20) Is there}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 a new way of mana\hich\af1\dbch\af31505\loch\f1 g\hich\af1\dbch\af31505\loch\f1 ing this comparison? Your Biomodels reference is from}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -2006. At the time, it was a\hich\af1\dbch\af31505\loch\f1 c\hich\af1\dbch\af31505\loch\f1 tually impossible to say who was 'right', because for}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 some models, many si}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 m}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -ulators disagreed with each other. If this\hich\af1\dbch\af31505\loch\f1 is something}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 you've put together yourself, some explanation would be great, and if it's}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -something that Biomodels has done since 2008 and published, a reference to}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 that would be great. If it's something they've done since 2008 but haven't}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 published -\loch\af1\dbch\af31505\hich\f1 \'85\hich\af1\dbch\af31505\loch\f1 I gues\hich\af1\dbch\af31505\loch\f1 s if you could quickly explain it, that'd be good? -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 Minor Essential Revisions: -\par \hich\af1\dbch\af31505\loch\f1 2. You make a point of stating in the Table 1 legend that iBioSim correctly}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 simulates the vast majority of the test suite, but doesn't do delay\loch\af1\dbch\af31505\hich\f1 \'85\hich\af1\dbch\af31505\loch\f1 but in the}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -table, iBioSim has a \hich\af1\dbch\af31505\loch\f1 checkmark for 'Fully SBML Test Suite Compliant'. I know}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 iBioSim has been working on implementing support for delay recently; was this a}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 last-minute update?}{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid5721557 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5721557 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5721557\charrsid8223699 \hich\af1\dbch\af31505\loch\f1 Thanks for pointing this out. }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5721557 -\hich\af1\dbch\af31505\loch\f1 This was a mistake on our side. -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5721557\charrsid5721557 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 3. You don't ex -\hich\af1\dbch\af31505\loch\f1 plicitly state what the deal is with LibSBMLSim's entry "L3, L2v4"}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 i}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 n}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 stead of a checkmark; this should go in the legend. (Also, why can't it}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -up-translate and simulate? I happen to know this is what iBioSim does\loch\af1\dbch\af31505\hich\f1 \'85\hich\af1\dbch\af31505\loch\f1 )}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid5721557 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5721557 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5721557\charrsid5721557 \hich\af1\dbch\af31505\loch\f1 There is now also a checkmark in brackets \hich\af1\dbch\af31505\loch\f1 -(just as in the case of events on COPASI) and the explanation to this table now contains a remark about its meaning. -\par -\par \hich\af1\dbch\af31505\loch\f1 Here, we indicate if a program can natively deal with all levels and versions of SBML. An uptranslation is not always possible because of \hich\af1\dbch\af31505\loch\f1 -incompatibilities between some levels and versions of SBML. It is therefore better to directly support all level/version combinations. -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5721557 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5721557\charrsid5721557 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -4. "The major difference between both is that an event with delay can trigger}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 multiple times before it is executed." Ac\hich\af1\dbch\af31505\loch\f1 tually, what with simultaneous events and}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -priorities, even events with no delays can trigger multiple times before being}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 executed. Case 978 tests this. -\par \hich\af1\dbch\af31505\loch\f1 5. p6: 'assignmens'}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid17104 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid17104 -\par \hich\af1\dbch\af31505\loch\f1 Corrected. -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid17104\charrsid17104 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -6. There are comma issues here and there.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid17104 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid17104 -\par \hich\af1\dbch\af31505\loch\f1 Corrected.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid17104\charrsid17104 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 Discretionary revisions: -\par \hich\af1\dbch\af31505\loch\f1 7. It would also be nice to see what other simulators did with the Biomodels}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 dat}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 base, though if it's a SED-ML thing, it looks like none of the others are going}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -to be able to do it straightforwardly, so that'd be a ton of work for \hich\af1\dbch\af31505\loch\f1 you, and not}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 worth it for a single column of data. Maybe if you ran those four models from the}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -db you failed through those other simulators? It might be that the db itself is}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 wrong for those four\loch\af1\dbch\af31505\hich\f1 \'85}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid7803810 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7803810 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid1975247 \hich\af1\dbch\af31505\loch\f1 Due to some improvements in}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6359808 \hich\af1\dbch\af31505\loch\f1 our lib}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid3421083 \hich\af1\dbch\af31505\loch\f1 rary we are no able to simulate\hich\af1\dbch\af31505\loch\f1 more Biomodel}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7299343 \hich\af1\dbch\af31505\loch\f1 \loch\af1\dbch\af31505\hich\f1 \'85\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid7299343\charrsid7299343 -\hich\af1\dbch\af31505\loch\f1 more}{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid7803810 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7803810\charrsid7803810 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -8. Speaking of the four failed biomodels models, providing \hich\af1\dbch\af31505\loch\f1 a statistic like '99.06%'}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 totally invites questions about the four you failed on, especially since you passed}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -100% of the test suite. Was it numerical issues? Something ill-formed? Are there}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 any other simulators which get the expected results? Even just a \hich\af1\dbch\af31505\loch\f1 sentence or two}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -would be great, but something should be done because everyone is going to}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 focus on the 4 instead of the other 420, unfortunately.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9771718 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9771718 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid4920708 \hich\af1\dbch\af31505\loch\f1 We addressed the matter of \hich\af1\dbch\af31505\loch\f1 problematic\hich\af1\dbch\af31505\loch\f1 \hich\af1\dbch\af31505\loch\f1 -models in the discussion}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid3504179 \hich\af1\dbch\af31505\loch\f1 as part of the lim}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid3504179\hres1\chhres0 -\hich\af1\dbch\af31505\loch\f1 i}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid3504179 \hich\af1\dbch\af31505\loch\f1 tations of our solvers.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9771718 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7803810\charrsid9771718 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -9. Model 966 is not really slow just because there are 23 events, but because}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 those 23 events have to be re-ev\hich\af1\dbch\af31505\loch\f1 aluated thousands of times. Might be worth}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 clarifying.}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid16528461 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 -{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid16528461 -\par \hich\af1\dbch\af31505\loch\f1 Thanks again for\hich\af1\dbch\af31505\loch\f1 pointing this out. \hich\af1\dbch\af31505\loch\f1 We \hich\af1\dbch\af31505\loch\f1 edited this \hich\af1\dbch\af31505\loch\f1 part}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid687199 \hich\af1\dbch\af31505\loch\f1 to clarify this issue}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid2047860 .}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid16528461\charrsid9771718 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid16528461\charrsid16528461 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -10. Both times you use 'SCL', you also explicitly say "Systems Biology Simul}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 tion}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 Core Library" which defeats the purpose of having an acronym. Probably best}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 just to leave the acronym off.}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -Level of int\hich\af1\dbch\af31505\loch\f1 erest: An article of outstanding merit and interest in its field}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9771718 .}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9771718 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9771718 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9177314 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -Quality of written English: Acceptable -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 Statistical review: No, the manuscript does not need to be seen by a}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7416744\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9177314\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 statistician.}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid3880907\charrsid9923232 -\par }\pard\plain \ltrpar\s1\qj \li0\ri0\sb480\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ab\af0\afs32\alang1025 \ltrch\fcs0 -\b\fs32\cf17\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31501\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31501\loch\f1 Reviewer number: 2 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid12800212\charrsid9923232 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 SUMMARY OF PAPER -\par \hich\af1\dbch\af31505\loch\f1 The authors describe an algorithm for solving models encoded in SBML, as well}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 as a Java-based implementation of the algorithm in the form of a software library,}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 and f}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 i}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -nally, the results of tests on the library. The algorithm is based on a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 well-known and \hich\af1\dbch\af31505\loch\f1 time-tested numerical integration algorithm by Rosenbrock, but}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -can evidently support other integrators in a plug-in fashion.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5784096 -\par -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 As a reader familiar with SBML, but someone who has not implemented a}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -simulator myself, I found the paper generally quite rea}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 d}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 able\hich\af1\dbch\af31505\loch\f1 , pleasant and easy}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 to follow, with helpful diagrams and flow charts. -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11417231 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 -{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11417231\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -OVERALL ISSUES: MAJOR COMPULSORY REVISIONS -\par \hich\af1\dbch\af31505\loch\f1 1) The authors concentrate on differential equation models as if this modeling}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 p}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 proach is the only one used in systems biology. This is certa\hich\af1\dbch\af31505\loch\f1 inly not the case:}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -there is a variety of approaches used in systems biology, such as stochastic}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 simulations, Boolean networks, rule-based modeling, etc. It is perfectly fine, and}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -even desirable, to develop an efficient and complete ODE solver focused on}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 SB\hich\af1\dbch\af31505\loch\f1 ML models (consi}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 -\hich\af1\dbch\af31505\loch\f1 d}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 e\hich\af1\dbch\af31505\loch\f1 r\hich\af1\dbch\af31505\loch\f1 -ing how popular SBML is and how complicated SBML}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 models are to solve fully), but the authors should position their work in the proper}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 context. I know for a fact that s} -{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 o}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 me of the coauthors are familiar with other}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 simulation frameworks, so\hich\af1\dbch\af31505\loch\f1 the problem is clearly one of how the paper is written}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -and not a lack of understanding of the vari}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 e}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 ty of approaches used in systems}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 biology. Here are a few places where the text would benefit from revisions:}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid15471139 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 -{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15471139\charrsid9771718 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15471139\charrsid15471139 \hich\af1\dbch\af31505\loch\f1 This is true. We have rewritten important part\hich\af1\dbch\af31505\loch\f1 s of the paper}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid15471139 \hich\af1\dbch\af31505\loch\f1 to point out that the inte}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15471139\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 r}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15471139 \hich\af1\dbch\af31505\loch\f1 pretation of SBML in terms of ODE models is just one }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid12391572 \hich\af1\dbch\af31505\loch\f1 -possible way to solve it}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15471139 .}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15471139\charrsid15471139 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15471139\charrsid9771718 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid15471139 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -- The first sentence of the abstract: "With the increasing availability of high}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 dime}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 n}{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 sional time course data for metabolites, genes, or fluxes the description of}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -dynamical systems by differential equation models becomes more and more}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 popular in systems biology." That is an assertion by the authors, and it reads as if}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 it is a statement abou -\hich\af1\dbch\af31505\loch\f1 t the growth of popularity of ODE models compared to other}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 techniques. Either the authors need to back it up with references showing that}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 ODE modeling is gaining p}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 o}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 pularity compared to other methods, or else the}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 statement should be modified.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15471139 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid5074791 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5074791 -\par \hich\af1\dbch\af31505\loch\f1 The implicit \hich\af1\dbch\af31505\loch\f1 -implication of a growing popularity of certain modeling aspects has been removed. This was actually not what the point should be here. We wanted to point out that modeling in general is important. In the first sentence, we have therefore now removed the s -\hich\af1\dbch\af31505\loch\f1 t\hich\af1\dbch\af31505\loch\f1 atement about a particular modeling framework. -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5074791\charrsid5074791 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -- p. 2: "The models encoded in these formats can be interpreted in terms of}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 differe}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 n}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 tial equation systems, with additional structures such as discrete events}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 and algebr}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -ic equations." They can be interpreted \hich\af1\dbch\af31505\loch\f1 in other ways too. -\par \hich\af1\dbch\af31505\loch\f1 - p. 3: "In order to derive an algorithm for the interpretation of SBML models ..."}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 The statement should be qualified, for example "In order to derive an algorithm}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -for the interpretation of SBML models in a differential equation framewor\hich\af1\dbch\af31505\loch\f1 k ..."}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 There are probably other places where this issue should be addressed; the}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -above are only some places where it was especially noticeable. -\par \hich\af1\dbch\af31505\loch\f1 2) The section on Background on p. 2 makes statements about SBML and}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 CellML, but the claims about CellML are ove\hich\af1\dbch\af31505\loch\f1 rstatements. E.g., "... a large variety}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -of programs supports these model description languages." Really? The authors}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 want to claim there is "a large variety" of programs that support CellML? Another}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -example: "Both communities offer standardized and manuall\hich\af1\dbch\af31505\loch\f1 y derived benchmark}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 test in order to evaluate the quality of simulation results." Benchmarks exist for}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -CellML? If that's true, would the authors mind providing a reference for that}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 claim? My impression has a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 -\hich\af1\dbch\af31505\loch\f1 l}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 ways been that CellML has nowhere the level of}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 a\hich\af1\dbch\af31505\loch\f1 -cceptance or testing that SBML has; therefore, to make such statements is not}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 scientifically rigorous. Further, to any reader familiar with SBML, it comes across}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -as a disingenuous attempt to make the authors' work seem more broadly}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 applicable. The bulk of \hich\af1\dbch\af31505\loch\f1 the text is intensely infl}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 u}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -enced by SBML, to the point}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 where it uses terms such as "kinetic laws" and "algebr}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 ic rules" -- terms that do}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 not exist outside of SBML, so the lip service paid to CellML support is not}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -particularly believable anyway. -\par \hich\af1\dbch\af31505\loch\f1 3) The desc\hich\af1\dbch\af31505\loch\f1 ription of how SBML constructs are handled is not complete.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 (Presum}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -bly this is a problem of exposition in the paper and not actually a failure}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 of the impl}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 e}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 mentation.) For example, SBML provides a facility for declaring new}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 function defin}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 i}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -tions, but the authors do not describe how their algorithm would}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 process such fun}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 c}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 tion definitions. The authors' software can probably handle}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 them easily, but still, in a p}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 per like this, it would be appropriate to include a few}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 words of explanation about \hich\af1\dbch\af31505\loch\f1 the stage at which function definitions are processed.}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -Another matter is the ability in SBML to reassign stoichiometry values}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 dynamically via the \hich\af1\dbch\af31505\loch\f1 "StoichiometryMath" \hich\af1\dbch\af31505\loch\f1 co}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 n}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -struct. Still another is whether the}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 system does anything with SBML's "Constra}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 -\hich\af1\dbch\af31505\loch\f1 i}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 nts" con\hich\af1\dbch\af31505\loch\f1 struct. The description of the}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -SBSCL seems incomplete without some explan}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 tions, or at least passing}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 mention, of these things.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9008586 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9008586 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid730977 \hich\af1\dbch\af31505\loch\f1 We}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13654333 \hich\af1\dbch\af31505\loch\f1 added}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid4875799 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7960638 \hich\af1\dbch\af31505\loch\f1 additional sections to describe the -\hich\af1\dbch\af31505\loch\f1 processing of \hich\af1\dbch\af31505\loch\f1 function definitions, }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid4875799 \loch\af1\dbch\af31505\hich\f1 \'93}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid4875799\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 StoichiometryMath}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid4875799 \loch\af1\dbch\af31505\hich\f1 \'94}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid7960638 \hich\af1\dbch\af31505\loch\f1 , \hich\af1\dbch\af31505\loch\f1 and }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid4875799 \loch\af1\dbch\af31505\hich\f1 \'93 -\hich\af1\dbch\af31505\loch\f1 Co\hich\af1\dbch\af31505\loch\f1 n\hich\af1\dbch\af31505\loch\f1 straints\loch\af1\dbch\af31505\hich\f1 \'94}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid7960638 .}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9008586 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9008586\charrsid9008586 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -4) There is very little discussion about the points of control that the user has to}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 deal with. What are the settings on the numer\hich\af1\dbch\af31505\loch\f1 ical methods that have to be}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 manually a}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 d}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -justed? (Or is the system so automatic that you can throw any model}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 at it and it will figure out what to do?) A sentence or two would help readers to}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -understand what they would be faced with if they tried to apply th\hich\af1\dbch\af31505\loch\f1 e library to a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 problem.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid5246403 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5246403 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6953150 \hich\af1\dbch\af31505\loch\f1 W\hich\af1\dbch\af31505\loch\f1 e addressed this point \hich\af1\dbch\af31505\loch\f1 at the end of our\hich\af1\dbch\af31505\loch\f1 - conclusions.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5246403 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6953150\charrsid5246403 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -5) There is very little discussion about the limitations of the algorithm and}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 software. It is implied that all possible SBML models can be handled, but are}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -there any cases where (e.g.) the system has more difficulty converging on}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 so\hich\af1\dbch\af31505\loch\f1 lutions than others? Are there other limitations?}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11493042 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 -{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11493042 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9838084 \hich\af1\dbch\af31505\loch\f1 This }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5733786 \hich\af1\dbch\af31505\loch\f1 point }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid1194370 \hich\af1\dbch\af31505\loch\f1 is also addressed \hich\af1\dbch\af31505\loch\f1 at the end of our\hich\af1\dbch\af31505\loch\f1 conclusions.}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid11229678 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13642216\charrsid11493042 -\par }\pard \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11417231 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11417231\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 MINOR ESSENTIAL REVISIONS -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 1: -\par \hich\af1\dbch\af31505\loch\f1 - "or fluxes" -> "and fluxes". -\par \hich\af1\dbch\af31505\loch\f1 - Comma after "fluxes". -\par \hich\af1\dbch\af31505\loch\f1 - "becomes more and more" -> "is becoming more". -\par \hich\af1\dbch\af31505\loch\f1 - In the last sentence of the first paragraph, "due to many special cases" is -\par \hich\af1\dbch\af31505\loch\f1 ambiguous. What has special cases? SBML or mathematical structures? -\par \hich\af1\dbch\af31505\loch\f1 - "This article describes an efficient algorithm to interpret and solve differential}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 equ}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 -a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 tion systems in SBML \hich\af1\dbch\af31505\loch\f1 models". This is not quite right. SBML models do not}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -contain differential equation systems, or at least not unless they are structured in}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 a very p}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 e}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 culiar way that avoids the use of the SBML reaction and uses rules}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 only. A stat}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 e}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -ment such as "derived from SB\hich\af1\dbch\af31505\loch\f1 ML models" would be more correct. -\par \hich\af1\dbch\af31505\loch\f1 - "pre-processing" does not need a hyphen.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid13635418 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 -{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11469972 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13635418 \hich\af1\dbch\af31505\loch\f1 Corrected.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13635418\charrsid13635418 -\par }\pard \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 2: -\par \hich\af1\dbch\af31505\loch\f1 - First paragraph: add "the" after "biology," and before "modeling". -\par \hich\af1\dbch\af31505\loch\f1 - "efforts like this require a strong collaboration": remove "a". -\par \hich\af1\dbch\af31505\loch\f1 - First sentence of 2nd paragraph: "or CellML" -> "and CellML". -\par \hich\af1\dbch\af31505\loch\f1 - "online data bases" -> "online databases". -\par \hich\af1\dbch\af31505\loch\f1 - "such as the BioModels database" -> "such as BioModels Database". -\par \hich\af1\dbch\af31505\loch\f1 - "or the CellML model repository" -> "and the CellML model repository". -\par \hich\af1\dbch\af31505\loch\f1 - "apr\hich\af1\dbch\af31505\loch\f1 oaches" -> "approaches". -\par \hich\af1\dbch\af31505\loch\f1 - The sentence beginning with "For efficient model analysis" is very awkward and -\par \hich\af1\dbch\af31505\loch\f1 almost incomprehensible. Please rewrite. -\par {\listtext\pard\plain\ltrpar \s17 \rtlch\fcs1 \ai\af0 \ltrch\fcs0 \f1\cf20\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -\tab}}\pard \ltrpar -\s17\qj \fi-360\li720\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls1\adjustright\rin0\lin720\itap0\pararsid6097275 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -"benchmark test in order to" -> "benchmark tests in order to". -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid1443162 \hich\af1\dbch\af31505\loch\f1 Corrected. (Look at the sentence beginning \hich\af1\dbch\af31505\loch\f1 with \loch\af1\dbch\af31505\hich\f1 \'93\hich\af1\dbch\af31505\loch\f1 -For efficient model \loch\af1\dbch\af31505\hich\f1 \'85\'94\hich\af1\dbch\af31505\loch\f1 ) -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid1443162\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 3: -\par \hich\af1\dbch\af31505\loch\f1 - "implicated" -> "implied" -\par \hich\af1\dbch\af31505\loch\f1 - "further systems biological" -> "other systems biology" (note: 2 changes). -\par \hich\af1\dbch\af31505\loch\f1 - "It comprises several" -> "It is comprised of several". -\par \hich\af1\dbch\af31505\loch\f1 - "re-use" does not need a hyphen. -\par \hich\af1\dbch\af31505\loch\f1 - "In order to derive an algorithm for the interpretation of SBML models": this is}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 one of the places where the paper implies ODEs are the only option. This}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -sentence should be qualified, for example by being rewritten to say "In order to}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 derive an alg}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 o}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 rithm\hich\af1\dbch\af31505\loch\f1 for the interpretation of SBML models in terms of differential}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 equations". -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5335191 \hich\af1\dbch\af31505\loch\f1 Corrected. -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5335191\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 4: -\par \hich\af1\dbch\af31505\loch\f1 - "non-linear" does not need a hyphen. -\par \hich\af1\dbch\af31505\loch\f1 - "Species, whose amounts": remove comma. -\par \hich\af1\dbch\af31505\loch\f1 - "in any reaction and do hence have only" -> "in any reaction and hence only}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 ha\hich\af1\dbch\af31505\loch\f1 ve". -\par \hich\af1\dbch\af31505\loch\f1 - "A further concept of SBML models are" -> "A further concept in SBML is". -\par }\pard\plain \ltrpar\qj \li0\ri0\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0\pararsid16667774 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid16667774 -\par \hich\af1\dbch\af31505\loch\f1 Corrected}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid16667774\charrsid9923232 . -\par }\pard \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid16667774\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 5: -\par \hich\af1\dbch\af31505\loch\f1 - "With the help of a bipartite matching" -> "With the help of bipartite matching". -\par \hich\af1\dbch\af31505\loch\f1 - "Sub-systems" does not need a hyphen. -\par \hich\af1\dbch\af31505\loch\f1 - "All kinetic laws of the react\hich\af1\dbch\af31505\loch\f1 ions": the term "kinetic laws" is odd, and presumably}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 s}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 o}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -mething borrowed from SBML. Could the statement be qualified somehow to}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 make that more clear? -\par \hich\af1\dbch\af31505\loch\f1 - "Deviating initial values defined by initial assignments and are now assigned".}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 The sentence doesn't mak\hich\af1\dbch\af31505\loch\f1 e sense. -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid2384365 \hich\af1\dbch\af31505\loch\f1 Corrected. (Look again at the corrected sentence in the last point.) -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid2384365\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 6: -\par \hich\af1\dbch\af31505\loch\f1 - "In order to deal with algebraic rules in an SBML model, these have to be}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 converted to assignment rules." This is written as a universal statement, but is it}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 not possib -\hich\af1\dbch\af31505\loch\f1 le that a different approach might choose to do things differently? The}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 u}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 thors should probably qualify that statement to say this is the approach taken}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 in their part}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 i}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -cular algorithm. -\par \hich\af1\dbch\af31505\loch\f1 - "these have to be" -> "they have to be". -\par \hich\af1\dbch\af31505\loch\f1 - Omit the comma ater "at least one variable,". -\par \hich\af1\dbch\af31505\loch\f1 - "other equations in model" -> "other equations in the model". -\par \hich\af1\dbch\af31505\loch\f1 - "the regarding algebraic rule": unfathomable. -\par \hich\af1\dbch\af31505\loch\f1 - Omit the comma after "to computing a matching,". -\par \hich\af1\dbch\af31505\loch\f1 - "An event in SBML is a function": no, it is not. It is a list of assignments. -\par \hich\af1\dbch\af31505\loch\f1 - "In addition, a delay may": it is not clear what the source of the delay is. I think -\par \hich\af1\dbch\af31505\loch\f1 the authors mean that the SBML event concept has an optional slot for defining a}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 delay; t\hich\af1\dbch\af31505\loch\f1 hey are not talking about some external source of delays. -\par \hich\af1\dbch\af31505\loch\f1 - "assignmens" -> "assignments". -\par \hich\af1\dbch\af31505\loch\f1 - "exeuted" -> "executed". -\par \hich\af1\dbch\af31505\loch\f1 - "but with an huge impact" -> "but these have a huge impact". -\par \hich\af1\dbch\af31505\loch\f1 - Insert "For example," before "the order in which events". -\par \hich\af1\dbch\af31505\loch\f1 - The statement\hich\af1\dbch\af31505\loch\f1 "the order in which events have to be processed used to be at}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 pr}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 o}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -grammers discretion" is confusing. I think the authors mean that it was the}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 case in SBML Level 2, and changed in SBML Level 3. -\par \hich\af1\dbch\af31505\loch\f1 - "there are events, whose trigger has" -> "there are events wh\hich\af1\dbch\af31505\loch\f1 ose triggers have"}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 (3 changes).}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589 - -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid5717130 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5717130 -\par \hich\af1\dbch\af31505\loch\f1 Corrected.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid5717130\charrsid5717130 -\par }\pard \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 7: -\par \hich\af1\dbch\af31505\loch\f1 - "non-persistent" does not need a hyphen. -\par \hich\af1\dbch\af31505\loch\f1 - What is a non-persistent event? Is it an SBML concept? -\par \hich\af1\dbch\af31505\loch\f1 - "This process repeats itself" -> "This process must be repeated". -\par \hich\af1\dbch\af31505\loch\f1 - Omit the comma in "The precise calc\hich\af1\dbch\af31505\loch\f1 ulation of the time, when events". -\par \hich\af1\dbch\af31505\loch\f1 - Add a comma before "Rosenbrock's method determines the new". -\par \hich\af1\dbch\af31505\loch\f1 - Add a comma after "that" in "After that the events". -\par \hich\af1\dbch\af31505\loch\f1 - Omit the comma in "the time, at which". -\par \hich\af1\dbch\af31505\loch\f1 - Change the colon to a period in "is calculated as follows:". -\par \hich\af1\dbch\af31505\loch\f1 - Omit the comma after "in all dimensions, in which". -\par \hich\af1\dbch\af31505\loch\f1 - Add a comma after "the second step" in "During the second step the derivatives}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 of all species". -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid14223803 \hich\af1\dbch\af31505\loch\f1 Corrected. -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid14223803\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 8: -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid4068990 \hich\af1\dbch\af31505\loch\f1 - There should be a reference given for the Apache Commons Math library. -\par \hich\af1\dbch\af31505\loch\f1 - The 2nd paragraph talks about the use of KiSAO, but no explanation is given}{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid6097275\charrsid4068990 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid4068990 \hich\af1\dbch\af31505\loch\f1 about the significance. What is it about? How is it used? -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 - "support for further community" -> "support for other community". -\par \hich\af1\dbch\af31505\loch\f1 - "Biomodel 206" -> "BioModels Database model #206". -\par \hich\af1\dbch\af31505\loch\f1 - "Biomodel 390" -> "BioModels Database model #390". -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 10: -\par \hich\af1\dbch\af31505\loch\f1 - "makes possible" -> "makes it possible". -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid12006280 -\par \hich\af1\dbch\af31505\loch\f1 Corrected.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid12006280 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 p. 11: -\par \hich\af1\dbch\af31505\loch\f1 - "a high performance of the overall library" -> "that the overall library offers high -\par \hich\af1\dbch\af31505\loch\f1 performance". -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid6097275 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 - Add comma after "SBML" in " -\hich\af1\dbch\af31505\loch\f1 models encoded in SBML returns". -\par \hich\af1\dbch\af31505\loch\f1 - "In the SBMLInterpreter events" -> "In the SBMLInterpreter object, events" -\par \hich\af1\dbch\af31505\loch\f1 - "currently stored in list" -> "currently stored in a list". -\par \hich\af1\dbch\af31505\loch\f1 - Omit comma after "One could argue,". -\par \hich\af1\dbch\af31505\loch\f1 - "where after" -> "whereafter".}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9595112 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9595112 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid9595112\charrsid9595112 \hich\af1\dbch\af31505\loch\f1 Corrected? -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9595112\charrsid9595112 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9595112 \hich\af1\dbch\af31505\loch\f1 - The last 2 -\hich\af1\dbch\af31505\loch\f1 sentences of that page are really unclear. I do not even know what t}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9595112\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 o}{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275\charrsid9595112 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9595112 \hich\af1\dbch\af31505\loch\f1 suggest.}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589 -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9595112 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 { -\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9595112\charrsid9595112 -\par }\pard \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid15345727 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15345727 \hich\af1\dbch\af31505\loch\f1 We -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15490856 \hich\af1\dbch\af31505\loch\f1 changed thi\hich\af1\dbch\af31505\loch\f1 s part }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid15490856\charrsid15490856 \hich\af1\dbch\af31505\loch\f1 slightly}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15490856 \hich\af1\dbch\af31505\loch\f1 . }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid9849930 \hich\af1\dbch\af31505\loch\f1 We hope this \hich\af1\dbch\af31505\loch\f1 change \hich\af1\dbch\af31505\loch\f1 makes }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6165173 -\hich\af1\dbch\af31505\loch\f1 it clearer.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid6097275 -\par }\pard \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9595112 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid9595112\charrsid9595112 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid4068990 \hich\af1\dbch\af31505\loch\f1 -Figures 2-4: I suspect the arrowheads on the arcs are too small for the final}{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid15822248\charrsid4068990 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\cf6\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid4068990 \hich\af1\dbch\af31505\loch\f1 public}{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid4068990\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a}{ -\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid4068990 \hich\af1\dbch\af31505\loch\f1 tion.}{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid15822248\charrsid4068990 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \cf6\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid4068990 \hich\af1\dbch\af31505\loch\f1 Captions: they all have more issues, but I did not have time to write them here. -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11417231 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 -{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11417231\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 DISCRETIONARY REVISIONS -\par \hich\af1\dbch\af31505\loch\f1 1) There is very little discussion about the performance of their algorithm beyond}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 -\af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 some words about the speed with which it can solve test models and the models}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -in the BioModels Database. The models in the SBML testing suite are app\hich\af1\dbch\af31505\loch\f1 arently}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 all rel}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 a -}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 tively small. How does the system performance scale with model size? It}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -would be useful to see some sort of plot or other comparison of (1) model size}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 versus run time as well as (2) memory consumption versus model size. If}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 available, a simu -\hich\af1\dbch\af31505\loch\f1 ltan}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 e}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 ous plot against some other software they tested such as}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 -\hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 BioUML might be interes}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 t}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -ing (but not crucial). -\par \hich\af1\dbch\af31505\loch\f1 2) SBML has a notion of extensions that add syntax to the basic definition of}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 SBML. Some recent extensions include support for such things as decom\hich\af1\dbch\af31505\loch\f1 posing}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 m}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 o}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -dels, and supporting rule-based models. It would be appropriate to mention}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 (perhaps in the discussion section) how the library handles SBML models with}{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 these extens}{\rtlch\fcs1 \af0 -\ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232\hres1\chhres0 \hich\af1\dbch\af31505\loch\f1 i}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -ons, or what the authors' plans are for dealing with them in the}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid15822248\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 }{\rtlch\fcs1 \af0 \ltrch\fcs0 -\lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 future. -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11417231\charrsid9923232 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 Level of interest: An article of outstanding merit and interest in its field -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11417231\charrsid9923232 -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 Quality of written English: Needs some language corrections before being -\par }{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11417231\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 P}{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -ublished -\par }\pard\plain \ltrpar\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11417231 \rtlch\fcs1 \af0\afs24\alang1025 \ltrch\fcs0 \fs24\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 -{\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid11417231\charrsid9923232 -\par }\pard\plain \ltrpar\s17\qj \li0\ri0\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid12800212 \rtlch\fcs1 \ai\af0\afs24\alang1025 \ltrch\fcs0 -\i\fs24\cf20\lang1031\langfe1031\loch\af1\hich\af1\dbch\af31505\cgrid\langnp1031\langfenp1031 {\rtlch\fcs1 \af0 \ltrch\fcs0 \lang1033\langfe1031\langnp1033\insrsid13246589\charrsid9923232 \hich\af1\dbch\af31505\loch\f1 -Statistical review: No, the manuscript does not need to be seen by a -\par \hich\af1\dbch\af31505\loch\f1 statistician. -\par 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a/doc/publications/2012_BMC_SystBiol/Review/Submitted_article.pdf b/doc/publications/2012_BMC_SystBiol/Review/Submitted_article.pdf deleted file mode 100644 index 8d17ccbe..00000000 Binary files a/doc/publications/2012_BMC_SystBiol/Review/Submitted_article.pdf and /dev/null differ diff --git a/doc/publications/2012_BMC_SystBiol/bmc_article.bib b/doc/publications/2012_BMC_SystBiol/bmc_article.bib index cde5aee7..6c46aaa0 100755 --- a/doc/publications/2012_BMC_SystBiol/bmc_article.bib +++ b/doc/publications/2012_BMC_SystBiol/bmc_article.bib @@ -1,91 +1,11 @@ % This file was created with JabRef 2.7.2. % Encoding: Cp1252 -@ARTICLE{Takizawa2013, - author = {Takizawa, Hiromu and Nakamura, Kazushige and Tabira, Akito and Chikahara, - Yoichi and Matsui, Tatsuhiro and Hiroi, Noriko and Funahashi, Akira}, - title = {{LibSBMLSim: A reference implementation of fully functional SBML - simulator}}, - journal = {Bioinformatics}, - year = {2013}, - month = apr, - abstract = {MOTIVATION: The Systems Biology Markup Language (SBML) is currently - supported by over 230 software tools, among which 160 support numerical - integration of ordinary differential equation (ODE) models. Although - SBML is a widely accepted standard within this field, there is still - no language-neutral library which supports all features of SBML for - simulating ODE models. Therefore, a demand exists for a simple, portable - implementation of a numerical integrator which supports SBML in order - to enhance the development of a computational platform for systems - biology. - - RESULTS: We implemented a library called libSBMLSim which supports - all the features of SBML and confirmed that the library passes all - tests in the SBML test suite including SBML Events, AlgebraicRules, - "fast" attribute on Reactions and Delay. LibSBMLSim is implemented - in the C programming language and does not depend on any third-party - library except libSBML, which is a library to handle SBML documents. - For the numerical integrator, both explicit and implicit methods - are written from scratch to support all the functionality of SBML - features in a straightforward implementation. We succeeded in implementing - libSBMLSim as a platform-independent library which can run on most - common operating systems (Windows, MacOSX, and Linux) and also provides - several language bindings (Java, C#, Python, and Ruby). - - AVAILABILITY: The source code of libSBMLSim is available from - \url{http://fun.bio.keio.ac.jp/software/libsbmlsim/}. - LibSBMLSim is distributed under the terms of LGPL. CONTACT: funa@bio.keio.ac.jp.}, - doi = {10.1093/bioinformatics/btt157}, - institution = {Department of Biosciences and Informatics, Keio University, 3-14-1 - Hiyoshi, Kouhoku-ku, Yokohama, Japan.}, - language = {eng}, - medline-pst = {aheadofprint}, - pii = {btt157}, - pmid = {23564843}, - url = {http://dx.doi.org/10.1093/bioinformatics/btt157} -} - - -@ARTICLE{Raymond2003, - author = {Raymond, G. M. and Butterworth, E. and Bassingthwaighte, J. B.}, - title = {{JSIM: Free software package for teaching physiological modeling - and research}}, - journal = {Experimental Biology}, - year = {2003}, - volume = {280}, - pages = {102--107} -} - @webpage{Funahashi2012, title = {{LibSBMLSim: The library for simulating SBML models}}, url = {http://fun.bio.keio.ac.jp/software/libsbmlsim/} } -@webpage{ApacheCommonsMath2013, - title = {{Commons Math: The Apache Commons Mathematics Library}}, - url = {http://commons.apache.org/proper/commons-math/} -} - -@webpage{SBMLsoftwareMatrix2012, - title = {{SBML Software Matrix (October 8\textsuperscript{th} 2012)}}, - url = {http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix} -} - -@webpage{SBMLsimulator2013, - title = {{SBMLsimulator---An efficient Java\texttrademark{} solver implementation for SBML}}, - url = {http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsimulator} -} - -@webpage{SBMLtestSuite2013, - title = {SBML Test Suite}, - url = {http://sbml.org/Software/SBML_Test_Suite} -} - -@webpage{jlibsedml2013, - title = {Java Resources for SED-ML}, - url = {http://jlibsedml.sourceforge.net} -} - @ARTICLE{Macilwain2011, author = {Macilwain, Colin}, title = {Systems biology: evolving into the mainstream}, @@ -467,7 +387,7 @@ @ARTICLE{Draeger2008 @ARTICLE{Draeger2011b, author = {Dr\"ager, Andreas and Rodriguez, Nicolas and Dumousseau, Marine and - D\"orr, Alexander and Wrzodek, Clemens and {Le Nov\`{e}re}, Nicolas + D\"orr, Alexander and Wrzodek, Clemens and Le Nov\`{e}re, Nicolas and Zell, Andreas and Hucka, Michael}, title = {{JSBML: a flexible Java library for working with SBML}}, journal = {Bioinformatics}, @@ -508,7 +428,7 @@ @INCOLLECTION{Ermentrout2012 booktitle = {Computational Systems Neurobiology}, publisher = {Springer Netherlands}, year = {2012}, - editor = {{Le Nov\`{e}re}, Nicolas}, + editor = {Le Nov{\`e}re, Nicolas}, pages = {519--531}, note = {10.1007/978-94-007-3858-4_17}, abstract = {This chapter describes the XPPAUT software package. XPPAUT is a general @@ -534,7 +454,7 @@ @TECHREPORT{Finney2003a } @TECHREPORT{Finney2006, - author = {Finney, Andrew and Hucka, Michael and {Le Nov\`{e}re}, Nicolas}, + author = {Finney, Andrew and Hucka, Michael and Le Nov\'ere, Nicolas}, title = {{Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions}}, year = {2006}, @@ -640,7 +560,7 @@ @ARTICLE{Hoops2006 @ARTICLE{hopcroft1973n, author = {Hopcroft, John E. and Karp, Richard M.}, - title = {An $n^{5/2}$ algorithm for maximum matchings in bipartite graphs}, + title = {An n\^{}5/2 algorithm for maximum matchings in bipartite graphs}, journal = {SIAM Journal on Computing}, year = {1973}, volume = {2}, @@ -710,7 +630,7 @@ @ARTICLE{Hucka2004 @TECHREPORT{Hucka2008, author = {Hucka, Michael and Finney, Andrew and Hoops, Stefan and Keating, - Sarah M. and {Le Nov\`{e}re}, Nicolas}, + Sarah M. and Le Nov\`ere, Nicolas}, title = {{Systems biology markup language (SBML) Level 2: structures and facilities for model definitions}}, institution = {Nature Precedings}, @@ -799,7 +719,7 @@ @TECHREPORT{Hucka2001 @TECHREPORT{Hucka2007, author = {Hucka, Michael and Finney, Andrew M. and Hoops, Stefan and Keating, - Sarah M. and {Le Nov\`{e}re}, Nicolas}, + Sarah M. and Le Nov\'ere, Nicolas}, title = {{Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions}}, year = {2007}, @@ -935,7 +855,7 @@ @INPROCEEDINGS{Kron10EvA2 } @ARTICLE{Novere2006a, - author = {{Le Nov\`{e}re}, Nicolas and Bornstein, Benjamin J. and Broicher, Alexander + author = {Le Nov{\`e}re, Nicolas and Bornstein, Benjamin J. and Broicher, Alexander and Courtot, M{\'e}lanie and Donizelli, Marco and Dharuri, Harish and Li, Lu and Sauro, Herbert and Schilstra, Maria and Shapiro, Bruce and Snoep, Jacky L. and Hucka, Michael}, @@ -945,7 +865,7 @@ @ARTICLE{Novere2006a year = {2006}, volume = {34}, pages = {D689--D691}, - abstract = {BioModels Database (\url{http://www.ebi.ac.uk/biomodels/}), part of the + abstract = {BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peerreviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to diff --git a/doc/publications/2012_BMC_SystBiol/bmc_article.tex b/doc/publications/2012_BMC_SystBiol/bmc_article.tex index 01a4061d..96d2fb58 100755 --- a/doc/publications/2012_BMC_SystBiol/bmc_article.tex +++ b/doc/publications/2012_BMC_SystBiol/bmc_article.tex @@ -67,10 +67,6 @@ \usepackage{rotating} \usepackage{multirow} \usepackage[normalem]{ulem} -\usepackage{xspace} -\usepackage[printonlyused]{acronym} -\usepackage[version=3]{mhchem} -\usepackage[normalem]{ulem} \definecolor{royalblue}{cmyk}{.93, .79, 0, 0} \definecolor{lightblue}{cmyk}{.10, .017, 0, 0} @@ -128,10 +124,10 @@ %\newenvironment{bmcformat}{\begin{raggedright}\baselineskip20pt\sloppy\setboolean{publ}{false}}{\end{raggedright}\baselineskip20pt\sloppy} %Publication style settings -\newenvironment{bmcformat}{\fussy\setboolean{publ}{true}}{\fussy} +%\newenvironment{bmcformat}{\fussy\setboolean{publ}{true}}{\fussy} %New style setting -%\newenvironment{bmcformat}{\baselineskip20pt\sloppy\setboolean{publ}{false}}{\baselineskip20pt\sloppy} +\newenvironment{bmcformat}{\baselineskip20pt\sloppy\setboolean{publ}{false}}{\baselineskip20pt\sloppy} @@ -161,26 +157,25 @@ \definecolor{winered}{cmyk}{0,1,0.331,0.502} \definecolor{lightgray}{gray}{0.97} -\newcommand{\TODO}[1]{\textcolor{red}{#1}} -\newcommand{\COR}[1]{\textcolor{blue}{#1}} -\newcommand{\AbstractDESSolver}{\texttt{Abstract\-DES\-Solver}\xspace} -\newcommand{\AlgebraicRule}{\texttt{Algebraic\-Rule}\xspace} -\newcommand{\AssignmentRule}{\texttt{Assignment\-Rule}\xspace} -\newcommand{\OverdeterminationValidator}{\texttt{Overdetermination\-Validator}\xspace} -\newcommand{\SBMLinterpreter}{\texttt{SBML\-interpreter}\xspace} -\newcommand{\FirstOrderSolver}{\texttt{First\-Order\-Solver}\xspace} -\newcommand{\AbstractIntegrator}{\texttt{AbstractIntegrator}\xspace} -\newcommand{\MultiTable}{\texttt{Multi\-Table}\xspace} -\newcommand{\Block}{\texttt{Block}\xspace} -\newcommand{\jlibsedml}{\texttt{jlibsedml}\xspace} -\newcommand{\EventInProgress}{\texttt{Event\-In\-Progress}\xspace} -\newcommand{\ASTNodeInterpreter}{\texttt{ASTNode\-In\-terpreter}\xspace} -\newcommand{\SBMLEventInProgressWithDelay}{\texttt{SBML\-Event\-In\-Progress\-With\-Delay}\xspace} -\newcommand{\true}{\emph{true}\xspace} -\newcommand{\false}{\emph{false}\xspace} - -\newcommand{\yes}{\ding{51}\xspace} %{\parbox[c]{1.3em}{\ding{51}}} %\Large\square\hspace{-.65em} -\newcommand{\no}{--\xspace} %{\parbox[c]{1.3em}{--} %\Large\square\hspace{-.62em}--} +\newcommand{\TODO}[1]{\textcolor{red}{\textbf{#1}}} +\newcommand{\AbstractDESSolver}{\texttt{Abstract\-DES\-Solver}} +\newcommand{\AlgebraicRule}{\texttt{Algebraic\-Rule}} +\newcommand{\AssignmentRule}{\texttt{Assignment\-Rule}} +\newcommand{\OverdeterminationValidator}{\texttt{Overdetermination\-Validator}} +\newcommand{\SBMLinterpreter}{\texttt{SBML\-interpreter}} +\newcommand{\FirstOrderSolver}{\texttt{First\-Order\-Solver}} +\newcommand{\AbstractIntegrator}{\texttt{AbstractIntegrator}} +\newcommand{\MultiTable}{\texttt{Multi\-Table}} +\newcommand{\Block}{\texttt{Block}} +\newcommand{\jlibsedml}{\texttt{jlibsedml}} +\newcommand{\EventInProgress}{\texttt{Event\-In\-Progress}} +\newcommand{\ASTNodeInterpreter}{\texttt{ASTNode\-In\-terpreter}} +\newcommand{\SBMLEventInProgressWithDelay}{\texttt{SBML\-Event\-In\-Progress\-With\-Delay}} +\newcommand{\true}{\emph{true}} +\newcommand{\false}{\emph{false}} + +\newcommand{\yes}{\ding{51}} %{\parbox[c]{1.3em}{\ding{51}}} %\Large\square\hspace{-.65em} +\newcommand{\no}{--} %{\parbox[c]{1.3em}{--} %\Large\square\hspace{-.62em}--} % centered columns with fixed width \newcolumntype{C}[1]{>{\centering\arraybackslash}p{#1}} @@ -219,11 +214,6 @@ % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\urlstyle{same} - -\hyphenation{ -J-SB-ML -} % Begin ... \begin{document} @@ -255,7 +245,7 @@ \author{% Roland Keller$^{1}$, %\email{Roland Keller - roland.keller@uni-tuebingen.de}, Alexander D\"orr$^{1}$, %\email{Alexander D\"orr - alexander.doerr@uni-tuebingen.de}, -Akito Tabira$^{2}$, %\email{Akito Tabira - tabira@fun.bio.keio.ac.jp} +Akito Tabira$^{2}$, %\email{Akito Tabira - mythosil_full_throttle@i.softbank.jp} Akira Funahashi$^{2}$, %\email{Akira Funahashi - funa@bio.keio.ac.jp} Michael J. Ziller$^{3}$, %\email{Michael J. Ziller - michael_ziller@harvard.edu} Richard Adams$^{4}$, %\email{Richard Adams - richard.adams@ed.ac.uk} @@ -306,23 +296,23 @@ \textbf{Background:} % Do not use inserted blank lines (ie \\) until main body of text. With the increasing availability of high dimensional time course data for -metabolites, genes, \COR{and} fluxes\COR{,} the \COR{mathematical} description -of dynamical systems -\sout{by differential equation models becomes more and more popular} -\COR{has become an essential aspect of research} -in systems biology. +metabolites, genes, or fluxes the description of dynamical systems by +differential equation models becomes more and more popular in systems biology. %driven by the aim to make biological phenomena predictable. -Models are often encoded in formats such as \acs{SBML}, whose \sout{mathematical} -structure is very complex and difficult to evaluate due to many special cases. -%A flexible interpreter for \acs{SBML} as well as numerical integrators are hence necessary to solve these models. +The diversity of modeling aproaches and experimental data requires customized +software solutions for very specific tasks. +Models are often encoded in formats such as SBML (Systems Biology Markup +Language), but +their mathematical structure is very complex and difficult to evaluate due to +many special cases. +%A flexible interpreter for SBML as well as numerical integrators are hence necessary to solve these models. \textbf{Results:} -This article describes an efficient algorithm to -\sout{interpret and} solve \sout{differential equation systems in} -\acs{SBML} models\COR{, which are interpreted in terms of ordinary differential equation systems}. +This article describes an efficient algorithm to interpret and solve the +differential equation systems of SBML models. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, -including several \COR{preprocessing} steps. +including several pre-processing steps. %Dynamic simulation of models describing biological phenomena is a key aspect of %research in systems biology. %This article describes an efficient and exhaustive algorithm to interpret and @@ -330,9 +320,9 @@ %Markup Language (SBML) and its implementation as part of the Systems Biology Simulation Core %Library for numerical computation in systems biology. We provide a flexible reference implementation of the algorithm as part of the -Systems Biology Simulation Core Library, a community-driven project providing a -large collection of numerical solvers and a sophisticated interface hierarchy -for the definition of custom differential equation systems. +Systems Biology Simulation Core Library, which is a community-driven project +that provides a large collection of numerical solvers and a sophisticated +interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and %also been used to simulate all models of BioModels Database. @@ -342,17 +332,19 @@ % TODO: Provide additional material %Supplementary data is available at Bioinformatics online. \textbf{Conclusions:} -The formal description of the mathematics behind the \acs{SBML} format facilitates the +The formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. +A similar approach would also be possible for further systems biological +community formats. %The reference implementation (Systems Biology Simulation Core Library) described in this article, reflects this formal structure within its abstract type hierarchy. -The reference implementation can be used as a simulation -backend for Java\texttrademark-based programs. -%Its abstract type hierarchy allows for customized extension. +For Java\texttrademark-based programs, this library can be used as a simulation +backend, whose abstract type hierarchy allows for customized extension. %, and can be used on every operating system for which a JVM %is available. % Source code, binaries, and documentation can be freely obtained under the terms -of the \acs{LGPL} version~3 from \COR{\url{http://simulation-core.sourceforge.net}}. +of the LGPL version~3 from the website +\url{http://sourceforge.net/projects/simulation-core/}. Feature requests, bug reports, contribution, or any further discussion can be directed to the mailing list \href{mailto:simulation-core-development@lists.sourceforge.net}{simulation-core-development@lists.sourceforge.net}. @@ -366,6 +358,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The Main Body begins here %% +%% %% %% Please refer to the instructions for %% %% authors on: %% %% http://www.biomedcentral.com/info/authors%% @@ -390,68 +383,61 @@ %% \section*{Background} -As part of the movement towards quantitative biology, \COR{the} modeling, +As part of the movement towards quantitative biology, modeling, simulation, and computer analysis of biological networks have become integral -parts of modern biological research \cite{Macilwain2011}. +parts of modern biological research \TODO{\cite{Macilwain2011}}. Ambitious national and international research projects such as the Virtual Liver Network \cite{Holzhuetter2012} strive to derive even organ-wide models of biological systems that include all kinds of processes taking place at several levels of detail. -Large-scale efforts like this require \COR{intensive} collaboration between various +Large-scale efforts like this require a strong collaboration between various research groups, including experimenters and modelers. The exchange, storage, -interoperability\COR{,} and the possibility to combine models have been recognized as +interoperability and the possibility to combine models have been recognized as key aspects of this endeavor \cite{Liebermeister2009sta}. -XML-based standard description formats \cite{Bray2000} such as the -\acf{SBML} \cite{Hucka2004} \COR{and} CellML \cite{Lloyd2004} +XML-based standard description formats \cite{Bray2000} such as the Systems +Biology Markup Language (SBML, \cite{Hucka2004}) or CellML \cite{Lloyd2004} enable encoding of quantitative biological network models. -To facilitate sharing and reuse of the models, online \COR{databases} such as -\COR{BioModels Database} \cite{Novere2006a} \COR{and} the CellML model repository +To facilitate sharing and reuse of the models, online data bases such as the +BioModels database \cite{Novere2006a} or the CellML model repository \cite{Lloyd2008} provide large collections of published models in various formats. Software libraries for reading and manipulating the content of these formats are also available \cite{Bornstein2008, Miller2010, -Draeger2011b} and a -\TODO{large variety of programs supports these model description languages}. - -The models encoded in these formats can be interpreted in terms of -\COR{several modeling frameworks, including without limitation} -differential equation systems, with additional structures such as -discrete events and algebraic equations. -The diversity of modeling \COR{approaches} and experimental data often requires -customized software solutions for very specific tasks. -\COR{For efficient analysis, simulation, and calibration (e.g., -the estimation of parameter values) of biological network models a multiple-purpose and efficient numerical -solver library is prerequisite.} -Although the language specifications of \acs{SBML} \cite{Hucka2001, Hucka2003, +Draeger2011b} and a large variety of programs supports these model formats. + +The models encoded in these formats can be interpreted in terms of differential +equation systems, with additional structures such as discrete events and +algebraic equations. +For efficient model analysis, simulation, and calibration (e.g., +the estimation of parameter values) a multiple-purpose and efficient numerical +solver library that has been designed with the requirements of biological +network models in mind is prerequisite. +Although the language specifications of SBML \cite{Hucka2001, Hucka2003, Finney2003a, Finney2006, Hucka2007, Hucka2008, Hucka2010a} and CellML \cite{Cuellar2006} describe the semantics of models in these formats and their interpretation, the algorithmic implementation is still not straightforward. -\TODO{Both communities} offer standardized and manually derived benchmark \COR{tests} in order -to evaluate the quality of simulation results, because it has been recognized -that in many cases different solver implementations lead to divergent results -\cite{Bergmann2008}. +Both communities offer standardized and manually derived benchmark test in order +to evaluate the quality of simulation results, because it has been recognized that in many cases +different solver implementations lead to divergent results \cite{Bergmann2008}. %In this work we address the question of how to precisely solve models encoded in -%the \acs{SBML} format, supporting all levels and versions. To this end, we here +%the SBML format, supporting all levels and versions. To this end, we here %describe a precise solver algorithm. -In this work we address the question of how to precisely interpret models -encoded in the \acs{SBML} format \COR{in terms of ordinary differential equation systems}. -Furthermore, we show how to adapt existing \COR{numerical} integration routines in order to simulate \sout{\acs{SBML}}\COR{these} models. -To this end, we derive a new algorithm for the \COR{accurate} interpretation and -simulation of all currently existing levels and versions of \acs{SBML}. -\sout{As a reference implementation, w}\COR{W}e introduce an exhaustive \COR{reference} implementation in \sout{the} -Java\texttrademark{} \sout{programming language}. The algorithm described in this paper -is, however, not limited to any particular programming language. It is also -important to note that the interpretation of these models must be strictly -separated from the numerical method that solves the \COR{implied} differential -equation system. In this way, a similar approach would also be possible for -\COR{other systems biology} community formats, such as CellML. +\TODO{In this work we address the question of how to precisely interpret models encoded in +the SBML format, supporting all levels and versions. Furthermore, we show how to adapt existing integration +routines in order to simulate SBML models. To this end, we here describe a precise interpretation and simulation algorithm.} +As a reference implementation, we introduce an exhaustive implementation in the Java\texttrademark{} programming +language. The algorithm described in this paper is, however, not limited to any +particular programming language. It is also important to note that the +interpretation of these models must be strictly separated from the numerical +method that solves the implicated differential equation system. In this way, a +similar approach can also be done for CellML or other formats. % -%The modeling language \acs{SBML} (Systems Biology Markup Language, +%The modeling language SBML (Systems Biology Markup Language, %\cite{Hucka2003}) constitutes an important \emph{de facto} standard for the %exchange of biochemical network models. %SBML defines a set of data structures and provides rules about how to interpret @@ -467,11 +453,11 @@ \section*{Background} %their objectives, e.g., the concentration of a reacting species. % % -The Systems Biology Simulation Core Library presented here is a platform-independent, +The Systems Biology Simulation Core Library (SCL) presented here is a platform-independent, well-tested generic library that is completely decoupled from any graphical user interface and can therefore easily be integrated into third-party programs. -It \COR{comprises} several ordinary differential equation (ODE) -solvers and an interpreter for \acs{SBML} models. It is the first simulation library +It comprises several Ordinary Differential Equation (ODE) +solvers and an interpreter for SBML models. It is the first simulation library based on JSBML \cite{Draeger2011b}. % the Java library JSBML % @@ -481,16 +467,16 @@ \section*{Background} %respect to given time-series of metabolite or gene expression values. % Furthermore, the Systems Biology Simulation Core Library contains classes to both export -simulation configurations to the \acf{SED-ML} \cite{Waltemath2011}, -and facilitate the \COR{reuse} and reproduction of these experiments by executing \acs{SED-ML} files. +simulation configurations to SED-ML (Simulation Experiment Description Markup Language, +\cite{Waltemath2011}), and facilitate the re-use and reproduction of these +experiments by executing SED-ML files. \section*{Results and discussion} -\COR{In order to derive an algorithm for the interpretation of \acs{SBML} models in a differential equation framework}, -it is first necessary to take a closer look at the mathematical equations implied by this data format. +\TODO{In order to derive an algorithm for the interpretation of SBML models, it is first necessary to +take a closer look at the mathematical equations implied by this data format. Based on this general description, we will then discuss all necessary steps -to deduce an algorithm that takes all special cases for the various levels and -versions of \acs{SBML} into account. +to deduce an algorithm that takes all special cases for the various levels and versions of SBML into account.} \subsection*{A formal representation of models in systems biology} @@ -498,19 +484,19 @@ \subsection*{A formal representation of models in systems biology} matrix $\mathbf{N}$, whose rows correspond to the reacting species $\vec{S}$ within the system, whereas its columns represent the reactions, i.e., bio-transformations, in which these species participate. -The velocities $\vec{\nu}$ of the \COR{reaction channels} $\vec{R}$ determine the rate of +The velocities $\vec{\nu}$ of the reactions $\vec{R}$ determine the rate of change of the species' amounts: \begin{equation} \frac{\D}{\D t}\vec{S} = \mathbf{N}\vec{\nu}(\vec{S}, t, \mathbf{N}, \mathbf{W}, \vec{p})\,. \label{eq:SpeciesChange} \end{equation} The parameter vector $\vec{p}$ contains rate constants and other, often -constant, quantities that influence the reactions' velocities. +constant, quantities that influence the reaction velocities. According to \cite{Liebermeister2006, Liebermeister2010} the modulation matrix $\mathbf{W}$ is defined as a matrix of size $|\vec{R}|\times|\vec{S}|$ containing the type of the regulatory influences of the species on the reactions, e.g., competetive inhibition or physical stimulation. -Integrating equation~(\ref{eq:SpeciesChange}) yields the predicted amounts of the +Integrating Equation~\ref{eq:SpeciesChange} yields the predicted amounts of the species at each time point of interest within the interval $[t_0, t_T]$: \begin{equation} \vec{S} = \int_{t_0}^{t_T} \mathbf{N}\vec{\nu}(\vec{S}, t, \mathbf{N}, \mathbf{W}, \vec{p}) @@ -519,68 +505,59 @@ \subsection*{A formal representation of models in systems biology} Depending on the units of the species, the same notation can also express the change of the species' concentrations. In this simple case, solving the homogeneous ordinary -differential equation system~(\ref{eq:SpeciesChange}) can be done in a +differential equation system~\ref{eq:SpeciesChange} can be done in a straightforward way using many (numerical) differential equation solvers. -The \COR{nonlinear} form of the kinetic equations in the vector function $\vec{\nu}$ +The non-linear form of the kinetic equations in the vector function $\vec{\nu}$ constitutes the major difficulty for this endeavor and is often the reason why an analytical solution of these systems is not possible or very hard to achieve. Generally, differential equation systems describing biological networks are, however, inhomogenious systems with a higher complexity. -Solving systems encoded in \acs{SBML} can be seen as computing the solution of the following +Solving systems encoded in SBML can be seen as computing the solution of the following equation: -\ifthenelse{\boolean{publ}}{\begin{multline} -\vec{Q} = \int_{t_0}^{t_T} \mathbf{N}\vec{\nu}(\vec{Q}, t, \mathbf{N}, \mathbf{W}, -\vec{p})\D t\\ -+ \int_{t_0}^{t_T} \vec{g}(\vec{Q}, t)\D t + \vec{f}_E(\vec{Q}, t) + \vec{r}(\vec{Q}, t)\,. -\label{eq:QuantityValue} -\end{multline}}{\begin{equation} +\begin{equation} \vec{Q} = \int_{t_0}^{t_T} \mathbf{N}\vec{\nu}(\vec{Q}, t, \mathbf{N}, \mathbf{W}, -\vec{p})\D t + \int_{t_0}^{t_T} \vec{g}(\vec{Q}, t)\D t + \vec{f}_E(\vec{Q}, t) + \vec{r}(\vec{Q}, t)\,. +\vec{p})\D t + \int_{t_0}^{t_T} \vec{g}(\vec{Q}, t)\D t + \vec{f}_E(\vec{Q}, t) + +\vec{r}(\vec{Q}, t)\,. \label{eq:QuantityValue} -\end{equation}} +\end{equation} The vector $\vec{Q}$ of quantities contains the sizes of the compartments $\vec{C}$, amounts (or concentrations) of reacting species $\vec{S}$, and the values of all global model parameters $\vec{P}$. It should be noted that these models may contain local parameters $\vec{p}$ that -influence the reactions' velocities, but which are not part of the global parameter -vector $\vec{P}$, and hence also not part of $\vec{Q}$. -All vector function terms may involve a delay function, i.e., an expression of -the form $\mathrm{delay}(x, \tau)$ with $\tau > 0$. In this way, it is possible -to address values of $x$ computed in the earlier integration step at time -$t - \tau$, turning equation~(\ref{eq:QuantityValue}) -into a \COR{delay-differential} equation. - -In the general case of equation~(\ref{eq:QuantityValue}), not all species' amounts +influence the reaction velocities, but which are not part of the global parameter +vector $\vec{P}$, and hence also not part of $\vec{Q}$. All vector function terms +may involve a delay function, i.e., an expression of the form $\mathrm{delay}(x, \tau)$ +with $\tau > 0$. In this way, it is possible to address values of $x$ computed in +the earlier integration step at time $t - \tau$, turning Equation~\ref{eq:QuantityValue} +into a delay differential equation. +In the general case of Equation~\ref{eq:QuantityValue}, not all species' amounts can be computed by integrating the transformation $\mathbf{N}\vec{\nu}$: The change of some model quantities may be given in form of rate rules (function $\vec{g}(\vec{Q}, t)$) that must be integrated separately. -\COR{Species, whose} amounts are determined by rate rules, must not participate \COR{in any -reaction and hence only have} zero-valued corresponding entries in the +Species, whose amounts are determined by rate rules, must not participate in any +reaction and do hence have only zero-valued corresponding entries in the stoichiometric matrix $\mathbf{N}$. Thereby, the rate rule function $\vec{g}(\vec{Q}, t)$ directly gives the rate of change of these quantities, and returns 0 for all others. - -In addition, \acs{SBML} introduces the concept of events $\vec{f}_E(\vec{Q}, t)$ and -assignment rules $\vec{r}(\vec{Q}, t)$. +In addition, SBML introduces the concept of events $\vec{f}_E(\vec{Q}, t)$ and +$\vec{r}(\vec{Q}, t)$ assignment rules. An event can directly manipulate the value of several quantities, for instance, reduce the size of a compartment to a certain portion of its current size, as soon as a trigger condition becomes satisfied. An assignment rule also influences the absolute value of some quantity. - -\COR{A further concept in \acs{SBML} are} algebraic rules, which are equations that +A further concept of SBML models are algebraic rules, which are equations that must evaluate to zero at all times during the simulation of the model. These rules can be solved to determine the values of quantities, whose values are not determined by other constructs. In this way, conservation relations or other complex interrelations can be expressed in a very convenient way. -With the help of \COR{bipartite} matching \cite{hopcroft1973n} and a subsequent conversion it is possible +With the help of a bipartite matching and a subsequent conversion it is possible to turn algebraic rules into assignment rules and hence include these into the term $\vec{r}(\vec{Q}, t)$. Such a transformation, however, requires symbolic computation and is -\COR{thus} a complicated endeavor. - +hence a complicated endeavor. In case that the system under study operates at multiple time scales, i.e., it -contains a fast and a slow \COR{subsystem}, a separation of the system is necessary +contains a fast and a slow sub-system, a separation of the system is necessary leading to differential algebraic equations. Some species can be declared to operate at the system's boundaries, assuming a constant pool of their amounts or concentrations. @@ -588,14 +565,14 @@ \subsection*{A formal representation of models in systems biology} certain condition division or multiplication with the sizes of their surrounding compartments is necessary in order to ensure the consistent interpretation of the models. -For all these reasons, solving equation~(\ref{eq:QuantityValue}) is much more -complicated than computing the solution of the simple equation~(\ref{eq:SpeciesChange}) +For all these reasons, solving Equation~\ref{eq:QuantityValue} is much more +complicated than computing the solution of the simple Equation~\ref{eq:SpeciesChange} alone. From the perspective of software engineering, a strict separation of the interpretation of the model and the numerical treatment of the differential equation system is necessary to ensure that regular numerical methods can be used -to solve equation~(\ref{eq:QuantityValue}). +to solve Equation~\ref{eq:QuantityValue}. In order to efficiently compute this solution, multiple pre-processing steps are required, such as the conversion of algebraic rules into assignment rules, or avoiding repeated re-computation of intermediate results. @@ -606,245 +583,226 @@ \subsection*{A formal representation of models in systems biology} \subsection*{Initialization} -At the beginning of the simulation the values of species, parameters and compartments are set to the initial values as given in the model. -All \COR{rate laws} of the reactions, assignment rules, transformed algebraic rules (see below), initial assignments, event assignments, rate rules and \COR{function definitions} are integrated into one directed acyclic syntax graph. This graph is hence the result of merging of the abstract syntax trees representing all those individual elements. Equivalent elements are only contained once. This significantly decreases the computation time needed for the evaluation of these syntax graphs during the simulation, in comparison to maintaining multiple syntax trees. -Figure~1 gives an example for such a syntax graph. - -After the creation of the abstract syntax graph, the initial assignments, and the +At the beginning of the simulation the values of species, parameters and +compartments are set to the initial values as given in the model. +All kinetic laws of the reactions, assignment rules, transformed algebraic +rules (see below), initial assignments, event assignments and rate rules +are integrated into a directed acyclic syntax graph. +This graph is hence the result of merging of the abstract syntax trees of +all those elements. +Equivalent elements are only contained once. +This significantly decreases the computation time needed for the +evaluation of these syntax trees during the simulation. +An example for such a syntax graph is given in Figure~1. + +After the creating of the abstract syntax graph, the initial assignments, and the assignment rules (including transformed algebraic rules) are processed. -\COR{Initial values defined by initial assignments or assignment rules are computed in this step.} +Deviating initial values defined by initial assignments and are now assigned. \subsection*{Solving algebraic rules} -\COR{In order to deal with algebraic rules in an \acs{SBML} model, \COR{they} are converted to assignment rules.} -In every equation of an algebraic rule, there should be at least one \COR{variable -whose} value is not yet defined through other equations in \COR{the} model. This variable has to be determined -for the purpose of interpreting the \COR{algebraic rule}. -At first, a bipartite graph according to the \acs{SBML} specifications is generated. This graph is used to -compute a \COR{matching using} the algorithm by Hopcroft and Karp +In order to deal with algebraic rules in an SBML model, these have to be converted to assignment rules. +In every equation of an algebraic rule, there should be at least one variable, +whose value is not yet defined through other equations in model. This variable has to be determined +for the purpose of interpreting the regarding algebraic rule. +At first, a bipartite graph according to the SBML specifications is generated. This graph is used to +compute a matching, using the algorithm from Hopcroft and Karp \cite{hopcroft1973n}. The initial greedy matching is extended with the use of augmenting paths. This process is repeated until no more augmenting paths can be found. Per definition, this results in a maximal matching. -\TODO{As stated in the \acs{SBML} specifications, if any equation vertex remains unconnected after augmenting the matching as far as possible, the model is considered overdetermined and thus is not a valid \acs{SBML} model.} -If this is not the case, every assignment rule is \COR{thereafter} converted into an algebraic rule. +As stated in the SBML specifications, if any equation vertex remains unconnected after augmenting the +matching as far as possible, the model is considered overdetermined and thus is not a valid SBML model. +But if we are indeed looking at a valid SBML model, every assignment rule is converted into an algebraic rule. To this end, the mathematical expression is transformed into an equation with the target variable on its left-hand side. The left-hand side is represented by the respective variable vertex, to which the considered algebraic rule has been matched. Figure~2 displays the described algorithm in form of a flow chart. \subsection*{Event handling} -An event in \acs{SBML} is a \COR{list of assignments} that is executed depending on whether a trigger -condition switches from \false to \true. -In addition, \COR{\acs{SBML} enables modellers to define a delay which may postpone the actual execution of the event's assignments -to a later point in time.} -With the release of \acs{SBML} Level~3 Version~1, the processing of events has been -raised to a higher level of complexity\COR{:} -\COR{In earlier versions} it was sufficient to determine, when an event triggers and when its \COR{assignments} are to be \COR{executed}. -In Level~3 Version~1 just a few new language elements have been added\COR{, but these have a huge impact} on how to handle events: -\COR{For example} the order in which events have been processed used to be at programmer\COR{'}s discretion \COR{in \acs{SBML} Level 2}, but \COR{in Level~3 Version~1} it is given by the event's priority element. +An event in SBML is a function that is executed depending on whether a trigger condition switches from \false{} to +\true. +In addition, a delay may postpone the actual execution of the event's assignments to a later point in time. +With the release of SBML Level~3 Version~1, the processing of events has been raised to a higher level of complexity. +Before Level~3 Version~1 it was sufficient to determine, when an event triggers and when its assignmens are to be exceuted. +In Level~3 Version~1 just a few new language elements have been added but with an huge impact on how to handle events: +The order in which events have been processed used to be at programmers discretion, but now it is given by the event's priority element. Coordinating the sequence, in which events are to be executed, has now become the crucial part of event handling. Furthermore, there exists the option to cancel an event during the time since its trigger has been activated and the actual time when the scheduler picks the event for execution. -\COR{Events that can be cancelled after the activation of their triggers are called nonpersistent.} For every time step, the events to be executed are a union of two subsets of the set of all events. -On the one hand, \COR{there are events whose triggers have} been activated at the \COR{current} time and which are to be evaluated without delay. +On the one hand, there are the events, whose trigger has been activated at the given time and which are to be evaluated without delay. On the other hand, there are events that triggered at some time point before, and whose delay reaches till the current point in time. For every element of the resulting set of events their priority rule must be evaluated. -One event is randomly chosen for execution from all events \COR{of} highest priority. +One event is randomly chosen for execution from all events with the highest priority. All other events could be handled in the same manner. However, the assignment of the first event can change the priority or even the trigger condition of the events that have not yet been executed. -Therefore, the trigger of \COR{nonpersistent} events and the priority of the remaining events have to be evaluated again. +Therefore, the trigger of non persistent events and the priority of the remaining events have to be evaluated again. In this case, another event that has now the highest priority is chosen. -This process \COR{must be repeated} until no further events are left \COR{for execution}. +This process repeats itself until no further events are left to be executed. Figure~3 shows the slightly simplified algorithm for event processing at a specific point in time. -\subsection*{Integrated calculation for a certain time step including event processing} -The precise calculation of the \COR{time when} events are triggered\COR{,} is crucial to -ensure exact results of the numerical integration process. -It could, for instance, happen that an event is triggered at time $t_{\tau}$, -which is between the two integration time points $t_{\tau - 1}$ and $t_{\tau + 1}$. -When processing the events only at time points $t_{\tau - 1}$ and $t_{\tau + 1}$ -it might happen that the trigger condition cannot be evaluated to \true at -neither of these time points. -The Rosenbrock solver \cite{Press1993} can adapt its step size $h$ if events -occur (see \COR{figure~4} for details). -For a certain time interval $[t_{\tau - 1}, t_{\tau + 1}]$ and the current vector -$\vec{Q}$\COR{,} Rosenbrock's method determines the new value of vector $\vec{Q}$ at a -point in time $t_{\tau - 1} + h$. -If the error tolerance cannot be ensured, $h$ is reduced and the procedure is -repeated. - -After that\COR{,} the events and the assignment rules are processed at the new point in -time $t_{\tau - 1} + h$. -If the previous step causes a change in $\vec{Q}$, the adaptive step size is -decreased by setting $h$ to $\nicefrac{h}{10}$ and the calculation is repeated -until the minimum step size is reached or the processing of events and rules -does not change $\vec{Q}$ anymore. -Hence, the \COR{time at which} an event takes place, is precisely determined. - \subsection*{Calculation of the derivatives for a certain point in time} -For given values $\vec{Q}$ at a point $t$ in time the current vector of derivatives $\dot{\vec{Q}}$ is calculated as follows\COR{.} -First, the rate rules are processed $\dot{\vec{Q}} = \vec{g}(\vec{Q}, t)$. Note that function $\vec{g}$ returns 0 in all \COR{dimensions -in which} no rate rule is defined. -Second, the velocity $\nu_i$ of each \COR{reaction channel} $R_i$ is computed with the help of the unified syntax graph (\COR{figure~1} shows an example of such a graph). +For given values $\vec{Q}$ at a point $t$ in time the current vector of derivatives $\dot{\vec{Q}}$ is calculated as follows: +First, the rate rules are processed $\dot{\vec{Q}} = \vec{g}(\vec{Q}, t)$. Note that function $\vec{g}$ returns 0 in all dimensions, +in which no rate rule is defined. +Second, the velocity $\nu_i$ of each reaction $R_i$ is computed with the help of the unified syntax graph (Figure~1 shows an example of such a graph). The velocity functions depend on $\vec{Q}$ at time $t$. -During the second step\COR{,} the derivatives of all species that participate in the current reaction $R_i$ need to be updated (see the flowchart in \COR{figure~5}). - -\subsection*{A reference implementation of the algorithm as part of the Systems -Biology Simulation Core Library} - -The algorithm described above has been implemented in Java\texttrademark{} and -included into the Systems Biology Simulation Core Library. -\COR{figure~6} displays \COR{an overview of} the software architecture of this library, which -has been designed as part of a community project aiming to provide an extensible -numerical backend for customized programs for research in computational systems -biology. -The \acs{SBML}-solving algorithm is based on the data structures provided by the JSBML -project \cite{Draeger2008}. -With the help of wrapper classes several numerical solvers originating from the -Apache Commons Math library \COR{\cite{ApacheCommonsMath2013}} could be included into the project. -In addition, the library provides an implementation of the explicit fourth order -Runge-Kutta method, Rosenbrock's solver, and Euler's method. - -Each solver has a method to directly access its corresponding \acf{KiSAO} term \cite{Courtot2011}. -Due to the strict separation between numerical differential equation solvers, -and the definition of the actual differential equation system, it is possible to -implement support for \COR{other} community standards, such as CellML -\cite{Lloyd2004}. - -In order to support the emerging standard \acf{MIASE} \cite{Waltemath2011a}, the -library also provides an interpreter of \acf{SED-ML} files \cite{Waltemath2011}. -These files allow users to store the details of a simulation, including the -selection and all settings of the numerical method, hence facilitating the -creation of reproducible results. -A simulation experiment can also be directly started by passing a \acs{SED-ML} file to -this interpreter. - -Many interfaces, abstract classes, and an exhaustive source code documentation -in form of JavaDoc facilitate the customization of the library. -For testing purposes, the library contains a sample program that benchmarks the -\acs{SBML} interpreter against the entire SBML Test Suite \COR{\cite{SBMLtestSuite2013}}. +During the second step the derivatives of all species that participate in the current reaction $R_i$ need to be updated (see the flowchart in Figure~4). + +\subsection*{Integrated calculation for a certain time step including event processing} +The precise calculation of the time, when events are triggered is crucial to ensure exact results of the numerical integration process. +It could, for instance, happen that an event is triggered at time $t_{\tau}$, which is between the two integration time points $t_{\tau - 1}$ and $t_{\tau + 1}$. +When processing the events only at time points $t_{\tau - 1}$ and $t_{\tau + 1}$ it might happen that the trigger condition cannot be evaluated to true at neither of these time points. +The Rosenbrock solver \cite{Press1993} can adapt its step size $h$ if events occur (see Figure~5 for details). +For a certain time interval $[t_{\tau - 1}, t_{\tau + 1}]$ and the current vector $\vec{Q}$ Rosenbrock's method determines the new value of vector $\vec{Q}$ at a point in time $t_{\tau - 1} + h$. +If the error tolerance cannot be ensured, $h$ is reduced and the procedure is repeated. + +After that the events and the assignment rules are processed at the new point in time $t_{\tau - 1} + h$. +If the previous step causes a change in $\vec{Q}$, the adaptive step size is decreased by setting $h$ to $\nicefrac{h}{10}$ and +the calculation is repeated until the minimum step size is reached or the processing of events and rules does not change $\vec{Q}$ anymore. +Hence, the time, at which an event takes place, is precisely determined. + +\subsection*{A reference implementation of the algorithm as part of the Systems Biology Simulation Core Library} + +The algorithm described above has been implemented in Java\texttrademark{} and included into the Systems Biology Simulation Core Library. +Figure~6 displays the software architecture of this library. +The Systems Biology Simulation Core Library has been designed as part of a community project aiming to provide an extensible numerical backend for customized programs for research in computational systems biology. +The SBML-solving algorithm is based on the data structures provided by the JSBML project \cite{Draeger2008}. +\TODO{We implemented wrapper classes in order to integrate several numerical solvers from the Apache Commons Math library into the project.} +In addition, the library provides an implementation of the explicit fourth order Runge-Kutta method, Rosenbrock's solver, and Euler's method. +Each solver has a method to directly access its corresponding KiSAO (Kinetic Simulation Algorithm Ontology) term \cite{Courtot2011}. +Due to the strict separation between numerical differential equation solvers, and the definition of the actual differential equation system, it is possible to implement support for further community standards, such as CellML \cite{Lloyd2004}. +Many interfaces, abstract classes, and an exhaustive source code documentation in form of JavaDoc facilitate the customization of the library. +In order to support the emerging standard MIASE (Minimal Information About a Simulation Experiment) \cite{Waltemath2011a}, the library also provides an interpreter of SED-ML files (Simulation Experiment Description Markup Language) \cite{Waltemath2011}. +These files allow users to store the details of a simulation, including the selection and all settings of the numerical method, hence facilitating the creation of reproducible results. +A simulation experiment can also be directly started by passing a SED-ML file to this interpreter. +For testing purposes, the library contains a sample program that benchmarks the SBML interpreter against the entire SBML Test Suite. \subsection*{Application to published models} The Systems Biology Simulation Core Library has been tested on all 424 curated -models from \COR{BioModels Database} \cite{Novere2006a} (release~23, October 2012). -As a result, \TODO{99.06\,\%} of these models could be correctly simulated. +models from BioModels database \cite{Novere2006a} (release~23, October 2012). +As a result, 99.06\,\% of these models could correctly be simulated. In the following, we use two models from this repository to illustrate the capabilities of this library: -\COR{BioModels Database model~\#206} by Wolf \emph{et al.} \cite{Wolf2000} and \COR{BioModels Database model~\#390} by Arnold +Biomodel~206 by Wolf \emph{et al.} \cite{Wolf2000} and Biomodel~390 by Arnold and Nikoloski \cite{Arnold2011}. The model by Wolf \emph{et al.} \cite{Wolf2000} mimics glycolytic oscillations that have been observed in yeast cells. The model describes how the dynamics propagate through the cellular network. Figure~7a displays the simulation results for the intracellular concentrations -of 3-phosphogylcerate, \acs{ATP}, glucose, glyceraldhyde 3-phosphate, and \acs{NAD$^+$}: +of 3-phosphogylcerate, ATP, glucose, glyceraldhyde 3-phosphate, and NAD$^+$: After an initial phase of approximately 15\,s all metabolites begin a steady-going rhythmic oscillation. Changes in the dynamics of the fluxes through selected reaction channels within -this model can be seen in \COR{figure~7b}. +this model can be seen in Figure~7b. By comparing a large collection of previous models of the Calvin-Benson cycle, Arnold and Nikoloski created a quantitative consensus model that comprises eleven species, six reactions, and one assignment rule \cite{Arnold2011}. All kinetic equations within this model call specialized function definitions. -Figure~8 shows the simulation results for the species \acs{RuBisCO}, -\acs{ATP}, and \acs{ADP} within this model. -As in the previous test case, \TODO{the simulation results reproduce the values provided by} \COR{BioModels Database}. +Figure~8 shows the simulation results for the species ribulose 1,5 bisphosphate, +ATP, and ADP within this model. +As in the previous test case, the simulation results reproduce the values +provided by BioModels database. \subsection*{Comparison to existing solver implementations for SBML} -In order to benchmark our software, we chose similar tools exhibiting the -following features from the \acs{SBML} software -matrix \TODO{\cite{SBMLsoftwareMatrix2012}}: -% -%\TODO{Many stand-alone programs providing simulation of SBML come with graphical user -%interfaces. -%For instance, the Virtual Cell \cite{Loew2001}, JSim \cite{Beard2012a}, iBioSim -%\cite{Myers2009}, PottersWheel \cite{Maiwald2008}, COPASI \cite{Hoops2006}, -%SYCAMORE \cite{Weidemann2008}, SBToolbox2 -%\cite{SBT_Schmidt2006}, JWS Online \cite{Olivier2004}, or the Systems Biology -%Workbench with Roadrunner (SBW, \cite{Bergmann06}). -%The vast majority of the internal solvers for these systems are part of -%larger software suites and can therefore not be easily integrated into custom -%programs. Some are implemented in programming languages that are either -%platform-dependent (e.g., C or C++) and/or require a commercial license (e.g., -%MATLAB\texttrademark{}) for their execution. -%The SBML ODE Solver Library \cite{Machne2006}, which is written in C, -%and is based on the libSBML library \cite{Bornstein2008}, -%provides such a simulation routine based on the SUNDIALS differential equation -%solver.} -% -%We therefore selected only those SBML-capable simulation programs, libraries, -%and frameworks -%that satisfy the following criteria: +\TODO{In order to benchmark our software, we chose similar tools exhibiting features X, Y, Z. They are A (), B (), C ()} +\TODO{Many stand-alone programs providing simulation of SBML come with graphical user +interfaces. +For instance, the Virtual Cell \cite{Loew2001}, JSim \cite{Beard2012a}, iBioSim +\cite{Myers2009}, PottersWheel \cite{Maiwald2008}, COPASI \cite{Hoops2006}, +SYCAMORE \cite{Weidemann2008}, SBToolbox2 +\cite{SBT_Schmidt2006}, JWS Online \cite{Olivier2004}, or the Systems Biology +Workbench with Roadrunner (SBW, \cite{Bergmann06}). +The vast majority of the internal solvers for these systems are part of +larger software suites and can therefore not be easily integrated into custom +programs. Some are implemented in programming languages that are either +platform-dependent (e.g., C or C++) and/or require a commercial license (e.g., +MATLAB\texttrademark{}) for their execution. +The SBML ODE Solver Library \cite{Machne2006}, which is written in C, +and is based on the libSBML library \cite{Bornstein2008}, +provides such a simulation routine based on the SUNDIALS differential equation +solver.} + +We therefore selected only those SBML-capable simulation programs, libraries, +and frameworks from the SBML software +matrix\footnote{\url{http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix} (October 8\textsuperscript{th} 2012)} +that satisfy the following criteria: \begin{itemize} \item The last updated version was released after the final release of - the specification for \acs{SBML} Level~3 Version~1 Core, i.e., October + the specification for SBML Level~3 Version~1 Core, i.e., October 6\textsuperscript{th} 2010. - \item Support for \acs{SBML} Level~3. \item Open-source software \item No dependency on commercial products that are not freely available (e.g., MATLAB\texttrademark{} or Mathematica\texttrademark) + \item Support for SBML Level~3. \end{itemize} -The selected programs are in alphabetical order: -%Only three other applications support the simulation of models containing events, algebraic rules and fast reactions completely: -BioUML \cite{Kolpakov2011, Kolpakov2006}, COPASI \cite{Hoops2006}, -iBioSim \cite{Myers2009}, JSim \cite{Raymond2003}, LibSBMLSim -\cite{Takizawa2013, Funahashi2012}, and VCell \cite{Moraru2008}. +Table~1 summarizes the comparison of six of these programs. +Only three other applications support the simulation of models containing events, algebraic rules and fast reactions completely: +iBioSim \cite{Myers2009}, BioUML \cite{Kolpakov2011}, \cite{Kolpakov2006}, and LibSBMLSim \cite{Funahashi2012}. %\TODO{Only three applications pass the four exemplary models (966, 988, 1083, 1000) of the SBML Test Suite (version 2.0.2):} %iBioSim \cite{Myers2009}, BioUML \cite{Kolpakov2011}, \cite{Kolpakov2006}, and LibSBMLSim \TODO{Citation}. -Table~1 summarizes the comparison of all six programs. -\TODO{It should be mentioned that all these programs are contineously improved and that this table can therefore only mirror a current snapshot\ldots} +The program iBioSim does not yet support the simulation of SBML models +containing the delay functions, except delayed events. +LibSBMLSim, which is a simulation API written in C, can only read models given +in SBML Level~2 Version~4 and SBML Level~3. +Hence, Systems Biology Simulation Core Library and BioUML are the only +simulation tools from this selection that pass all models of the SBML Test Suite +for all levels and versions of SBML. \section*{Conclusions} -The \acs{SBML} implementation has successfully passed the -SBML Test Suite (version~2.0.2) using Rosenbrock's solver. +The SBML implementation has successfully passed the +SBML Test Suite (version 2.0.2) using Rosenbrock solver. The results are shown in Table~2. - All models together can be simulated within seconds, which means that the simulation -of one \acs{SBML} model takes only milliseconds on average, using regular desktop computers. -The total simulation time for all models in \acs{SBML} Level~3 Version~1 is significantly -higher than for the models in other \acs{SBML} levels and versions. -This can be explained by the fact that there are some models in \acs{SBML} Level~3 -Version~1, in which a time-consuming processing of a large number of events is -necessary. -In particular, the simulation of model 966 of the SBML Test Suite \COR{\cite{SBMLtestSuite2013}}, which is only provided in \acs{SBML} Level~3 Version~1, takes 21\,s because it contains 23 events to be processed. -\COR{Event handling is the most time consuming step during the simulation of an \acs{SBML} model, especially since two of these 23 events fire every $.01$ seconds. Therefore these events -have to be evaluated thousandfold.} The evaluation of this model accounts for 60~\% of the total simulation time for the models in \acs{SBML} Level~3 Version~1. -Furthermore, the Systems Biology Simulation Core Library solves \TODO{99.06\,\%} of the -models from the \href{http://biomodels.net}{BioModels.net} \COR{Database} (release 23, -\cite{Novere2006a}) simulating from $t = 0$ to $t = 10$ using Rosenbrock solver -and a step size of $0.1$. -These results suggest the reliability of the simulation algorithm described in -this work. - -Our tests indicate that \COR{at the moment} only two programs pass the entire \COR{test suite} for all -\acs{SBML} levels and versions: BioUML, which is a workbench for modelling, simulation, -and parameter fitting, and the Systems Biology Simulation Core Library. -The Systems Biology Simulation Core Library is therefore the only \acs{API} simulation -library exhibiting this capability. +of one SBML model takes only milliseconds on average, using regular desktop computers. +The total simulation time for all models in SBML Level~3 Version~1 is significantly +higher than for the models in other SBML levels and versions. +This can be explained by the fact that there are some models in SBML Level~3 Version~1, +in which a time-consuming processing of a large number of events is necessary. +The simulation of model 966 of the SBML Test Suite, which is only provided in +SBML Level~3 Version~1 and contains many events to be processed, takes 21 seconds. +This accounts for 60~\% of the total simulation time for the models in SBML +Level~3 Version~1. +Our tests indicate that BioUML, which is a workbench for modelling, simulating +and parameter fitting, and the Systems Biology Simulation Core Library are the +only SBML applications that pass the entire Test Suite for all SBML levels and +versions. +The Systems Biology Simulation Core Library is therefore the only API simulation +library that supports the whole SBML Test Suite for all SBML levels and versions. %Compared to BioUML the Simulation Core Library simulates all models of the Test Suite much faster. %(see %\href{http://sbml.org/Software/SBML_Test_Suite}{http://sbml.org/Software/SBML\_Test\_Suite}): - -Therefore, the Systems Biology Simulation Core Library is an efficient Java tool for the simulation of differential equation systems used in systems biology. It can be easily integrated into larger customized applications. For instance, \COR{CellDesigner \cite{Funahashi2003} has already been using it since version~4.2} as one of its simulation libraries. The stand-alone application SBMLsimulator \COR{\cite{SBMLsimulator2013}.} provides a convenient graphical user interface for the simulation of \acs{SBML} models and uses it as a computational back-end. The abstract class structure of the library supports the integration of additional model formats, such as CellML, besides its \acs{SBML} implementation. To this end, it is only necessary to implement a suitable interpreter class. -%Points of Control: - -\COR{The standard preferences for simulating an SBML model consist of the Rosenbrock solver with an absolute tolerance of \TODO{xxx} and a relative tolerance of \TODO{xxx}. On the basis of our experiments this setup can handle most of the problems without further ado. The Rosenbrock solver with its adaptive step size is the most able solver in this library concerning stiff ODEs. Nevertheless the user has the possibility the choose another solver for integration. According to the SBML specifications a model has to be simulated from time point 0. The user has the possibility to specify the end of the simulation. Modifying the relative and absolute tolerance can increase the accuracy of the results or decrease computation time. \TODO{...}} - -\COR{As mentioned before the Rosenbrock solver is basically capable of solving stiff ODEs. Albeit there are some models from the BioModels Database that constitute very stiff problems and large ODEs (408, 235) for which the Rosenbrock solver has some difficulty solving them. This issue reflects in a higher time consumption for simulation because the step size is decreased on and on to maintain the desired accuracy. Tuning the relative and absolute tolerance may help but sometimes the Rosenbrock is stretched to its limits. This behavior can also be observed for the Runge-Kutta-Fehlberg method included in iBioSim. To clarify the focus of iBioSim lies not in the use of ODE solvers but in the stochastic analysis of systems with the Reb2Sac stochastic simulator and abstraction techniques to make the models easier to analyze. However the performance of the Runge-Kutta-Fehlberg and Rosenbrock show that some ODE solvers can have more difficulties with some biological models than. More advanced solvers like CVODE from SUNDIALS \TODO{quote} integrated as a ported to java version into BioUML can handle complicated ODEs much better. Since the SUNDIALS are not distrusted under the LGPL and no version of these solvers in Java only we disregarded their use. But as a community-driven project, new solvers can be contributed by the community.} - +Furthermore, Systems Biology Simulation Core Library solved 99.06\,\% of the +models from the +\href{http://biomodels.net}{BioModels.net} database (release 23, +\cite{Novere2006a}) simulating from $t = 0$ to $t = 10$ using Rosenbrock solver +and a step size of $0.1$. +Therefore, the Systems Biology Simulation Core Library is an efficient Java tool +for the +simulation of differential equation systems used in systems biology. It can be +easily integrated into larger customized applications. +For instance, CellDesigner version~4.2 \cite{Funahashi2003} already uses it as +one of its simulation libraries. +The stand-alone application SBMLsimulator\footnote{SBMLsimulator is available at +\url{http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsimulator}.} +provides a convenient graphical user interface for the simulation of SBML +models and uses it as a computational backend. +The abstract class structure of the library supports the integration of +additional model formats, such as CellML, besides its SBML implementation. To +this end, it is only necessary to implement a suitable interpreter class. %The SBML ODE Solver Library \cite{Machne2006}, which is written in C, %and based on the libSBML library \cite{Bornstein2008}, %provides such a simulation routine based on the SUNDIALS differential equation %solver. -By including support for the emerging standard \acs{SED-ML}, we hope to facilitate the +By including support for the emerging standard SED-ML, we hope to facilitate the exchange, archival and reproduction of simulation experiments performed using the Systems Biology Simulation Core Library. @@ -852,39 +810,49 @@ \section*{Methods} \subsection*{Implementation} -All the solver classes are derived from the abstract class \AbstractDESSolver (\COR{figure~6}). -Several solvers of the Apache Commons Math library (version 3.0) \COR{\cite{ApacheCommonsMath2013}} are integrated with the help of wrapper classes. -Numerical methods and the actual differential equation systems are strictly separated. -The class \MultiTable stores the results of a simulation within its \Block data structures. +All the solver classes are derived from the abstract class \AbstractDESSolver{} +(Figure~6). +Several solvers of the Apache Commons Math library (version 3.0) are integrated +with the help of wrapper classes. Numerical methods and the actual differential +equation systems are strictly separated. The class \MultiTable{} stores the +results of a simulation within its \Block{} data structures. % -The abstract description of differential equation systems, with the help of several distinct interfaces, makes \COR{it} possible to decouple them from a particular type of biological network. It is therefore possible to pass an instance of an interpreter for a respective model description format to any available solver. +The abstract description of differential equation systems, with the help of +several distinct interfaces, makes possible to decouple them from a particular +type of biological network. It is therefore possible to pass an instance of an +interpreter for a respective model description format to any available solver. %\marginpar{I would not quote SBML and CellML. CellML is % actually not supported at the moment} % %A specialized interpreter class is required for the evaluation of a biological -%model. -\TODO{DISCUSSION-BEGIN!!!} +%model. This interpretation is the most time consuming step of the integration procedure. -This is why efficient and clearly organized data structures are required to ensure \COR{that the overall library offers high performance}. -\TODO{DISCUSSION-END!!!} -The interpretation of \acs{SBML} models is split between evaluation of events and rules, computation of stoichiometric information, and computation of the current values for all model components (such as species and compartments). +This is why efficient and clearly organized data structures are required to +ensure a high performance of the overall library. The interpretation of SBML +models is split between evaluation of events and rules, computation of +stoichiometric information, and computation of the current values for all model +components (such as species and compartments). % -For a given state of the ODE system, the class \SBMLinterpreter, responsible -for the evaluation of models encoded in \acs{SBML}\COR{,} returns the current set of +For a given state of the ODE system, the class \SBMLinterpreter{}, responsible +for the evaluation of models encoded in SBML returns the current set of time-derivatives of the variables. It is connected to an efficient MathML interpreter of the expressions contained -in kinetic laws, rules and events (\ASTNodeInterpreter). -The nodes of the syntax graph for those expressions depend on the current state of the ODE system. -If the state has changed, the values of the nodes have to be recalculated (see Results). +in kinetic laws, rules and events (\ASTNodeInterpreter{}). The nodes of the syntax graph for those +expressions depend on the current state of the ODE system. If the state has +changed, the values of the nodes have to be recalculated (see Results). % -An important aspect in the interpretation of \acs{SBML} models is the determination of the exact time at which an event occurs, as this influences the precision of the system's variables. -To this end, we adjusted the Rosenbrock solver \cite{Kotcon2011}, an integrator with an adaptive step size, to a very precise timing of the events. %\sout{Rosenbrock's method is well-suited even for stiff systems.} -% +An important aspect in the interpretation of SBML models is the +determination of the exact time at which an event occurs, as this influences +the precision of the system's variables. To this end, we adjusted the Rosenbrock +solver \cite{Kotcon2011}, an integrator with an adaptive step size, to a very +precise timing of the events. +%\sout{Rosenbrock's method is well-suited even for stiff systems.} +% In addition to events, rules are also treated during integration. Basically, rules are events that occur at every given point in time and are therefore processed in the same manner. -For every object of the type \AlgebraicRule, a new \AssignmentRule object is generated by means of the preceding bipartite matching. -They represent only temporary rules, that are incorporated in the simulation process but do not influence the model in the \acs{SBML} file. +For every object of the type \AlgebraicRule{}, a new \AssignmentRule{} object is generated by means of the preceding bipartite matching. +They represent only temporary rules, that are incorporated in the simulation process but do not influence the model in the SBML file. %\marginpar{This is only valid for polynomes. And for those, %assignmentRules should have been used anyway. How do-you proceed for %cos(x)=0?: Yes, that's true. People should use assignments there, but the @@ -892,69 +860,76 @@ \subsection*{Implementation} %currently not sure if we could solve cos(x) = 0 or similar cases.} % -In the \SBMLinterpreter \COR{class,} events are represented via an array containing an object of the class \EventInProgress for every event in the model. +In the \SBMLinterpreter{} events are represented via an array containing an object of the class \EventInProgress{} for every event in the model. Thereby the distinction between events with and without delays is made. -\COR{Both types of events can trigger multiple times before being executed, but an event with delay can produce multiple assignments even before the assignment of its first triggering is executed. The assignment of an event without delay is executed at the same point in time as the event is being triggered or not at all, if the event is being canceled before execution.} -In order to deal with such an issue, the class \SBMLEventInProgressWithDelay keeps track of this via the help of a list containing the points in time, at which the respective event has to executed. When events trigger more than once before execution, they have to be ordered according to their delay because the delay of the very same event may vary. - -When the \SBMLinterpreter \COR{class} is processing events with priority, the events with the highest priority are currently stored in \COR{a} list until one of them is selected for \COR{execution}. \COR{The handling of a priority queue could be done with the in computer science well known concept of a binary max heap. The element at the root represents the largest value in the heap and after its extraction, the heap property is restored so that the next largest value is moved to the root. However,} as stated in the Results section, the execution of one event can influence the priority \TODO{of} the remaining events. \TODO{Considering the binary max heap, there is the possibility that many priorities change whereby the standard method to restore the max heap characteristic after extraction is not sufficient any more. Therefore, we disregarded the use of other data structures for now.} - -% -%The simulation algorithm then proceeds as follows: For each time step, the ODE %solver gets the current variable values and calculates the system's state for the next point in time. After that, events and rules are processed, that can change the values. The modified values then become the initial values for the next time step. The event processing of the Rosenbrock solver \sout{is different from other solvers, as it} is directly integrated in the solver class and influences the step size. The time-accurate handling of events and rules leads to very precise results of the simulation. +The major difference between both is that an event with delay can trigger multiple times before it is executed. +In order to deal with such an issue, the class \SBMLEventInProgressWithDelay{} keeps track of this via the help of a list containing the points in time, at which the respective event has to executed. +When events trigger more than once before execution, they have to be ordered according to their delay because the delay of the very same event may vary. + +When the \SBMLinterpreter{} is processing events with priority, the events with the highest priority +are currently stored in list until one of them is selected for execution. One could argue, that all events can +be kept in the same data structure, e.g., in a binary max heap, where after the extraction of the element with the largest value, the heap is restructured so that that next largest value is at the top. +As stated in a previous section, the execution of one event can influence the priority off the remaining events. +Considering the binary max heap, there is the possibility that many priorities change whereby the standard +method to restore the max heap characteristic after extraction is not sufficient any more. +Therefore, we disregarded the use of other data structures for now. % -\COR{Besides the subset of MathML functions provided by the different specification \acs{SBML} there exists also the possibility to apply user-defined functions from a given \acs{SBML} file. As mentioned in the initialization, additional function definitions are also represented via an abstract syntax graph. For each function definition the arguments defined in the their lambda expression are mapped to their corresponding nodes in the abstract syntax graph. The evaluation of a MathML element with a user-defined function take place in several steps. The arguments of the respective function are evaluated and then passed to their corresponding node in the graph via the mapping established before. After this step the nodes representing arguments have a specific value attached to them. At last the complete MathML element can be evaluated.} -\COR{During the calculation of reaction velocities the "StoichiometryMath" construct allows a dynamic change of a reaction's stoichiometry during simulation. The \SBMLinterpreter class flags reactions with changing stoichiometry during initialization and evaluates the corresponding MathML anew if the stoichiometry is needed for calculation. Constant stoichiometry values are computed once and stored in an array.} -\COR{The definition of constraints introduce assumptions how a model is supposed to act during simulation. Analogous to the trigger of events, the MathML element of each constraint is evaluated for every time step. The \SBMLinterpreter class keeps a record of which constrained is violated at what point in time during simulation. After the simulation of a model the violated constrains are reported.} -\acs{SED-ML} support is enabled by inclusion of the \jlibsedml library \COR{\cite{jlibsedml2013}} in the binary download. -Clients of the the Systems Biology Simulation Core Library can choose to use the \jlibsedml \acs{API} directly, or access \acs{SED-ML} support via facade classes in the \texttt{org.simulator.sedml} package that do not require direct dependencies on \jlibsedml in their code. +%The simulation algorithm then proceeds as follows: For each time step, the ODE +%solver gets the current variable values and +%calculates the system's state for the next point in time. After that, events +%and rules are processed, that can change the values. The modified values then +%become the initial values for the next time step. The event processing of the +%Rosenbrock solver +%\sout{is different from other solvers, as it} +%is directly integrated in the solver class and influences the +%step size. The time-accurate handling of events and rules leads to very precise +%results of the simulation. +% +SED-ML support is enabled by inclusion of the \jlibsedml{} library +(\href{http://www.jlibsedml.org}{http://www.jlibsedml.org}) in the binary +download. Clients of the the Systems Biology Simulation Core Library can choose +to use the \jlibsedml{} API directly, or access SED-ML support via facade +classes in the \texttt{org.simulator.sedml} package that do not require direct +dependencies on \jlibsedml{} in their code. \section*{Availability and Requirements} -The current version of Systems Biology Simulation Core Library is available on the project homepage. The entire project, including source code and documentation, several versions of jar files containing only binaries, binaries together with source code, can be downloaded, optionally also as a version including all required third-party libraries. -\begin{description} - \item{Project name:} \COR{Systems Biology Simulation Core Library} - \item{Project homepage:} \COR{\url{http://simulation-core.sourceforge.net}} - \item{Operating systems:} Platform independent, i.e., for all systems for which a JVM - is available. The Systems Biology Simulation Core Library was successfully - tested under Linux (Ubuntu version 10.4), Mac OS X (versions 10.6.8 and 10.8.2), - and \COR{Microsoft\textsuperscript{\textregistered} Windows\textsuperscript{\textregistered}~7}. - \item{Programming language:} Java\texttrademark - \item{Other requirements} \COR{Java runtime environment (JRE)} 1.6 or above - \item{License:} \COR{\acf{LGPL}} version~3 -\end{description} - -\section*{Acronyms} -\ifthenelse{\boolean{publ}}{\small}{} -\begin{acronym} - \acro{ADP} {adenosine diphosphate} - \acro{API} {application programing interface} - \acro{ATP} {adenosine-5'-triphosphate} - \acro{DHAP} {dihydroxyacetone phosphate} - \acro{F1,6BP} {fructose 1,6-bisphosphate} - \acro{GA3P} {glyceraldehyde 3-phosphate} - \acro{GUI} {graphical user interface} - \acro{JAR} {Java archive file} - \acro{JDK} {Java Development Kit} - \acro{JVM} {Java Virtual Machine} - \acro{KiSAO} {kinetic simulation algorithm ontology} - \acro{MIASE} {minimal information about a simulation experiment} - \acro{LGPL} {GNU Lesser General Public License} - \acro{ODE} {ordinary differential equation} - \acro{RuBisCO} {ribulose-1,5-bisphosphate carboxylase oxygenase} - \acro{NAD$^+$} {nicotinamide adenine dinucleotide} - \acro{SBML} {systems biology markup language} - \acro{SED-ML} {simulation experiment description markup language} -\end{acronym} +The current version of Systems Biology Simulation Core Library is available on +the project homepage. Either the source code or a jar file with binaries can be +downloaded. + +Project name: Simulation Core Library + +Project homepage: \url{http://sourceforge.net/projects/simulation-core/} + +Operating Systems: Systems Biology Simulation Core Library was successfully +tested under Linux (Ubuntu version 10.4), Mac OS X (versions 10.6.8 and 10.8.2), +and Windows~7. + +Programming Language: Java\texttrademark{} + +Other Requirements: Java Runtime Environment 1.6 or above + +License: LGPL version~3 + +\bigskip %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section*{Author's contributions} -RK and AlD contributed equally, implemented the majority of the source code, and declare shared first authorship. -MJZ and HP designed and implemented the abstraction scheme between solvers and ODE systems. -NR and NLN designed, implemented, and coordinated the data structures for a smooth integration of JSBML. -RA implemented support for \acs{SED-ML}. AT and AF incorporated the Simulation Core Library into CellDesigner. -AnD initialized and coordinated the project, drafted the manuscript, and supervised the work together with AZ. -All authors contributed to the implementation, read and approved the final manuscript. +RK and AlD contributed equally, implemented the majority of the source code, and +declare shared first authorship. +AnD drafted the first version of the manuscript, initialized and coordinated the +project, and supervised the work together with AZ. +MJZ and HP designed and implemented the abstraction scheme between solvers and +ODE systems. +NR and NLN designed, implemented, and coordinated the data structures for a +smooth integration of JSBML. +RA implemented support for SED-ML. +AT and AF incorporated the Simulation Core Library into CellDesigner. +All authors contributed to the implementation, read and approved the final +manuscript. + %%%%%%%%%%%%%%%%%%%%%%%%%%% \section*{Acknowledgements} @@ -964,11 +939,11 @@ \section*{Acknowledgements} A.~Becker, E.~Harley, and C.~Moore, Harvey Mudd College, USA, for providing a Java implementation of Rosenbrock's method, and to Michael T.~Cooling, University of Auckland, New Zealand, for fruitful discussion. The authors thank -D.~M.~Wouamba, P.~Stevens, M.~Zwie\ss{}ele, M.~Kronfeld, and A.~Schr\"oder for +D.~M.~Wouamba, P.~Stevens, M.~Zwie\ss{}ele, M.~Kronfeld, and A.~Schr''oder for source code contribution and fruitful discussion. This work was funded by the Federal Ministry of Education and Research (BMBF, -Germany) as part of the Virtual Liver Network (grant number 0315756). +Germany) in the project Virtual Liver (grant number 0315756). %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% The Bibliography %% @@ -1012,68 +987,63 @@ \section*{Acknowledgements} \section*{Figures} \subsection*{Figure 1 - Example for the creation of an abstract syntax graph of a small model} -\COR{This figure displays a unified representation of kinetic equations from an example model that} consists of the following reactions: +The model consists of the following reactions: \begin{center} \parbox[c]{.35\textwidth}{\begin{align*} -R_{1}&:& \ce{F1,6BP} &\rightleftharpoons \ce{DHAP + GA3P}\\ -R_{2}&:& \ce{DHAP} &\rightleftharpoons \ce{GA3P} +R_{1}&:& F1,6BP &\rightleftharpoons DHAP + GA3P\\ +R_{2}&:& DHAP &\rightleftharpoons GA3P \end{align*}} \end{center} -\COR{Both} reactions are part of the glycolysis\COR{. T}he contained molecules are \acf{F1,6BP}, -\acf{DHAP}\COR{,} and \acf{GA3P}. +The two reactions are part of the glycolysis, the contained molecules are fructose 1,6-bisphosphate (F1,6BP), +dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GA3P). Using the program SBMLsqueezer \cite{Draeger2008} the following mass action kinetics have been created: \begin{align*} -\nu_{R_{1}} &= k_{+1} \cdot [\ce{F1,6BP}] - k_{-1} \cdot[\ce{DHAP}] \cdot [\ce{GA3P}]\\ -\nu_{R_{2}} &= k_{+2} \cdot [\ce{DHAP}] - k_{-2} \cdot[\ce{GA3P}] +\nu_{R_{1}} &= k_{+1} \cdot [F16BP] - k_{-1} \cdot[DHAP] \cdot [GA3P]\\ +\nu_{R_{2}} &= k_{+2} \cdot [DHAP] - k_{-2} \cdot[GA3P] \end{align*} The nodes for [DHAP] and [GA3P] are only contained in the syntax graph once and connected to more than one multiplication node. This figure clearly indicates that the syntax graph is not a tree. -\COR{As can be seen in this picture, the outdegree of syntax trees does not necessaryly have to be binary.} \subsection*{Figure 2 - Algorithm for transforming algebraic rules to assignment rules} The first step is to decide whether the model is overdetermined by creating a matching of the variables. If this is not the case, every algebraic rule is solved to the matched variable, -which provides the basis for the creation of an equivalent assignment rule. \TODO{MORE DESCRIPTION!} +which provides the basis for the creation of an equivalent assignment rule. \subsection*{Figure 3 - Processing of events: simpflified algorithm (handling of delayed events omitted)} Let $E$ be the set of all events in a model, and $I_E$ be the set of events, whose trigger -conditions have already been evaluated to \true in the previous time step. We refer to elements within +conditions have already been evaluated to \true{} in the previous time step. We refer to elements within $I_E$ as \emph{inactive} events. We define the set $A_E$ as the subset of $E$ containing those events, -whose trigger condition switches from \false to \true in the current point $t$ in time. At the beginning -of the event handling, $A_E$ is empty. We call an event \emph{persistent}\COR{,} if it can only be removed from +whose trigger condition switches from \false{} to \true{} in the current point $t$ in time. At the beginning +of the event handling, $A_E$ is empty. We call an event \emph{persistent} if it can only be removed from $A_E$ under the condition that all of its assignments have been evaluated. This means that a -\COR{\emph{nonpersistent}} event can be removed from $A_E$ in case that its trigger condition becomes \false -during the evaluation of other events. Here, the function $\mathrm{trig}(e)$ returns \COR{1 or 0} depending -on whether or not the trigger condition of event $e \in E$ is satisfied. Similarly, the function +\emph{non-persistent} event can be removed from $A_E$ in case that its trigger condition becomes \false{} +during the evaluation of other events. Here, the function $\mathrm{trig}(e)$ returns 0 or 1 depending +on whether or not the trigger condition of the event $e$ is satisfied. Similarly, the function $\mathrm{persist}(e)$ returns 0 if event $e$ is not persistent, or 1 otherwise. In each iteration the trigger conditions of those active events $a_e \in A_E$ that are not persistent are checked. -If the trigger condition of such an event has changed from \true (1) to \false (0), it is removed from $A_E$. +If the trigger condition of such an event has changed from \true{} (1) to \false{} (0), it is removed from $A_E$. The next step comprises the evaluation of the triggers of all events. -If its trigger changes from \false to \true, an event is added to the set of active events $A_E$. -An event with its trigger changed from \true to \false is removed from the list of inactive events. -After the procession of all triggers the event $e$ of highest priority in the set of active events is chosen for execution by the function $\mathrm{choose}(A_E)$. +If its trigger changes from \false{} to \true{}, an event is added to the set of active events $A_E$. +An event with its trigger changed from \true{} to \false{} is removed from the list of inactive events. +After the procession of all triggers the event $e$ with the highest priority in the set of active events is chosen for execution by the function $\mathrm{choose}(A_E)$ . Note that priorities are not always defined, or multiple events may have an identical priority. The function $\mathrm{choose}(A_E)$ is therefore more complex than can be shown in this figure. This event is then processed, i.e., all of its assignments are evaluated, and afterwards the triggers of all events in $E$ have to be evaluated again, because of possible mutual influences between the events. -The algorithm proceeds until the \COR{set $A_E$ of active} events is empty. -\TODO{Should we rename $A_E$ to $E_\mathrm{A}$ and $I_E$ to $E_\mathrm{I}$? If yes, this has also to be done in the images.} +The algorithm proceeds until the list of acitve events is empty. -\subsection*{Figure 4 - Integrated calculation of new values for a time step including event processing} -For a certain time interval the Rosenbrock solver \COR{(\acs{KiSAO} term 33)} always tries to increase time $t$ by the current adaptive +\subsection*{Figure 4 - Calculation of the derivatives at a specific point in time} +First, the vector for saving the derivatives of all quantities $\dot{\vec{Q}}$ is set to the null vector $\vec{0}$. +Then the rate rules of the model are processed by solving the function $\vec{g}(\vec{Q}, t)$, which can change $\dot{\vec{Q}}$ in some dimensions. +After that for every reaction $R_i$ its velocity $\nu_i$ is computed. +The derivatives of each species (with index $s$) participating in the currently processed reaction $R_i$ are updated +in each step adding the product of the stoichiometry $n_{is}$ and the reaction's velocity $\nu_i$. + +\subsection*{Figure 5 - Integrated calculation of new values for a time step including event processing} +For a certain time interval the Rosenbrock solver always tries to increase time $t$ by the current adaptive step size $s$ and calculates a new vector of quantities $\vec{Q}_{\mathrm{res}}$. After a successful step the events and rules of the model are processed. If this causes a change in $\vec{Q}$, $h$ is first decreased and then the Rosenbrock solver calculates another vector $\vec{Q}_{t}$ using this adapted step size. The precision of the event processing is therefore determined by the minimum step size $h_{\min}$. -The $\mathrm{adapt}$ function is defined by Rosenbrock's method \cite{Press1993}. -\TODO{Should we rename $\vec{Q}_{\mathrm{res}}$ to $\vec{Q}_{\mathrm{next}}$?} - -\subsection*{Figure 5 - Calculation of the derivatives at a specific point in time} -First, the vector for saving the derivatives of all quantities $\dot{\vec{Q}}$ is set to the null vector $\vec{0}$. -Then the rate rules of the model are processed by solving the function $\vec{g}(\vec{Q}, t)$, which can change $\dot{\vec{Q}}$ in some dimensions. -After that for every \COR{reaction channel} $R_i$ its velocity $\nu_i$ is computed. -The derivatives of each species (with index $s$) participating in the currently processed \COR{reaction channel} $R_i$ are updated -in each step adding the product of the stoichiometry $n_{is}$ and the reaction's velocity $\nu_i$. -\TODO{Explain that stoichiometric values can be variable! Recomputation is necessary!} -\TODO{Should we note here that in simple cases, in which such a sophisticated step-size adaptation is not required, all available ODE solvers can be used, which will be faster?} +The $\mathrm{adapt}$ function is defined by Rosenbrock's method \TODO{cite}. \subsection*{Figure 6 - Architecture of the Systems Biology Simulation Core Library (simplified)} Numerical methods are strictly separated from differential equation systems. The @@ -1081,47 +1051,25 @@ \subsection*{Figure 6 - Architecture of the Systems Biology Simulation Core Libr methods. The middle part shows the interfaces defining several special types of the differential equations to be solved by the numerical methods. -The class \SBMLinterpreter (bottom part) implements all of these interfaces -with respect to the information content of a given \acs{SBML} model. Similarly, an +The class \SBMLinterpreter{} (bottom part) implements all of these interfaces +with respect to the information content of a given SBML model. Similarly, an implementation of further data formats can be included into the library. -\TODO{Why does Rosenbrock not extend FirstOrderSolver?} \subsection*{Figure 7 - Simulation of glycolytic oscillations} -This figure displays the results of a simulation computed with the Systems -Biology Simulation Core Library based on model 206 from BioModels \COR{Database} -\cite{Novere2006a, Wolf2000}. -Shown are the changes of the concentration (7a) of the most characteristic -intracellular metabolites 3-phosphogylcerate, \acs{ATP}, glucose, glyceraldhyde -3-phosphate, and \acs{NAD$^+$} within yeast cells. -Figure~7b displays a selection of the dynamcis of relevant fluxes -(\textsc{d}-glucose 6-phosphotransferase, glycerone-phosphate-forming, -phosphoglycerate kinase, pyruvate 2-O-phosphotransferase, acetaldehyde forming, -\acs{ATP} biosynthetic process) +This figure displays the results of a simulation computed with the Systems Biology Simulation Core Library based on model 206 from BioModels database \cite{Novere2006a, Wolf2000}. +Shown are the changes of the concentration (a) of the most characteristic intracellular metabolites 3-phosphogylcerate, ATP, glucose, glyceraldhyde 3-phosphate, and NAD$^+$ within yeast cells. +Figure 7b displays a selection of the dynamcis of relevant fluxes +(\textsc{D}-glucose 6-phosphotransferase, glycerone-phosphate-forming, phosphoglycerate kinase, pyruvate 2-O-phosphotransferase, acetaldehyde forming, ATP biosynthetic process) that were computed as intermediate results by the algorithm. -The computation was performed using the Adams-Moulton solver \cite{Hairer2000} -(\acs{KiSAO} term 280) with 200 integration steps, $10^{-10}$ as absolute error -tolerance and $10^{-5}$ as relative error tolerance. -Due to the importance of feedback regulation the selection of an appropriate -numerical solver is of crucial importance for this model. -Methods without step-size adaptation, such as the fourth order Runge-Kutta -algorithm (\acs{KiSAO} term 64), might only be able to find a high quality solution -with an appropriate number of integration steps. -The simulation results obtained by using the algorithm described in this work -reproduces the results provided by \COR{BioModels Database}. -\TODO{Where are these results provided?} -\TODO{Add more information about the number of species and reactions etc. in the model.} +The computation was performed using the Adams-Moulton solver \cite{Hairer2000} (KiSAO term 280) with 200 integration steps, $10^{-10}$ as absolute error tolerance and $10^{-5}$ as relative error tolerance. +Due to the importance of feedback regulation the selection of an appropriate numerical solver is of crucial importance for this model. +Methods without step-size adaptation, such as the fourth order Runge-Kutta algorithm, might only be able to find a high quality solution with an appropriate number of integration steps. +The simulation results obtained by using the algorithm described in this work reproduces the results provided by BioModels database. \subsection*{Figure 8 - Simulation of the Calvin-Benson cycle} -Another example of the capabilities of the Simulation Core Library has been -obtained by solving model 390 from BioModels \COR{Database} -\cite{Novere2006a, Arnold2011}. -This model was simulated using Euler's method (\acs{KiSAO} term 30) with 200 -integration steps for the time interval $[0, 35]$ seconds. -This figure shows the evolution of the concentrations of ribulose 1,5 -bisphosphate\COR{, a key metabolite for \ce{CO2} fixation in the reaction catalzed by \acf{RuBisCO},} and the currency metabolites \acs{ATP} and \acs{ADP} during the first 35\,s of -the photosynthesis. -\TODO{Add more information about the number of species and reactions etc. in the model.} +Another example of the capabilities of the Simulation Core Library has been obtained by solving model 390 from BioModels database \cite{Novere2006a, Arnold2011}. +This model was simulated using Euler's method (KiSAO term 30) with 200 integration steps for the time interval $[0, 35]$ seconds. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -1134,45 +1082,32 @@ \subsection*{Figure 8 - Simulation of the Calvin-Benson cycle} %% \section*{Tables} -\subsection*{Table 1 - Comparison of SBML-capable simulators} -The table gives an overview about the most characteristic features of -\acs{SBML}-capable simulation programs. As one aspect, it shows, which programs -support the most difficult \acs{SBML} elements (fast reactions, algebraic rules, and -events). Another key point is whether all models of the most recent SBML Test -Suite \COR{\cite{SBMLtestSuite2013}} can be correctly solved. -Please note that in the column for the SBML Test Suite, a dash means that -\emph{not all} of its models can be correctly solved, because not all \acs{SBML} -elements are supported. -\COR{In its current version, t}he program iBioSim, for instance, solves the vast majority of the test cases -correctly, but does not yet support the delay function, except delayed events. -LibSBMLSim, which is a simulation \acs{API} written in C, can only read models given -in \acs{SBML} Level~2 Version~4 and \acs{SBML} Level~3 -\COR{(indicated by the checkmark in brackets)}. -Similarly, a dash in the column for events means that not \emph{all} possible -cases for this language element can be correctly solved. -COPASI, for instance, supports events in \acs{SBML}, but not all of the current -constructs. -Hence, Systems Biology Simulation Core Library and BioUML are the only -simulation tools from this selection that pass \emph{all} models of the SBML -Test Suite \COR{(version~2.0.2)} across all levels and versions of \acs{SBML}. -\TODO{This table must be updated!} +\subsection*{Table 1 - Other simulators for SBML models: SBML language support} +The table shows which SBML elements (fast reactions, algebraic rules, events) +are supported by other SBML-capable simulation software and whether all models +of the SBML Test Suite can be correctly solved. +COPASI supports events in SBML, but not all of the current constructs. +The library LibSBMLSim can correctly solve the SBML Test Suite, but is limited +to SBML Level~3 Version~1 and Level~2 Version~4. +In the test suite column, a dash means that +\TODO{not the full test suite can be solved, because not all SBML elements are supported.} %\par \mbox{} \begin{landscape} -\rowcolors{4}{white}{lightblue} -\begin{tabular}{p{2cm}lccccC{1cm}C{1.2cm}p{2.5cm}C{.5cm}p{1cm}p{3.3cm}p{1.65cm}} +\rowcolors{3}{white}{lightblue} +\begin{tabular}{p{2cm}lccccC{1cm}C{1.2cm}p{2.5cm}p{.5cm}lp{3.3cm}p{1.65cm}} \toprule Program & Version & -\multicolumn{3}{C{2.4cm}}{Difficult SBML elements} & +\multicolumn{3}{C{2.5cm}}{Difficult SBML elements} & & \multirow{2}{1.5cm}{ - \begin{sideways}Fully SBML Test\end{sideways} - \begin{sideways}Suite compliant\end{sideways} + \begin{sideways}Fully SBML Test\end{sideways} + \begin{sideways}Suite compliant\end{sideways} } - & \acs{SED-ML} + & SED-ML & \multirow{2}{2.5cm}{Programming language} - & \acs{GUI} - & \acs{API} access + & GUI + & API access & Platform & Comments \\ \cline{3-5} @@ -1189,13 +1124,13 @@ \subsection*{Table 1 - Comparison of SBML-capable simulators} \begin{sideways}Events\end{sideways} } \\ \midrule -BioUML & 0.9.4 & \yes & \yes & \yes & & \yes & In $\upalpha$ version & Java & \yes & Java\-Script & independent & \\ -COPASI & 4.8 & \no & \no & (\yes) & & \no & \no & C++ (with multiple bindings) & \yes & \yes & Windows, Mac OS X, Linux, Solaris & \\ -iBioSim & 2.0 & \yes & \yes & \yes & & \no & \no & Java & \yes & \no & Fedora 15, Windows, Mac OS X $\geq$ 10.6 & \\ -JSim & 2.07 & \no & \yes & \no & & \no & \no & Java & \yes & \yes & Windows, Mac OS X, Linux & \\ -LibSBMLSim & 1.0 & \yes & \yes & \yes & & (\yes) & \no & C & \no & \yes & Windows, Mac OS X, Linux, Free BSD & \\ -VCell & 5.0 & \yes & \no & \yes & & \no & \no & Java frontend, C/C++ server backend & \yes & \no & independent & Internet connection required \\ -\COR{Simulation Core Library} & \COR{1.2} & \yes & \yes & \yes & & \yes & \yes & Java & \no & \yes & independent & \\ +BioUML & 0.9.3 & \yes & \yes & \yes & & \yes & In $\upalpha$ version & Java & \yes & JavaScript & independent & \\ +COPASI & 4.8 & \no & \no & (\yes) & & \no & \no & C++ (plus multiple bindings) & \yes & \yes & Windows, Linux, Mac OS X, Solaris & \\ +iBioSim & 2.0 & \yes & \yes & \yes & & \yes & \no & Java & \yes & \no & Fedora 15, Windows, Mac OS $>$ 10.6 & \\ +JSim & 2.07 & \no & \yes & \no & & \no & \no & Java & \yes & \yes & Windows, Linux, Mac OS X & \\ +LibSBMLSim & 1.0 & \yes & \yes & \yes & & L3, L2V4 & \no & C & \no & \yes & Windows, Linux, Free BSD, Mac OS X & \\ +VCell & 5.0 & \yes & \no & \yes & & \no & \no & Java frontend, C/C++ server backend & \yes & \no & independent & Internet connection required \\ +Simulation Core & 1.0 & \yes & \yes & \yes & & \yes & \yes & Java & \no & \yes & independent & \\ \bottomrule \end{tabular} \rowcolors{1}{white}{white} @@ -1220,12 +1155,10 @@ \subsection*{Table 1 - Comparison of SBML-capable simulators} %VCell & http://www.vcell.org/ & \cite{Moraru2008}, \cite{ Loew2001} & \yes & & &Error adding features & Cannot generate math & & No rate rules supported & Java frontend C/C++ server backend & \no & open source & VCML & 5.0.0 & Nov 11 2011 & Platform independent (Java) & Requires internet connection & \no\\\hline %XPPAUT 1 http://www.math.pitt.edu/~bard/xpp/xpp.html Ermentrout2012 -\subsection*{Table 2 - Simulation of the models from the SBML Test Suite (version 2.0.2) using Rosenbrock's solver} -The table shows the number of tested models and the total running times of the tests for all \acs{SBML} levels and versions. +\subsection*{Table 2 - Simulation of the models from the SBML Test Suite (version 2.0.2) using Rosenbrock solver} +The table shows for all SBML levels and versions the number of tested models and the total running times of the tests. An Intel\textsuperscript{\textregistered} Core\texttrademark{} i5 CPU with 3.33\,GHz and 4\,GB RAM was used with -Windows\textsuperscript{\textregistered}~7 (Version 6.1.7600) as operating system. -\TODO{JVM version? What is exactly measured here?} -\par \mbox{} +Windows\textsuperscript{\textregistered}~7 (Version 6.1.7600) as operating system.\par \mbox{} \par \mbox{ \rowcolors{2}{white}{lightblue} diff --git a/doc/publications/2012_BMC_SystBiol/img/Figure2.tex b/doc/publications/2012_BMC_SystBiol/img/Figure2.tex index bcd8ce22..1cf3afc4 100644 --- a/doc/publications/2012_BMC_SystBiol/img/Figure2.tex +++ b/doc/publications/2012_BMC_SystBiol/img/Figure2.tex @@ -2,11 +2,9 @@ \usepackage[latin1]{inputenc} \usepackage{tikz} -\usepackage{scalefnt} -\usepackage{amssymb} \usepackage[papersize={12.3cm,23.5cm},left=.13cm,right=.5cm,bottom=.1cm,top=.1cm]{geometry} +\usetikzlibrary{shapes,arrows} \begin{document} -\usetikzlibrary{shapes,arrows,decorations.pathmorphing,backgrounds,positioning,fit,petri} \pagestyle{empty} @@ -18,9 +16,8 @@ \tikzstyle{line} = [draw, -latex'] \tikzstyle{cloud} = [draw, ellipse,fill=red!20, node distance=3cm, minimum height=2em] - -\tikzstyle{io} = [trapezium,trapezium left angle=70,trapezium right angle=-70,minimum height=0.8cm, draw, fill=blue!20, text width=8em, text badly centered, node distance=3cm, inner sep=0pt,minimum height=2.5em] - +\tikzstyle{io} = [trapezium,trapezium left angle=70,trapezium right angle=-70,minimum height=0.6cm, draw, fill=blue!20, +text width=8em, text badly centered, node distance=3cm, inner sep=0pt,minimum height=2em] \begin{figure} \begin{tikzpicture}[node distance = 2cm, auto] @@ -35,28 +32,28 @@ \node [block, right of=overdetermined?, node distance=4.5cm] (exception) {Throw exception}; \node [block, below of=i0, node distance=2.5cm] (solve) {Solve $i$\textsuperscript{th} algebraic rule according to matching}; \node [block, left of=solve, node distance=4.5cm] (i++) {$i := i + 1$}; - \node [io, below of=solve, node distance=1.75cm] (newassignment) {New assignment rule}; + \node [io, below of=solve, node distance=2cm] (newassignment) {New assignment rule}; - \node [decision, below of=newassignment, node distance=2.25cm] (rulesleft?) {More algebraic rules?}; + \node [decision, below of=newassignment, node distance=2cm] (rulesleft?) {More algebraic rules?}; \node [cloud, below of=rulesleft?, node distance=2.5cm] (stop) {Stop}; - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (start) -- (graph); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (graph) -- (findpaths); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (findpaths) -- (matching?); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (matching?) -- node {Yes}(augment); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (augment) |- (findpaths); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (matching?) -- node {No} (overdetermined?); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (overdetermined?) -- node {No} (i0); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (overdetermined?) -- node {Yes}(exception); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (i0) -- (solve); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (i++) -- (solve); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (solve) -- (newassignment); - - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (newassignment) -- (rulesleft?); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (rulesleft?) -| node {Yes} (i++); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (rulesleft?) -- node {No} (stop); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (exception) |- (stop); + \path [line] (start) -- (graph); + \path [line] (graph) -- (findpaths); + \path [line] (findpaths) -- (matching?); + \path [line] (matching?) -- node {Yes}(augment); + \path [line] (augment) |- (findpaths); + \path [line] (matching?) -- node {No} (overdetermined?); + \path [line] (overdetermined?) -- node {No} (i0); + \path [line] (overdetermined?) -- node {Yes}(exception); + \path [line] (i0) -- (solve); + \path [line] (i++) -- (solve); + \path [line] (solve) -- (newassignment); + + \path [line] (newassignment) -- (rulesleft?); + \path [line] (rulesleft?) -| node {No} (i++); + \path [line] (rulesleft?) -- node {Yes} (stop); + \path [line] (exception) |- (stop); \end{tikzpicture} \end{figure} diff --git a/doc/publications/2012_BMC_SystBiol/img/Figure3.tex b/doc/publications/2012_BMC_SystBiol/img/Figure3.tex index 4d0c57da..c1342d74 100644 --- a/doc/publications/2012_BMC_SystBiol/img/Figure3.tex +++ b/doc/publications/2012_BMC_SystBiol/img/Figure3.tex @@ -2,10 +2,9 @@ \usepackage[latin1]{inputenc} \usepackage{tikz} -\usepackage{scalefnt} \usepackage{amsmath} \usepackage[papersize={16.4cm,20.5cm},left=.13cm,right=.5cm,bottom=.1cm,top=.1cm]{geometry} -\usetikzlibrary{shapes,arrows,decorations.pathmorphing,backgrounds,positioning,fit,petri} +\usetikzlibrary{shapes,arrows} \begin{document} \pagestyle{empty} @@ -36,7 +35,7 @@ \node [block, right of=updateRunningEvents, node distance=5cm] (increase2) {$j := j + 1$}; - \node [decision, right of=increase2, node distance=4cm] (decision3) {$j > |E|$?}; + \node [decision, right of=increase2, node distance=4cm] (decision3) {$j > |E|$}; \node [decision, below of=decision3] (noRunningEvents) {$A_E = \emptyset$?}; \node [block, left of=noRunningEvents, node distance=4cm] (chooseEvent) {$e := \mathrm{choose}(A_E)$}; @@ -47,28 +46,29 @@ \node [blank,below of=initLoop, node distance=1.2cm] (aux2) {}; \node [blank,right of=decision2, node distance=2.2cm] (aux4) {}; + \node [cloud, below of=processEvent, node distance=3cm] (stop) {Stop}; % Draw edges - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (start) -- (init); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (init) -- (initLoop); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (initLoop) -- (triggerEvents); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (triggerEvents) -- node{No} (updateInactive); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (triggerEvents) -- node{Yes} (decision2); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (updateInactive) -- (increase2); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (decision2) -- node{No} (updateRunningEvents); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (decision2) -- node{Yes} (aux4) -| (increase2); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (increase2) -- (decision3); + \path [line] (start) -- (init); + \path [line] (init) -- (initLoop); + \path [line] (initLoop) -- (triggerEvents); + \path [line] (triggerEvents) -- node{No} (updateInactive); + \path [line] (triggerEvents) -- node{Yes} (decision2); + \path [line] (updateInactive) -- (increase2); + \path [line] (decision2) -- node{No} (updateRunningEvents); + \path [line] (decision2) -- node{Yes} (aux4) -| (increase2); + \path [line] (increase2) -- (decision3); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (updateRunningEvents) -- (increase2); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (decision3) -- node{Yes} (noRunningEvents); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (decision3) -- node [right, very near start] {No}(aux3)|- (aux2); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (noRunningEvents) |- node{Yes} (stop); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (noRunningEvents) -- node{No} (chooseEvent); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (chooseEvent) -- (processEvent); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (processEvent) -| (update); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (update) -- (removeEvents); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (removeEvents) |- (initLoop); + \path [line] (updateRunningEvents) -- (increase2); + \path [line] (decision3) -- node{Yes} (noRunningEvents); + \path [line] (decision3) -- node{No}(aux3)|- (aux2); + \path [line] (noRunningEvents) |- node{Yes} (stop); + \path [line] (noRunningEvents) -- node{No} (chooseEvent); + \path [line] (chooseEvent) -- (processEvent); + \path [line] (processEvent) -| (update); + \path [line] (update) -- (removeEvents); + \path [line] (removeEvents) |- (initLoop); \end{tikzpicture} \end{figure} -\end{document} +\end{document} \ No newline at end of file diff --git a/doc/publications/2012_BMC_SystBiol/img/Figure4.tex b/doc/publications/2012_BMC_SystBiol/img/Figure4.tex index 59b97659..5a7e5cf2 100644 --- a/doc/publications/2012_BMC_SystBiol/img/Figure4.tex +++ b/doc/publications/2012_BMC_SystBiol/img/Figure4.tex @@ -2,62 +2,42 @@ \usepackage[latin1]{inputenc} \usepackage{tikz} -\usepackage{scalefnt} -\usepackage{amsmath} -\usepackage[papersize={15.27cm,18cm},left=.13cm,right=.5cm,bottom=.1cm,top=.1cm]{geometry} -\usetikzlibrary{shapes,arrows,decorations.pathmorphing,backgrounds,positioning,fit,petri} +\usepackage[papersize={12cm,16cm},left=.13cm,right=.5cm,bottom=.1cm,top=.1cm]{geometry} +\usetikzlibrary{shapes,arrows} \begin{document} \pagestyle{empty} % Define block styles \tikzstyle{decision} = [diamond, draw, fill=blue!20, - text width=4.5em, text badly centered, node distance=3cm, inner sep=0pt] + text width=5em, text badly centered, node distance=3cm, inner sep=0pt] \tikzstyle{block} = [rectangle, draw, fill=blue!20, - text width=8em, text centered, minimum height=4em] + text width=14em, text centered, rounded corners, minimum height=4em] \tikzstyle{line} = [draw, -latex'] \tikzstyle{cloud} = [draw, ellipse,fill=red!20, node distance=3cm, minimum height=2em] -\tikzstyle{io} = [trapezium,trapezium left angle=70,trapezium right angle=-70,minimum height=0.6cm, draw, fill=blue!20, -text width=14em, text badly centered, node distance=2.5cm, inner sep=4pt,minimum height=2em] -\tikzstyle{blank} = [coordinate]%[rectangle, text width=0em, text centered, rounded corners, minimum height=0em] - + \begin{figure} \begin{tikzpicture}[node distance = 2cm, auto] % Place nodes - \node [cloud] (start) {Start}; - \node [block, below of=start] (init) {\vspace{-.5cm}\begin{align*}t &:= t_{0}\\\vec{Q} &:= \vec{Q}_{0}\\h &:= h_0\end{align*}}; - \node [io, below of=init, text width=15em] (output) {($\vec{Q}_{\mathrm{res}}, t_{\mathrm{res}}) := \mathrm{Rosenbrock}(t, \vec{Q}, h)$}; - \node [block, below of=output,text width=17em] (pevents) {$\vec{Q}_{\mathrm{tmp}} :=$\\$\vec{Q}_{\mathrm{res}} + \vec{e}(\vec{Q}_{\mathrm{res}}, t_{\mathrm{res}}) + \vec{r}(\vec{Q}_{\mathrm{res}}, t_{\mathrm{res}})$}; - \node [decision, below of=pevents, node distance=3cm] (xpxres?) {$\vec{Q}_{\mathrm{tmp}} = \vec{Q}_{\mathrm{res}}$?}; - \node [block, left of=xpxres?, below of=xpxres?, node distance=4cm] (newvalues) {\vspace{-.5cm}\begin{align*}t &:= t_{\mathrm{res}}\\\vec{Q} &:= \vec{Q}_{\mathrm{res}}\\h &:= \mathrm{adapt}(h)\end{align*}}; - \node [decision, right of=xpxres?, node distance=3.5cm] (larger?) {$h\ge h_{\min} \cdot 10$?}; - \node [block, right of=larger?, node distance=3.75cm] (stepsize) {$h := \frac{h}{10}$}; - - \node [decision, below of=newvalues, node distance=3cm] (end?) {$t \ge t_{T}$?}; - \node [cloud, right of=end?, node distance=4cm] (stop) {Stop}; - \node [blank, left of=newvalues] (aux){}; - \node [blank, left of=xpxres?] (aux2){}; - - - - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (start) -- (init); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (init) -- (output); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (output) -- (pevents); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (pevents) -- (xpxres?); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (xpxres?) -- node [above] {Yes}(aux2)-| (newvalues); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (xpxres?) -- node [above,near start] {No}(larger?); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (larger?) |- node {No}(newvalues); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (larger?) -- node [above,near start] {Yes}(stepsize); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (stepsize) |- (output); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (newvalues) -- (end?); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (end?) -- node {Yes}(stop); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (end?) -| (aux) |- node {No}(output); - - - - + \node [cloud] (start) {Start}; + \node [block, below of=start] (rateRules) {Compute all assignment rules:\\$\dot{\vec{Q}} := \vec{g}(\vec{Q}, t)$}; + \node [block, below of=rateRules] (initLoop) {$j := 1$}; + \node [block,below of=initLoop] (reaction) {Compute flux $J_j$ through $R_j$:\\$J_j := \nu_j(\vec{Q}, t, \mathbf{N}, \mathbf{W}, \vec{p})$}; + \node [block,below of=reaction] (updateX) {for each species $i$ in $R_j$:\\$\dot{Q}_i := \dot{Q_i} + n_{ij} \cdot J_j$}; + \node [block, below of=updateX] (increase) {$j := j + 1$}; + \node [decision, right of=increase, node distance=8cm] (endOfLoop) {$j > |R|$}; + \node [cloud, below of=increase, node distance=5cm] (stop) {Stop}; + % Draw edges + \path [line] (start) -- (rateRules); + \path [line] (rateRules) -- (initLoop); + \path [line] (initLoop) -- (reaction); + \path [line] (reaction) -- (updateX); + \path [line] (updateX) -- (increase); + \path [line] (increase) -- (endOfLoop); + \path [line] (endOfLoop) |- node{Yes} (stop); + \path [line] (endOfLoop) |- node{No} (reaction); \end{tikzpicture} \end{figure} -\end{document} +\end{document} \ No newline at end of file diff --git a/doc/publications/2012_BMC_SystBiol/img/Figure5.tex b/doc/publications/2012_BMC_SystBiol/img/Figure5.tex index 16f0bb25..f162378b 100644 --- a/doc/publications/2012_BMC_SystBiol/img/Figure5.tex +++ b/doc/publications/2012_BMC_SystBiol/img/Figure5.tex @@ -1,46 +1,88 @@ \documentclass{article} \usepackage[latin1]{inputenc} -\usepackage{tikz} -\usepackage{scalefnt} -\usepackage[papersize={6.3cm,15.9cm},left=.13cm,right=.5cm,bottom=.1cm,top=.1cm]{geometry} -\usetikzlibrary{shapes,arrows,decorations.pathmorphing,backgrounds,positioning,fit,petri} +\usepackage{tikz} +\usepackage{amsmath} +\usepackage[papersize={15.2cm,20cm},left=.13cm,right=.5cm,bottom=.1cm,top=.1cm]{geometry} +\usetikzlibrary{shapes,arrows} \begin{document} \pagestyle{empty} % Define block styles \tikzstyle{decision} = [diamond, draw, fill=blue!20, - text width=5em, text badly centered, node distance=3cm, inner sep=0pt] + text width=4.5em, text badly centered, node distance=3cm, inner sep=0pt] \tikzstyle{block} = [rectangle, draw, fill=blue!20, - text width=14em, text centered, rounded corners, minimum height=4em] + text width=8em, text centered, minimum height=4em] \tikzstyle{line} = [draw, -latex'] \tikzstyle{cloud} = [draw, ellipse,fill=red!20, node distance=3cm, minimum height=2em] +\tikzstyle{io} = [trapezium,trapezium left angle=70,trapezium right angle=-70,minimum height=0.6cm, draw, fill=blue!20, +text width=14em, text badly centered, node distance=2.5cm, inner sep=4pt,minimum height=2em] \tikzstyle{blank} = [coordinate]%[rectangle, text width=0em, text centered, rounded corners, minimum height=0em] \begin{figure} \begin{tikzpicture}[node distance = 2cm, auto] % Place nodes - \node [cloud] (start) {Start}; - \node [block, below of=start] (rateRules) {Compute all assignment rules:\\$\dot{\vec{Q}} := \vec{g}(\vec{Q}, t)$}; - \node [block, below of=rateRules] (initLoop) {$j := 1$}; - \node [block,below of=initLoop] (reaction) {Compute flux $J_j$ through $R_j$:\\$J_j := \nu_j(\vec{Q}, t, \mathbf{N}, \mathbf{W}, \vec{p})$}; - \node [block,below of=reaction] (updateX) {for each species $i$ in $R_j$:\\$\dot{Q}_i := \dot{Q_i} + n_{ij} \cdot J_j$}; - \node [block, below of=updateX] (increase) {$j := j + 1$}; - \node [decision, below of=increase, node distance=2.5cm] (endOfLoop) {$j > |R|$?}; - \node [cloud, below of=endOfLoop, node distance=2.5cm] (stop) {Stop}; - \node [blank, right of=endOfLoop, node distance=3.5cm] (aux){}; - % Draw edges - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (start) -- (rateRules); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (rateRules) -- (initLoop); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (initLoop) -- (reaction); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (reaction) -- (updateX); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (updateX) -- (increase); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (increase) -- (endOfLoop); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (endOfLoop) -- node[right]{Yes} (stop); - \draw [color = black, line width = 1.0pt, ->, -triangle 60] (endOfLoop) -- node[very near start] {No} (aux) |- (reaction); + \node [cloud] (start) {Start}; + \node [block, below of=start] (init) {\vspace{-.5cm}\begin{align*}t &:= t_{0}\\\vec{Q} &:= \vec{Q}_{0}\\h &:= h_0\end{align*}}; + \node [io, below of=init, text width=15em] (output) {($\vec{Q}_{\mathrm{res}}, t_{\mathrm{res}}) := \mathrm{Rosenbrock}(t, \vec{Q}, h)$}; + \node [block, below of=output,text width=17em] (pevents) {$\vec{Q}_{\mathrm{tmp}} :=$\\$\vec{Q}_{\mathrm{res}} + \vec{e}(\vec{Q}_{\mathrm{res}}, t_{\mathrm{res}}) + \vec{r}(\vec{Q}_{\mathrm{res}}, t_{\mathrm{res}})$}; + \node [decision, below of=pevents, node distance=3cm] (xpxres?) {$\vec{Q}_{\mathrm{tmp}} = \vec{Q}_{\mathrm{res}}$?}; + \node [block, left of=xpxres?, below of=xpxres?, node distance=4cm] (newvalues) {\vspace{-.5cm}\begin{align*}t &:= t_{\mathrm{res}}\\\vec{Q} &:= \vec{Q}_{\mathrm{res}}\\h &:= \mathrm{adapt}(h)\end{align*}}; + \node [decision, right of=xpxres?, node distance=3.5cm] (larger?) {$h\ge h_{\min} \cdot 10$?}; + \node [block, right of=larger?, node distance=3.5cm] (stepsize) {$h := \frac{h}{10}$}; + + \node [decision, below of=newvalues, node distance=3cm] (end?) {$t \ge t_{T}$?}; + \node [cloud, below of=end?, node distance=2.5cm] (stop) {Stop}; + \node [blank, left of=newvalues] (aux){}; + \node [blank, left of=xpxres?] (aux2){}; + +% \node [decision, below of=findpaths] (matching?) {At least one path available?}; +% \node [block, left of=matching?, node distance=4.5cm] (augment) {Augment matching}; +% \node [decision, below of=matching?, node distance=3.5cm] (overdetermined?) {Model ovedetermined?}; +% \node [block, below of=overdetermined?, node distance=3cm] (i0) {i:=0}; +% \node [block, right of=overdetermined?, node distance=4.5cm] (exception) {Throw exception}; +% \node [block, below of=i0, node distance=2.5cm] (solve) {Solve i-th algebraic rule according to matching}; +% \node [block, left of=solve, node distance=4.5cm] (i++) {i:=i+1}; +% \node [io, below of=solve, node distance=2cm] (newassignment) {New assignment rule}; +% +% \node [decision, below of=newassignment, node distance=2cm] (rulesleft?) {i=\#algebraic rules?}; +% \node [cloud, below of=rulesleft?, node distance=2.5cm] (stop) {Stop}; + + + \path [line] (start) -- (init); + \path [line] (init) -- (output); + \path [line] (output) -- (pevents); + \path [line] (pevents) -- (xpxres?); + \path [line] (xpxres?) -- node {Yes}(aux2)-| (newvalues); + \path [line] (xpxres?) -- node {No}(larger?); + \path [line] (larger?) |- node {No}(newvalues); + \path [line] (larger?) -- node {Yes}(stepsize); + \path [line] (stepsize) |- (output); + \path [line] (newvalues) -- (end?); + \path [line] (end?) -- node {Yes}(stop); + \path [line] (end?) -| (aux) |- node {No}(output); + + + +%\path [line] (end?) |- node {No})([xshift=-0.5cm,yshift=-0.5cm]newvalues.south west) |- (init); +% \path [line] (findpaths) -- (matching?); +% \path [line] (matching?) -- node {Yes}(augment); +% \path [line] (augment) |- (findpaths); +% \path [line] (matching?) -- node {No} (overdetermined?); +% \path [line] (overdetermined?) -- node {No} (i0); +% \path [line] (overdetermined?) -- node {Yes}(exception); +% \path [line] (i0) -- (solve); + %\path [line] (i++) -- (solve); +% \path [line] (solve) -- (newassignment); + + %\path [line] (newassignment) -- (rulesleft?); + %\path [line] (rulesleft?) -| node {No} (i++); + %\path [line] (rulesleft?) -- node {Yes} (stop); + %\path [line] (exception) |- (stop); + \end{tikzpicture} \end{figure} -\end{document} +\end{document} \ No newline at end of file diff --git a/doc/publications/2012_BMC_SystBiol/img/Figure6.pdf b/doc/publications/2012_BMC_SystBiol/img/Figure6.pdf index 37240909..0a6baebc 100644 Binary files a/doc/publications/2012_BMC_SystBiol/img/Figure6.pdf and b/doc/publications/2012_BMC_SystBiol/img/Figure6.pdf differ diff --git a/doc/publications/2012_BMC_SystBiol/img/Figure7.pdf b/doc/publications/2012_BMC_SystBiol/img/Figure7.pdf deleted file mode 100644 index 349abe4c..00000000 Binary files a/doc/publications/2012_BMC_SystBiol/img/Figure7.pdf and /dev/null differ diff --git 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b/doc/publications/2012_BMC_SystBiol/plots/plot.R @@ -30,21 +30,21 @@ bounds <- function(matrix, indices) { } plot_species <- function(b, indices, names, matrix) { - plot(c(b[1,1], b[2,1]) * 60, c(b[1,2], b[2,2]), type="n", xlab="Time in s", ylab=expression(paste("Concentration in ", mmol%.%l^-1)), las=1) + plot(c(b[1,1], b[2,1]) * 60, c(b[1,2], b[2,2]), type="n", xlab="Time in s", ylab=expression(paste("Concentration in ", mmol%.%l^-1))) legend("topleft", names, col=2:(length(indices)+1), lty=1, lwd=2) for (i in 1:length(indices)) { lines(matrix[,1] * 60, matrix[,indices[i]], type="l", col=i+1, lty=1, lwd=2) } - title("Species in model 206") + #title("Species in model 206") } plot_fluxes <- function(b, indices, names, matrix) { - plot(c(b[1,1], b[2,1]) * 60, c(b[1,2], b[2,2]) / 60, type="n", xlab="Time in s", ylab=expression(paste("Flux in ", mmol%.%s^-1)), las=1) + plot(c(b[1,1], b[2,1]) * 60, c(b[1,2], b[2,2]) / 60, type="n", xlab="Time in s", ylab=expression(paste("Flux in ", mmol%.%s^-1))) legend("topleft", names, col=2:(length(indices)+1), lty=1, lwd=2) for (i in 1:length(indices)) { lines(matrix[2:length(matrix[,1]),1] * 60, matrix[2:length(matrix[,indices[i]]),indices[i]] / 60, type="l", col=i+1, lty=1, lwd=2) } - #title("Fluxes in model 206") + title("Fluxes in model 206") } @@ -90,10 +90,10 @@ dev.off() ###### Figure 7a plot_species <- function(b, indices, names, matrix) { - plot(c(b[1,1], b[2,1]) * 60, c(b[1,2], b[2,2]), type="n", xlab="Time in s", ylab=expression(paste("Concentration in ", mmol%.%l^-1)), las=1) - legend("topleft", names, col=2:(length(indices)+1), lty=1, lwd=3, ncol=2, bty="n") + plot(c(b[1,1], b[2,1]) * 60, c(b[1,2], b[2,2]), type="n", xlab="Time in s", ylab=expression(paste("Concentration in ", mmol%.%l^-1))) + legend("topleft", names, col=2:(length(indices)+1), lty=1, lwd=2, ncol=2, bty="n") for (i in 1:length(indices)) { - lines(matrix[,1] * 60, matrix[,indices[i]], type="l", col=i+1, lty=1, lwd=3) + lines(matrix[,1] * 60, matrix[,indices[i]], type="l", col=i+1, lty=1, lwd=2) } #title("Species in model 206") } @@ -111,10 +111,10 @@ dev.off() ###### Figure 7b plot_fluxes <- function(b, indices, names, matrix) { - plot(c(b[1,1], b[2,1]) * 60, c(b[1,2], b[2,2]) / 60, type="n", xlab="Time in s", ylab=expression(paste("Flux in ", mmol%.%s^-1)), las=1) - legend("topleft", names, col=2:(length(indices)+1), lty=1, lwd=3, bty="n") + plot(c(b[1,1], b[2,1]) * 60, c(b[1,2], b[2,2]) / 60, type="n", xlab="Time in s", ylab=expression(paste("Flux in ", mmol%.%s^-1))) + legend("topleft", names, col=2:(length(indices)+1), lty=1, lwd=2, bty="n") for (i in 1:length(indices)) { - lines(matrix[2:length(matrix[,1]),1] * 60, matrix[2:length(matrix[,indices[i]]),indices[i]] / 60, type="l", col=i+1, lty=1, lwd=3) + lines(matrix[2:length(matrix[,1]),1] * 60, matrix[2:length(matrix[,indices[i]]),indices[i]] / 60, type="l", col=i+1, lty=1, lwd=2) } } @@ -126,31 +126,6 @@ names <- c("D-glucose 6-phosphotransferase", "glycerone-phosphate-forming", "pho plot_fluxes(b, indices, names, x) dev.off() -############################################################################################ -###### Figure 7 (a and b in one image) - -pal <- palette() -pal[7] <- pal[8] -palette(pal) - -pdf("test.pdf", width=23.4, height=8.3) -layout(matrix(1:2, ncol=2)) -par(cex=2, mai=c(1.7, 1.7, 0.1, 0.3)) -indices <- c(3, 4, 6, 7, 8) -names <- c("glucose", "ATP", "glyceraldehyde 3-phosphate", expression(NAD^"+"), "3-phosphoglycerate") -b <- bounds(x, indices) -b[2,2] <- 3.6 #3.3 -plot_species(b, indices, names, x) -mtext("A", line=-1.08, at=-6.15, cex=3) - -par(cex=2, mai=c(1.7, 1.9, 0.1, 0.1)) -indices <- c(30:35) -b <- bounds(x, indices) -names <- c("D-glucose 6-phosphotransferase", "glycerone-phosphate-forming", "phosphoglycerate kinase", "pyruvate 2-O-phosphotransferase", "acetaldehyde forming", "ATP biosynthetic process") -plot_fluxes(b, indices, names, x) -mtext("B", line=-1.08, at=-6.15, cex=3) -dev.off() - ############################################################################################ @@ -160,10 +135,10 @@ indices <- c(4, 9, 10) names <- c("Ribulose 1,5 bisphosphate", "ATP", "ADP") b <- bounds(y, indices) plot_species <- function(b, indices, names, matrix) { - plot(c(b[1,1], b[2,1]), c(b[1,2], b[2,2]), type="n", xlab="Time in s", ylab=expression(paste("Concentration in ", mmol%.%l^-1)), las=1) - legend("topright", names, col=2:(length(indices)+1), lty=1, lwd=3, bty="n") + plot(c(b[1,1], b[2,1]), c(b[1,2], b[2,2]), type="n", xlab="Time in s", ylab=expression(paste("Concentration in ", mmol%.%l^-1))) + legend("topright", names, col=2:(length(indices)+1), lty=1, lwd=2, bty="n") for (i in 1:length(indices)) { - lines(matrix[,1], matrix[,indices[i]], type="l", col=i+1, lty=1, lwd=3) + lines(matrix[,1], matrix[,indices[i]], type="l", col=i+1, lty=1, lwd=2) } #title("Species in model 206") } diff --git a/doc/publications/2012_BMC_SystBiol/plots/test.pdf b/doc/publications/2012_BMC_SystBiol/plots/test.pdf index 19e18998..f6230768 100644 Binary files a/doc/publications/2012_BMC_SystBiol/plots/test.pdf and b/doc/publications/2012_BMC_SystBiol/plots/test.pdf differ diff --git a/doc/publications/2012_Bioinformatics/Decision.txt b/doc/publications/2012_Bioinformatics/Decision.txt deleted file mode 100644 index 0d800732..00000000 --- a/doc/publications/2012_Bioinformatics/Decision.txt +++ /dev/null @@ -1,69 +0,0 @@ -27-Jun-2012 -Manuscript ID: BIOINF-2012-0686 -Title: Simulation Core Library: a Java library for numerical computation in systems biology - -Dear Dr. DrŠger, - -The reviews of your manuscript are now in hand. The reviewers had substantial concerns about the manuscript and the Associate Editor, Olga Troyanskaya, has decided to reject your manuscript based on their advice. Specifically, the reviewers had substantial concerns about the biological impact of this library on it's own and about it's relationship to other existing software. - -As the journal receives more publishable manuscripts than its space will accommodate acceptance must be limited to manuscripts receiving the most favourable recommendations from reviewers. Unfortunately, I must decline your request to have the manuscript published in Bioinformatics. The Associate Editor's general comments and those of the reviewers can be found at the foot of this e-mail. We will not consider any further versions of this manuscript, but I hope that you find the comments useful should you decide to revise your manuscript for another journal. - -On behalf of the Executive Editor, I would like to thank you for considering Bioinformatics to present your work and I look forward to the possibility of receiving other manuscripts from you in the future. - -Best regards, -Alison Hutchins -Bioinformatics Editorial office - - -Here are the Editor's comments: - ----------------------------------------- ----------------------------------------- - -Here are the comments of the reviewers: ----------------------------------------- -Reviewer: 1 -Comments to the Author -1) General comments - -In this Applications Note, the authors present "Simulation Core Library", a Java library for ODE simulations of SBML models. - -2) Specific comments -a) major - -The target audience for this software is Java developers who are looking for a Java ODE solver for SBML models. This audience is likely to be most interested in 1) the API that they will use, and 2) why they should use this particular library; and less interested in implementation details (which they don't care about) and object-oriented design (which they understand and expect). Given this, and the short format of the Applications Note, it might be beneficial to emphasize the motivation (why this library is important) and the unique contribution of this work (what programming challenges does this library alleviate for developers) by shortening and tightening the Implementation section and expanding the Introduction and the Results and Conclusion sections. - -There is no mention of existing Java ODE libraries, except for the reference to the Apache Commons Math library. If Java ODE libraries already exist, they should be referenced, along with an explanation of what they cannot do that the "Simulation Core Library" can do. One of the primary contributions of this work seems to be the interface between the existing JSBML and Apache Commons Math libraries. If this was a significant challenge, this should be highlighted in the paper. - -Perhaps the biggest strength of the paper (independent of the software itself) is the mention that the software is currently used by existing applications CellDesigner and SBMLsimulator. But CellDesigner has been around for many years and users of that software were able to run ODE simulations long before "Simulation Core Library". This might be confusing to readers. If the ability to run ODE simulations in CellDesigner is not new, then it might be worthwhile to provide some clarity on why this is mentioned. Does the "Simulation Core Library" somehow perform better than previous ODE solvers in CellDesigner? Or is the use in CellDesigner mentioned only to show a proof-of-concept that the library "can be easily integrated in larger applications"? If the latter is true, can you expand on how easy it was to integrate into CellDesigner, or the relationship/comparison between the "Simulation Core Library" versus the other simulation libraries in CellDesigner? Also, it seems SBMLsimulator was written by a group closely related to, and including some members of, the authors of this paper. This should be explicitly mentioned. - -b) minor -Typo in the first sentence of the Abstract: "is a the" should be "is a" or "is the". - -The process of determining the exact time at which an event occurs is mentioned a couple times, but this must have been previously solved by existing SBML ODE solvers. If this is trivial, it might not be worth mentioning. If this is non-trivial, then perhaps citing a reference to a previous implementation might be appropriate. - -The claim that the software solved 99.27% of the models from the BioModels.net database piqued my curiosity as to what happened in the failed 0.73%. - - -Reviewer: 2 -Comments to the Author -Drager et al describes a Java library, Simulation Core Library (SCL), for numerical computation in systems biology. I personally do not like the name ÔSimulation Core LibraryÕ or the project name Ôsimulation-coreÕ because they do not reflect the (limited) application area of this library, but I guess software authors have the freedom to name their applications. The library is certainly useful, because it provides a large number of solvers, and perhaps more importantly, classes to work with SBML (based on JSBML) and SED-ML. Although I do not completely agree with the authors about the lack of reusability of existing C/C++ or matlab based simulators, having an alternative implementation in Java is certainly welcome. - -The biggest problem I have with this paper is that I do not understand why the authors decided to publish the library instead of the application SBMLSimulator. When I clicked the link ÒSimulation Core Library Web SiteÓ from their sourceforge.net website, I saw a website for SBMLSimulator. It took me a while to figure out that SCL is the simulation engine of SBMLSimulator that has been deliberately separated so that other programs can make use of it. Other than a javadoc generated API documentation, I could not find any description about the design and structure of SCL, and how exactly potential users can make use of this library. It appeared to me that SBMLSimulator is the main application and SCL is only one of the components, and perhaps a side product of this software. - -I am confused with the aim of this paper because, if for some reason (SBMLSimulator is not ready?) the authors would like to emphasize the library instead of the program, they should create a dedicated webpage with detailed information. There should be introduction, tutorials and examples about different classes in this library so that uses can make efficient use of the library. The current status of the website is unacceptable for the publication of this library. - -If SBMLSimulator is mature and provides unique features compared to other simulators, it might be better to publish SBMLSimulator and list SCL as one of the features that makes SBMLSimulator useful not only to users, but also to developers of similar applications. This is a very common approach because many modern applications provide APIs and libraries that can be reused by others. A paper about SBMLSimulator would reach a much larger audience because there are many more users than developers. - -The paper is generally readable but there are some minor language issues: -¥ The first sentence of abstract: É is a the keyÉ ? -¥ Page 1, Line 20: of BioModels Database, should be Òin the BioModels DatabaseÓ? -¥ Page 1, Line 56, However, É does not read well. Perhaps need to reorganize with words like Òis currently lackingÓ. -¥ Page 1 right, Line 38: Òcan therefore easily beÓ should be Òcan therefore be easilyÓ -¥ Page 2, line 33, adding Òthat isÓ before Òresponsible for Ò? - - - -Reviewer: 3 -Comments to the Author -This short note introduce a new dynamic simulation Java library for numerical computation in systems biology. The introduction is very clear. Although with the length of the note, it is hard to fully grasp details of this software package, from the description in this note and more details from their website, their work seems interesting to readers in systems biology areas. \ No newline at end of file diff --git a/doc/publications/2012_Bioinformatics/Cover_Letter.pdf b/doc/publications/2012_bioinformatics_applications_note/Cover_Letter.pdf similarity index 100% rename from doc/publications/2012_Bioinformatics/Cover_Letter.pdf rename to doc/publications/2012_bioinformatics_applications_note/Cover_Letter.pdf diff --git a/doc/publications/2012_Bioinformatics/PLAIN.BST b/doc/publications/2012_bioinformatics_applications_note/PLAIN.BST similarity index 100% rename from doc/publications/2012_Bioinformatics/PLAIN.BST rename to doc/publications/2012_bioinformatics_applications_note/PLAIN.BST diff --git a/doc/publications/2012_Bioinformatics/alltt.sty b/doc/publications/2012_bioinformatics_applications_note/alltt.sty similarity index 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- - - - - -
- - - - - - - - - - -
Introduction Capabilities Documentation Download Mailing list License Acknowledgments 
- 		- -
-
- -

Systems Biology Simulation Core Library

- -

- Welcome to the Systems Biology Simulation Core Library! -

-

- The Systems Biology Simulation Core Library provides an efficient and exhaustive Java™ implementation of methods to interpret - the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution. - This library is based on the JSBML project and can be used on every operating system, - for which a Java Virtual Machine is available. -

-

- Please note that this project does not contain any user interface, neither a command-line interface, nor a graphical user interface. - This project has been developed as a pure programming library. To support the Minimum Information About a Simulation Experiment - (MIASE) effort, it understands Simulation Experiment Description Markup Language - (SED-ML) files. -

-

- Its abstract type and interface hierarchy facilitates the implementation of further community standards, such as - CellML. -

- -

Capabilities

- -

Numerical simulation of SBML models

- -
    -
  • Several solvers from the Apache Commons Math Library included
    • -
  • Rosenbrock solver for integration of stiff differential equation systems
    • -
  • Clear separation of SBML interpretation and integration routines
    • -
  • Fast SBML interpretation by using a transformed syntax graph
    • -
  • Full support of SBML events, algebraic rules and fast reactions
    • -
  • Support of all all models from the SBML Test Suite - (v. 2.2) for all levels and versions: Simulation results
    • -
- -

Support for SED-ML

- -
    -
  • Several quality functions for computation of the distance from simulated data to some given data
    • -
- - -

Documentation of the application programing interfaces

- - To get startet with this library, please see the API documentation (JavaDoc) - for the version you like to use: - - -

Download

- - You can obtain all versions of this library by going to the - sourceforge download area - of the project. - - -

Mailing list and tracker

- -

- Please don't hesitate to contact the developer's mailing list - simulation-core-development@lists.sourceforge.net. -

-

- If you encounter any bugs, or like to ask for a feature request, - please use the tracker. -

- -

Authors and license

- -

- This library is free software; you can redistribute it and/or modify - it under the terms of the GNU Lesser General Public License as - published by the Free Software Foundation. A copy of the license - agreement is provided in the file named "LICENSE.txt" included with - this each version of software distribution and also available online as - LGPL 3.0. -

- Copyright © 2007-2013 jointly by the following organizations: -

    -
  1. University of Tuebingen, Germany
    2. -
  2. Keio University, Japan
    3. -
  3. Harvard University, USA
    4. -
  4. The University of Edinburgh, UK
    5. -
  5. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
    6. -
-

-

- The main developers of this library are: -

- Contributors (in alphabetic order): -
    -
  • Richard Adams
    • -
  • Akira Funahashi
    • -
  • Nicolas Le Novère
    • -
  • Hannes Planatscher
    • -
  • Nicolas Rodriguez
    • -
  • Akito Tabira
    • -
  • Andreas Zell
    • -
  • Michael J. Ziller
    • -
- Your contribution is welcome. If you like to participate in this effort, please contact the - developers' mailing list and join the team! -

- -

Acknowledgments

- -

- Many thanks to B. Kotcon, S. Mesuro, D. Rozenfeld, A. Yodpinyanee, A. Perez, E. Doi, - R. Mehlinger, S. Ehrlich, M. Hunt, G. Tucker, P. Scherpelz, A. Becker, E. Harley, - and C. Moore, Harvey Mudd College, USA, for providing a Java implementation of - Rosenbrock's method as part of the ODEToolkit. -

- We like to thank Michael T. Cooling, - University of Auckland, New Zealand, for fruitful discussion. -

- Special thanks to D. M. Wouamba, P. Stevens, M. Zwießele, - M. Kronfeld, and - A. Schröder for - source code contribution and fruitful discussion. -

- This work was funded by the Federal Ministry of Education and Research - (BMBF, Germany) as part of - the Virtual Liver Network. -

- -
- - - - - -
- - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -org.simulator -
-Enum SBMLTestSuiteRunner.Options

-
-java.lang.Object
-  extended by java.lang.Enum<SBMLTestSuiteRunner.Options>
-      extended by org.simulator.SBMLTestSuiteRunner.Options
-
-
-
All Implemented Interfaces:
Serializable, Comparable<SBMLTestSuiteRunner.Options>
-
-
-
Enclosing class:
SBMLTestSuiteRunner
-
-
-
-
public static enum SBMLTestSuiteRunner.Options
extends Enum<SBMLTestSuiteRunner.Options>
- - -

-Commannd-line options for this test program. -

- -

-

-
Since:
-
1.2
-
Version:
-
$Rev: 331 $
-
Author:
-
Andreas Dräger
-
-
- -

- - - - - - - - - - - - - -
-Enum Constant Summary
all - -
-           
sedml - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static SBMLTestSuiteRunner.OptionsvalueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static SBMLTestSuiteRunner.Options[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-all

-
-public static final SBMLTestSuiteRunner.Options all
-
-
-
-
-
- -

-sedml

-
-public static final SBMLTestSuiteRunner.Options sedml
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static SBMLTestSuiteRunner.Options[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (SBMLTestSuiteRunner.Options c : SBMLTestSuiteRunner.Options.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static SBMLTestSuiteRunner.Options valueOf(String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
IllegalArgumentException - if this enum type has no constant -with the specified name -
NullPointerException - if the argument is null
-
-
- -
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org.simulator.SBMLTestSuiteRunner.Options

-
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-Packages that use SBMLTestSuiteRunner.Options
org.simulatorThis package simply contains a default main program to display very - basic licensing terms and other information. 
-  -

- - - - - -
-Uses of SBMLTestSuiteRunner.Options in org.simulator
-  -

- - - - - - - - - - - - - -
Methods in org.simulator that return SBMLTestSuiteRunner.Options
-static SBMLTestSuiteRunner.OptionsSBMLTestSuiteRunner.Options.valueOf(String name) - -
-          Returns the enum constant of this type with the specified name.
-static SBMLTestSuiteRunner.Options[]SBMLTestSuiteRunner.Options.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

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-Package org.simulator.gui.img -

-This package contains images and icons for the Simulation Core Library. -

-See: -
-          Description -

-

-Package org.simulator.gui.img Description -

- -

-This package contains images and icons for the Simulation Core Library. - These pictures can be used in graphical user interfaces. -

- -

-

-
Since:
-
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-
Andreas Dräger
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-Package org.simulator.gui -

-Contains classes that provide very basic functions that facilitate the creation of graphical user interfaces. -

-See: -
-          Description -

-

-Package org.simulator.gui Description -

- -

-Contains classes that provide very basic functions that facilitate the creation of graphical user interfaces. -

- -

-

-
Since:
-
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- - - diff --git a/resources/org/simulator/gui/img/package-info.java b/resources/org/simulator/gui/img/package-info.java index affec050..afcd821a 100644 --- a/resources/org/simulator/gui/img/package-info.java +++ b/resources/org/simulator/gui/img/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/resources/org/simulator/gui/package-info.java b/resources/org/simulator/gui/package-info.java index 398413c9..2f07883e 100644 --- a/resources/org/simulator/gui/package-info.java +++ b/resources/org/simulator/gui/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/About.java b/src/org/simulator/About.java index 1cb90f87..12189e05 100644 --- a/src/org/simulator/About.java +++ b/src/org/simulator/About.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -38,7 +38,7 @@ public static void main(String[] args) { String message = "This is the Systems Biology Simulation Core Library.\n\n" + "Main authors: Roland Keller, Alexander D\u00f6rr, and Andreas Dr\u00e4ger\n" + - "Copyright \u00A9 2007-2013 jointly by the following organizations:\n" + + "Copyright \u00A9 2007-2012 jointly by the following organizations:\n" + "1. University of Tuebingen, Germany\n" + "2. Keio University, Japan\n" + "3. Harvard University, USA\n" + diff --git a/src/org/simulator/io/CSVImporter.java b/src/org/simulator/io/CSVImporter.java index a75719b3..4ddf1a3d 100644 --- a/src/org/simulator/io/CSVImporter.java +++ b/src/org/simulator/io/CSVImporter.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/io/package-info.java b/src/org/simulator/io/package-info.java index d800f737..efa77185 100644 --- a/src/org/simulator/io/package-info.java +++ b/src/org/simulator/io/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/ArithmeticMean.java b/src/org/simulator/math/ArithmeticMean.java index 5c2e5580..7d636b7b 100644 --- a/src/org/simulator/math/ArithmeticMean.java +++ b/src/org/simulator/math/ArithmeticMean.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/DistanceSum.java b/src/org/simulator/math/DistanceSum.java index 60c265f9..3de00a6f 100644 --- a/src/org/simulator/math/DistanceSum.java +++ b/src/org/simulator/math/DistanceSum.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/EuclideanDistance.java b/src/org/simulator/math/EuclideanDistance.java index 8541dc0b..e65c71ae 100644 --- a/src/org/simulator/math/EuclideanDistance.java +++ b/src/org/simulator/math/EuclideanDistance.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/ManhattanDistance.java b/src/org/simulator/math/ManhattanDistance.java index 1f4d550a..b81a2126 100644 --- a/src/org/simulator/math/ManhattanDistance.java +++ b/src/org/simulator/math/ManhattanDistance.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/Mathematics.java b/src/org/simulator/math/Mathematics.java index e7e0aee9..86ee95a4 100644 --- a/src/org/simulator/math/Mathematics.java +++ b/src/org/simulator/math/Mathematics.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/MeanFunction.java b/src/org/simulator/math/MeanFunction.java index e0e585c6..eee7e582 100644 --- a/src/org/simulator/math/MeanFunction.java +++ b/src/org/simulator/math/MeanFunction.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/N_Metric.java b/src/org/simulator/math/N_Metric.java index cdf05936..4e102b70 100644 --- a/src/org/simulator/math/N_Metric.java +++ b/src/org/simulator/math/N_Metric.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -22,8 +22,7 @@ */ package org.simulator.math; - -import org.simulator.math.odes.MultiTable.Block.Column; +import java.util.Iterator; /** * An implementation of an n-metric. An n-metric is basically the n-th root of @@ -87,25 +86,29 @@ public N_Metric(double root) { return Math.pow(Math.abs(x_i - y_i), root); } - /* - * + /* (non-Javadoc) + * @see org.sbml.simulator.math.Distance#distance(java.lang.Iterable, java.lang.Iterable, double) */ - public double distance(Column x, - Column y, double defaultValue) { - if (root == 0d) { + public double distance(Iterable x, + Iterable y, double defaultValue) { + if(root == 0d) { return defaultValue; } double d = 0; double x_i; double y_i; - for (int i=0; i!= Math.min(x.getRowCount(), y.getRowCount()); i++) { - x_i = x.getValue(i); - y_i = y.getValue(i); + Iterator yIterator = y.iterator(); + for (Number number : x) { + if (!yIterator.hasNext()) { + break; + } + x_i = number.doubleValue(); + y_i = yIterator.next().doubleValue(); if (computeDistanceFor(x_i, y_i, root, defaultValue)) { d += additiveTerm(x_i, y_i, root, defaultValue); } } - return overallDistance(d, root, defaultValue); + return overallDistance(d,root,defaultValue); } @@ -136,25 +139,5 @@ public void setRoot(double root) { this.root = root; } - /** - * @param expected - * @param defaultValue - * @return - */ - public double distanceToZero(Column x, double defaultValue) { - if(root == 0d) { - return defaultValue; - } - double d = 0; - double x_i; - for (int i=0; i!= x.getRowCount(); i++) { - x_i = x.getValue(i); - if (computeDistanceFor(x_i, 0d, root, defaultValue)) { - d += additiveTerm(x_i, 0d, root, defaultValue); - } - } - return overallDistance(d,root,defaultValue); - } - } diff --git a/src/org/simulator/math/PearsonCorrelation.java b/src/org/simulator/math/PearsonCorrelation.java index 9bb4745d..c9ec7cb0 100644 --- a/src/org/simulator/math/PearsonCorrelation.java +++ b/src/org/simulator/math/PearsonCorrelation.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -22,8 +22,7 @@ */ package org.simulator.math; - -import org.simulator.math.odes.MultiTable.Block.Column; +import java.util.Iterator; /** * Implementation of the Pearson correlation. @@ -61,8 +60,10 @@ public PearsonCorrelation(double defaultValue) { /* (non-Javadoc) * @see org.sbml.simulator.math.Distance#distance(java.lang.Iterable, java.lang.Iterable, double) */ - public double distance(Column x, - Column y, double defaultValue) { + public double distance(Iterable x, + Iterable y, double defaultValue) { + Iterator yIterator = y.iterator(); + MeanFunction meanF = new ArithmeticMean(); double meanX = meanF.computeMean(x); double meanY = meanF.computeMean(y); @@ -71,9 +72,12 @@ public double distance(Column x, double sumXSquared = 0d; double sumYSquared = 0d; - for (int i=0; i != Math.min(x.getRowCount(), y.getRowCount()); i++) { - double x_i = x.getValue(i); - double y_i = y.getValue(i); + for (Number number : x) { + if (!yIterator.hasNext()) { + break; + } + double x_i = number.doubleValue(); + double y_i = yIterator.next().doubleValue(); sumNumerator+= (x_i-meanX)*(y_i-meanY); sumXSquared+= (x_i-meanX)*(x_i-meanX); sumYSquared+= (y_i-meanY)*(y_i-meanY); diff --git a/src/org/simulator/math/QualityMeasure.java b/src/org/simulator/math/QualityMeasure.java index b495cdec..b49fbac1 100644 --- a/src/org/simulator/math/QualityMeasure.java +++ b/src/org/simulator/math/QualityMeasure.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -26,7 +26,6 @@ import java.util.ArrayList; import org.simulator.math.odes.MultiTable; -import org.simulator.math.odes.MultiTable.Block.Column; /** * This class is the basis of various implementations of distance functions. @@ -116,8 +115,8 @@ boolean computeDistanceFor(double x_i, double y_i, double root, * @return distance the distance between the two vectors * @throws IllegalArgumentException */ - public double distance(Column x, - Column y) { + public double distance(Iterable x, + Iterable y) { return distance(x, y,defaultValue); } @@ -138,8 +137,8 @@ public double distance(Column x, * @return The distance between the two arrays x and y. * @throws IllegalArgumentException */ - public abstract double distance(Column x, - Column y,double defaultValue); + public abstract double distance(Iterable x, + Iterable y,double defaultValue); /** * diff --git a/src/org/simulator/math/RNG.java b/src/org/simulator/math/RNG.java index 14a1cb29..baef9ca1 100644 --- a/src/org/simulator/math/RNG.java +++ b/src/org/simulator/math/RNG.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/RelativeEuclideanDistance.java b/src/org/simulator/math/RelativeEuclideanDistance.java index ca590317..2c6b7ad4 100644 --- a/src/org/simulator/math/RelativeEuclideanDistance.java +++ b/src/org/simulator/math/RelativeEuclideanDistance.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/RelativeManhattanDistance.java b/src/org/simulator/math/RelativeManhattanDistance.java index 5c9d6d5f..11aa9c89 100644 --- a/src/org/simulator/math/RelativeManhattanDistance.java +++ b/src/org/simulator/math/RelativeManhattanDistance.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/RelativeSquaredError.java b/src/org/simulator/math/RelativeSquaredError.java index 4cd42400..5c0ddbbf 100644 --- a/src/org/simulator/math/RelativeSquaredError.java +++ b/src/org/simulator/math/RelativeSquaredError.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/Relative_N_Metric.java b/src/org/simulator/math/Relative_N_Metric.java index 8eba31ed..4127fc54 100644 --- a/src/org/simulator/math/Relative_N_Metric.java +++ b/src/org/simulator/math/Relative_N_Metric.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -22,8 +22,8 @@ */ package org.simulator.math; - -import org.simulator.math.odes.MultiTable.Block.Column; +import java.util.LinkedList; +import java.util.List; /** * Computes the relative distance of two vectors based on the {@link N_Metric} distance. @@ -85,11 +85,15 @@ public Relative_N_Metric(N_Metric metric) { /* (non-Javadoc) * @see org.sbml.simulator.math.Distance#distance(java.lang.Iterable, java.lang.Iterable, double) */ - public double distance(Column x, - Column expected, double defaultValue) { + public double distance(Iterable x, + Iterable expected, double defaultValue) { double numerator=metric.distance(x, expected, defaultValue); - double denominator = metric.distanceToZero(expected, defaultValue); - double denominator2 = metric.distanceToZero(x, defaultValue); + List nullVector = new LinkedList(); + for(@SuppressWarnings("unused") Number n : expected) { + nullVector.add(0d); + } + double denominator=metric.distance(expected,nullVector,defaultValue); + double denominator2=metric.distance(x,nullVector,defaultValue); if ((denominator != 0) && (denominator2 != 0) ) { return numerator / denominator; } else if((denominator == 0) && (denominator2 == 0)){ diff --git a/src/org/simulator/math/odes/AbstractDESSolver.java b/src/org/simulator/math/odes/AbstractDESSolver.java index 45b896f6..806158ea 100644 --- a/src/org/simulator/math/odes/AbstractDESSolver.java +++ b/src/org/simulator/math/odes/AbstractDESSolver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -25,7 +25,6 @@ import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.math.BigDecimal; -import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.LinkedList; @@ -112,7 +111,7 @@ public static long getSerialversionuid() { /** * A cloned version of this object */ - protected AbstractDESSolver clonedSolver; + private AbstractDESSolver clonedSolver; /** * Initialize with default integration step size and non-negative attribute @@ -292,7 +291,6 @@ else if (Double.isInfinite(yPrev[k])) { * @param change * The vector for the resulting change of the system. * @param steadyState - * * @return The change. * @throws Exception */ @@ -302,7 +300,7 @@ public abstract double[] computeChange(DESystem DES, double[] y, double t, /* (non-Javadoc) * @see org.simulator.math.odes.DelayValueHolder#computeValue(double, java.lang.String) */ - public double computeDelayedValue(double time, String id, DESystem DES, double[] initialValues, int yIndex) { + public double computeDelayedValue(double time, String id) { //get interval double[] timepoints=data.getTimePoints(); int leftIndex=-1; @@ -313,9 +311,6 @@ public double computeDelayedValue(double time, String id, DESystem DES, double[] if ((i>0) && (timepoints[i]>time)) { leftIndex=i-1; } - else if((timepoints[i]==time)) { - leftIndex=rightIndex; - } break; } } @@ -333,45 +328,14 @@ else if((timepoints[i]==time)) { } if (rightIndex!=-1) { rightValue=c.getValue(rightIndex); - if(Double.isNaN(rightValue) && Math.abs(time - leftValue) < 10E-12) { - rightValue = leftValue; - } } - if(Double.isNaN(rightValue)) { - boolean calculated = true; - double[] yCopy = new double[initialValues.length]; - double[] change = new double[initialValues.length]; - System.arraycopy(initialValues, 0, yCopy, 0, initialValues.length); - try { - DES.setDelaysIncluded(false); - if(clonedSolver == null) { - clonedSolver = this.clone(); - clonedSolver.reset(); - } - clonedSolver.computeChange(DES, yCopy, 0, time, change, false); - } catch (DerivativeException e) { - rightIndex=-1; - calculated = false; - } - DES.setDelaysIncluded(true); - if(calculated) { - return yCopy[yIndex] + change[yIndex]; - - } - - - } - if (leftIndex==-1) { return rightValue; } else if (rightIndex==-1) { return leftValue; } - else if(rightIndex == leftIndex) { - return leftValue; - } else { return leftValue + (rightValue-leftValue)*((time-timepoints[leftIndex])/(timepoints[rightIndex]-timepoints[leftIndex])); } @@ -395,8 +359,6 @@ else if(rightIndex == leftIndex) { * whether or not to increase the given time by the given step * size. * @param steadyState - * - * * @return the time increased by the step size * @throws DerivativeException */ @@ -442,7 +404,7 @@ protected double[] computeSteadyState(FastProcessDESystem DES, int step=0; while (!noChange(oldValues, newValues, step)) { System.arraycopy(newValues, 0, oldValues, 0, newValues.length); - ft = computeNextState(DES, ft, stepSize * 1000, oldValues, change, + ft = computeNextState(DES, ft, stepSize, oldValues, change, newValues, true, true); step++; } @@ -562,9 +524,6 @@ protected MultiTable initResultMatrix(DESystem DES, protected MultiTable initResultMatrix(DESystem DES, double[] initialValues, double[] timePoints) { double result[][] = new double[timePoints.length][initialValues.length]; - for(int i=0; i!= result.length; i++) { - Arrays.fill(result[i], Double.NaN); - } System.arraycopy(initialValues, 0, result[0], 0, initialValues.length); data = new MultiTable(timePoints, result, DES .getIdentifiers()); @@ -609,10 +568,10 @@ private boolean noChange(double newValues[], double oldValues[], int step) { for (int i = 0; i < newValues.length; i++) { double distance = Math.abs(newValues[i]-oldValues[i]); double relativeDistance = 0; - if((Math.abs(newValues[i]) > 1E-10) || (Math.abs(oldValues[i]) > 1E-10)) { + if(!(newValues[i] == 0) || !(oldValues[i] == 0)) { relativeDistance = Math.abs((newValues[i]-oldValues[i])/Math.max(newValues[i],oldValues[i])); } - if(((distance > 1E-6) || (relativeDistance > 1E-6)) && (step < 10000)) { + if(((distance > 1E-5) || (relativeDistance > 1E-5)) && (step < 10000)) { return false; } } @@ -839,7 +798,7 @@ public MultiTable solve(DESystem DES, double[] initialValues, result[i], timeBegin); System.arraycopy(yTemp, 0, result[i], 0, yTemp.length); } - v = additionalResults(DES, t, result[i], data, i); + v = additionalResults(DES, t - stepSize, result[i - 1], data, i); firePropertyChange(oldT * intervalFactor, t * intervalFactor); } diff --git a/src/org/simulator/math/odes/AdamsBashforthSolver.java b/src/org/simulator/math/odes/AdamsBashforthSolver.java index fbe03cd4..67d1cdba 100644 --- a/src/org/simulator/math/odes/AdamsBashforthSolver.java +++ b/src/org/simulator/math/odes/AdamsBashforthSolver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/AdamsMoultonSolver.java b/src/org/simulator/math/odes/AdamsMoultonSolver.java index b6ba47fc..19a56bce 100644 --- a/src/org/simulator/math/odes/AdamsMoultonSolver.java +++ b/src/org/simulator/math/odes/AdamsMoultonSolver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/AdaptiveStepsizeIntegrator.java b/src/org/simulator/math/odes/AdaptiveStepsizeIntegrator.java index 96b8fa35..d0d1d2fa 100644 --- a/src/org/simulator/math/odes/AdaptiveStepsizeIntegrator.java +++ b/src/org/simulator/math/odes/AdaptiveStepsizeIntegrator.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -37,11 +37,11 @@ public abstract class AdaptiveStepsizeIntegrator extends AbstractDESSolver { /** * Default absolute allowable vectorial tolerance. */ - protected double absTol = 1E-14d; + protected double absTol = 1E-10d; /** * Default relative allowable vectorial tolerance. */ - protected double relTol = 1E-10d; + protected double relTol = 1E-5d; /** * diff --git a/src/org/simulator/math/odes/DESSolver.java b/src/org/simulator/math/odes/DESSolver.java index 72a45345..5030c459 100644 --- a/src/org/simulator/math/odes/DESSolver.java +++ b/src/org/simulator/math/odes/DESSolver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/DESystem.java b/src/org/simulator/math/odes/DESystem.java index 3701ed13..fd60ba87 100644 --- a/src/org/simulator/math/odes/DESystem.java +++ b/src/org/simulator/math/odes/DESystem.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -63,11 +63,4 @@ public interface DESystem extends Serializable, FirstOrderDifferentialEquations */ public int getPositiveValueCount(); - /** - * @param delaysIncluded - * Determines whether delay expression should be included in the calculation. - */ - public void setDelaysIncluded(boolean delaysIncluded); - - } diff --git a/src/org/simulator/math/odes/DelayValueHolder.java b/src/org/simulator/math/odes/DelayValueHolder.java index 8c5d3732..87950f6d 100644 --- a/src/org/simulator/math/odes/DelayValueHolder.java +++ b/src/org/simulator/math/odes/DelayValueHolder.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -41,17 +41,9 @@ public interface DelayValueHolder extends Serializable { * computed for the element with the given id. * @param id * the id of the delayed value - * @param DES - * the DESystem - * @param initialValues - * the initialValues of the DES - * @param yIndex - * the index corresponding to the id in the vector of the DES - * - * * @return the computed value for the element with the given identifier at * the time point in the past. */ - public double computeDelayedValue(double time, String id, DESystem DES, double[] initialValues, int yIndex); + public double computeDelayedValue(double time, String id); } diff --git a/src/org/simulator/math/odes/DelayedDESystem.java b/src/org/simulator/math/odes/DelayedDESystem.java index b2ce1526..c759bbc7 100644 --- a/src/org/simulator/math/odes/DelayedDESystem.java +++ b/src/org/simulator/math/odes/DelayedDESystem.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/DormandPrince54Solver.java b/src/org/simulator/math/odes/DormandPrince54Solver.java index aafd9c3a..a9c371e4 100644 --- a/src/org/simulator/math/odes/DormandPrince54Solver.java +++ b/src/org/simulator/math/odes/DormandPrince54Solver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/DormandPrince853Solver.java b/src/org/simulator/math/odes/DormandPrince853Solver.java index ad0dbcf8..30e49dd1 100644 --- a/src/org/simulator/math/odes/DormandPrince853Solver.java +++ b/src/org/simulator/math/odes/DormandPrince853Solver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/EulerMethod.java b/src/org/simulator/math/odes/EulerMethod.java index 56ceb8de..f0d9dafc 100644 --- a/src/org/simulator/math/odes/EulerMethod.java +++ b/src/org/simulator/math/odes/EulerMethod.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/EventDESystem.java b/src/org/simulator/math/odes/EventDESystem.java index 5f29ac33..89c64c0f 100644 --- a/src/org/simulator/math/odes/EventDESystem.java +++ b/src/org/simulator/math/odes/EventDESystem.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/EventInProgress.java b/src/org/simulator/math/odes/EventInProgress.java index 4a596f47..a9b68f81 100644 --- a/src/org/simulator/math/odes/EventInProgress.java +++ b/src/org/simulator/math/odes/EventInProgress.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/FastProcessDESystem.java b/src/org/simulator/math/odes/FastProcessDESystem.java index 1d396a00..8ee3e46f 100644 --- a/src/org/simulator/math/odes/FastProcessDESystem.java +++ b/src/org/simulator/math/odes/FastProcessDESystem.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/FirstOrderSolver.java b/src/org/simulator/math/odes/FirstOrderSolver.java index 9f5ceac2..a291f467 100644 --- a/src/org/simulator/math/odes/FirstOrderSolver.java +++ b/src/org/simulator/math/odes/FirstOrderSolver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/GraggBulirschStoerSolver.java b/src/org/simulator/math/odes/GraggBulirschStoerSolver.java index 16fdab14..22a9c97e 100644 --- a/src/org/simulator/math/odes/GraggBulirschStoerSolver.java +++ b/src/org/simulator/math/odes/GraggBulirschStoerSolver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -84,7 +84,7 @@ public GraggBulirschStoerSolver clone() { * @see org.simulator.math.odes.FirstOrderSolver#createIntegrator() */ protected void createIntegrator() { - integrator = new GraggBulirschStoerIntegrator(Math.min(1e-8, Math.min(1.0,getStepSize())), Math.min(1.0,getStepSize()), getAbsTol(), getRelTol()); + integrator=new GraggBulirschStoerIntegrator(Math.min(1e-8,Math.min(1.0,getStepSize())), Math.min(1.0,getStepSize()), getAbsTol(), getRelTol()); } /* (non-Javadoc) diff --git a/src/org/simulator/math/odes/HighamHall54Solver.java b/src/org/simulator/math/odes/HighamHall54Solver.java index 9da880db..1ca8b4e4 100644 --- a/src/org/simulator/math/odes/HighamHall54Solver.java +++ b/src/org/simulator/math/odes/HighamHall54Solver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/MultiTable.java b/src/org/simulator/math/odes/MultiTable.java index d9e42afc..a585f1d2 100644 --- a/src/org/simulator/math/odes/MultiTable.java +++ b/src/org/simulator/math/odes/MultiTable.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -62,7 +62,7 @@ public class MultiTable extends AbstractTableModel implements Iterable(); } - + /** * Checks whether or not this {@link Block} contains a {@link Column} * with the given identifier. @@ -337,7 +337,7 @@ public String getColumnName(int column) { public String[] getColumnNames() { return columnNames; } - + /** * @return the data */ @@ -474,7 +474,6 @@ public void setRowData(int rowIndex, double[] array) { /* (non-Javadoc) * @see javax.swing.table.AbstractTableModel#setValueAt(java.lang.Object, int, int) */ - @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) { if (!(aValue instanceof Double)) { throw new IllegalArgumentException(ONLY_DOUBLE_VALUES_ACCEPTED); @@ -490,7 +489,6 @@ public void setValueAt(Object aValue, int rowIndex, int columnIndex) { /* (non-Javadoc) * @see java.lang.Object#toString() */ - @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append(Arrays.toString(getIdentifiers())); @@ -629,33 +627,33 @@ public void addBlock(String[] identifiers) { * @param timepoints * @return table the filtered table */ - public MultiTable filter(double[] timepoints) { - ArrayList rowIndices = new ArrayList(); - int i=0; - for(double time: timepoints) { - while((i rowIndices = new ArrayList(); + int i=0; + for(double time: timepoints) { + while((i -1 ? getColumn(index) : null; } - + /** * Returns the index of a column for a given identifier. * @@ -839,7 +837,6 @@ public Double getValueAt(int rowIndex, int columnIndex) { /* (non-Javadoc) * @see javax.swing.table.AbstractTableModel#isCellEditable(int, int) */ - @Override public boolean isCellEditable(int rowIndex, int columnIndex) { // Maybe we want to change this later return false; @@ -925,7 +922,7 @@ public void setTimePoints(double[] timePoints) { && (listOfBlocks.get(0).getRowCount() != timePoints.length)) { throw new IllegalArgumentException(String.format( UNEQUAL_DATA_AND_TIME_POINTS, listOfBlocks.get(0) - .getRowCount(), timePoints.length)); + .getRowCount(), timePoints.length)); } this.timePoints = timePoints; } @@ -933,7 +930,7 @@ public void setTimePoints(double[] timePoints) { /* (non-Javadoc) * @see javax.swing.table.AbstractTableModel#setValueAt(java.lang.Object, int, int) */ - public void setValueAt(Double aValue, int rowIndex, int columnIndex) { + public void setValueAt(Object aValue, int rowIndex, int columnIndex) { if (!(aValue instanceof Double)) { throw new IllegalArgumentException(ONLY_DOUBLE_VALUES_ACCEPTED); } @@ -948,7 +945,6 @@ public void setValueAt(Double aValue, int rowIndex, int columnIndex) { /* (non-Javadoc) * @see java.lang.Object#toString() */ - @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append('['); diff --git a/src/org/simulator/math/odes/ParameterizedDESystem.java b/src/org/simulator/math/odes/ParameterizedDESystem.java index c2c2fcfa..54b37046 100644 --- a/src/org/simulator/math/odes/ParameterizedDESystem.java +++ b/src/org/simulator/math/odes/ParameterizedDESystem.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/RichDESystem.java b/src/org/simulator/math/odes/RichDESystem.java index a67b5ead..022663d4 100644 --- a/src/org/simulator/math/odes/RichDESystem.java +++ b/src/org/simulator/math/odes/RichDESystem.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/RosenbrockSolver.java b/src/org/simulator/math/odes/RosenbrockSolver.java index 89586eb2..102ef106 100644 --- a/src/org/simulator/math/odes/RosenbrockSolver.java +++ b/src/org/simulator/math/odes/RosenbrockSolver.java @@ -160,21 +160,7 @@ public class RosenbrockSolver extends AdaptiveStepsizeIntegrator { */ private boolean[] ignoreNaN; - /** - * Precision for event timing - */ - private static final double precisionTimingEventsAndRules = 1E-7; - - /** - * Precision for fast reaction timing - */ - private static final double precisionTimingFastReactions = 1E-3; - - /** - * Precision for fast reactions - */ - private static final double precisionFastReactions = 1E-3; - + private static final double precisionEventsAndRules = 1E-7; /** * default constructor @@ -252,7 +238,7 @@ private void init(int size, double stepsize, int nTimepoints) { /* (non-Javadoc) * @see org.simulator.math.odes.AbstractDESSolver#clone() */ - public RosenbrockSolver clone() { + public AbstractDESSolver clone() { return new RosenbrockSolver(this); } @@ -560,38 +546,14 @@ public double[] computeChange(DESystem DES, double[] y2, double time, changed=processEventsAndRules(true, EDES, Math.min(newTime,timeEnd), t, yTemp); } } - if ((!changed) && (DES instanceof FastProcessDESystem) && (!steadyState)) { - FastProcessDESystem FDES = (FastProcessDESystem) DES; - if(FDES.containsFastProcesses()) { - double[] yTemp2 = new double[yTemp.length]; - System.arraycopy(yTemp, 0, yTemp2, 0, yTemp.length); - if(clonedSolver == null) { - clonedSolver = this.clone(); - } - double[] result = clonedSolver.computeSteadyState(FDES, - yTemp2, 0); - System.arraycopy(result, 0, yTemp, 0, yTemp.length); - for(int i=0; i!=result.length; i++) { - double difference = Math.abs(yTemp[i]-oldY[i]); - if((Math.abs(yTemp[i]) > 1E-10) || (Math.abs(oldY[i]) > 1E-10)) { - difference = Math.abs((yTemp[i]-oldY[i])/ Math.max(yTemp[i], oldY[i])); - } - if((difference > precisionFastReactions) && (h > precisionTimingFastReactions)) { - changed = true; - break; - } - } - - } - } if(changed) { //if(h/10>hMin) { - if(h>precisionTimingEventsAndRules) { + if(h>precisionEventsAndRules) { //h=h/10; - h = Math.max(h / 10,precisionTimingEventsAndRules); - if(h - precisionTimingEventsAndRules < precisionTimingEventsAndRules) { - h = precisionTimingEventsAndRules; + h = Math.max(h / 10,precisionEventsAndRules); + if(h - precisionEventsAndRules < precisionEventsAndRules) { + h = precisionEventsAndRules; } System.arraycopy(oldY, 0, y, 0, numEqn); } @@ -605,7 +567,6 @@ public double[] computeChange(DESystem DES, double[] y2, double time, } } else { - System.arraycopy(yTemp, 0, y, 0, numEqn); t=Math.min(newTime,timeEnd); // change stepsize (see Rodas.f) require 0.2<=hnew/h<=6 hAdap = Math.max(fac1, diff --git a/src/org/simulator/math/odes/RungeKutta_EventSolver.java b/src/org/simulator/math/odes/RungeKutta_EventSolver.java index 132eb721..396f0adb 100644 --- a/src/org/simulator/math/odes/RungeKutta_EventSolver.java +++ b/src/org/simulator/math/odes/RungeKutta_EventSolver.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/odes/package-info.java b/src/org/simulator/math/odes/package-info.java index 6887201d..eebf7896 100755 --- a/src/org/simulator/math/odes/package-info.java +++ b/src/org/simulator/math/odes/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/math/package-info.java b/src/org/simulator/math/package-info.java index c05b7da7..f50ecf8a 100644 --- a/src/org/simulator/math/package-info.java +++ b/src/org/simulator/math/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/package-info.java b/src/org/simulator/package-info.java index 3178b8f8..d441452d 100644 --- a/src/org/simulator/package-info.java +++ b/src/org/simulator/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sbml/AlgebraicRuleConverter.java b/src/org/simulator/sbml/AlgebraicRuleConverter.java index 4ad9f27e..90206dac 100644 --- a/src/org/simulator/sbml/AlgebraicRuleConverter.java +++ b/src/org/simulator/sbml/AlgebraicRuleConverter.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sbml/SBMLEventInProgress.java b/src/org/simulator/sbml/SBMLEventInProgress.java index b7ee3d8f..c46ad9ea 100644 --- a/src/org/simulator/sbml/SBMLEventInProgress.java +++ b/src/org/simulator/sbml/SBMLEventInProgress.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sbml/SBMLEventInProgressWithDelay.java b/src/org/simulator/sbml/SBMLEventInProgressWithDelay.java index 64177436..3a6c1d3a 100644 --- a/src/org/simulator/sbml/SBMLEventInProgressWithDelay.java +++ b/src/org/simulator/sbml/SBMLEventInProgressWithDelay.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sbml/SBMLValueHolder.java b/src/org/simulator/sbml/SBMLValueHolder.java index 0d990b32..90398d02 100644 --- a/src/org/simulator/sbml/SBMLValueHolder.java +++ b/src/org/simulator/sbml/SBMLValueHolder.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sbml/SBMLinterpreter.java b/src/org/simulator/sbml/SBMLinterpreter.java index 0ed9e2ca..206274fa 100644 --- a/src/org/simulator/sbml/SBMLinterpreter.java +++ b/src/org/simulator/sbml/SBMLinterpreter.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -393,11 +393,6 @@ public class SBMLinterpreter implements DelayedDESystem, EventDESystem, * Is the SBase in the Y vector an amount? */ private boolean[] isAmount; - - /** - * Are delays included in the computation? - */ - private boolean delaysIncluded; /** @@ -462,7 +457,6 @@ public SBMLinterpreter(Model model, double defaultSpeciesValue, double defaultP this.astNodeTime = 0d; this.priorities = new HashSet(); this.highOrderEvents = new LinkedList(); - this.delaysIncluded = true; Map speciesReferenceToRateRule = new HashMap(); int speciesReferencesInRateRules = 0; @@ -574,7 +568,7 @@ public String[] getAdditionalValueIds() { public double[] getAdditionalValues(double t, double[] Y) throws DerivativeException { if ((t - currentTime > 1E-15) - || ((Y != this.Y) && !Arrays.equals(Y, this.Y)) || (t == 0)) { + || ((Y != this.Y) && !Arrays.equals(Y, this.Y))) { /* * We have to compute the system for the given state. But we are not * interested in the rates of change, but only in the reaction velocities. @@ -652,7 +646,7 @@ public double getCurrentStoichiometry(String id) { if ((sr != null) && sr.isSetStoichiometryMath()) { try { - return ((ASTNodeValue)sr.getStoichiometryMath().getMath().getUserObject(TEMP_VALUE)).compileDouble(astNodeTime, 0d); + return ((ASTNodeValue)sr.getStoichiometryMath().getMath().getUserObject(TEMP_VALUE)).compileDouble(astNodeTime); } catch (SBMLException exc) { logger.log(Level.WARNING, String.format( "Could not compile stoichiometry math of species reference %s.", id), @@ -715,14 +709,14 @@ public EventInProgress getNextEventAssignments(double t, double previousTime, do } else { ASTNodeValue priorityObject=events[index].getPriorityObject(); if (priorityObject != null) { - events[index].changePriority(priorityObject.compileDouble(astNodeTime, 0d)); + events[index].changePriority(priorityObject.compileDouble(astNodeTime)); priorities.add(events[index].getPriority()); } } } else { ASTNodeValue priorityObject=events[index].getPriorityObject(); if (priorityObject != null) { - events[index].changePriority(priorityObject.compileDouble(astNodeTime, 0d)); + events[index].changePriority(priorityObject.compileDouble(astNodeTime)); priorities.add(events[index].getPriority()); } } @@ -759,7 +753,7 @@ else if ((events[index].getLastTimeFired()<=currentTime) && (events[index].getLa if ((events[index].hasExecutionTime()) && (events[index].getTime() <= currentTime) && !aborted) { if (ev.getPriority() != null) { - priority = events[index].getPriorityObject().compileDouble(astNodeTime, 0d); + priority = events[index].getPriorityObject().compileDouble(astNodeTime); if (!priorities.contains(priority)) { priorities.add(priority); @@ -783,7 +777,7 @@ else if ((events[index].getLastTimeFired()<=currentTime) && (events[index].getLa // event has a delay ASTNodeValue delayObject = events[i].getDelayObject(); if (delayObject != null) { - execTime += delayObject.compileDouble(astNodeTime, 0d); + execTime += delayObject.compileDouble(astNodeTime); if (!delayedEvents.contains(i)) { delayedEvents.add(i); } @@ -791,7 +785,7 @@ else if ((events[index].getLastTimeFired()<=currentTime) && (events[index].getLa } else { ASTNodeValue priorityObject = events[i].getPriorityObject(); if (priorityObject != null) { - priority = events[i].getPriorityObject().compileDouble(astNodeTime, 0d); + priority = events[i].getPriorityObject().compileDouble(astNodeTime); priorities.add(priority); events[i].changePriority(priority); } @@ -1094,7 +1088,7 @@ public void init(boolean renewTree, double defaultSpeciesValue, double defaultPa if (rule.isRate()) { RateRule rr = (RateRule) rule; SpeciesReference sr = model.findSpeciesReference(rr.getVariable()); - if ((sr != null) && !sr.isConstant()) { + if ((sr != null) && sr.isConstant()) { speciesReferencesInRateRules++; speciesReferenceToRateRule.put(sr.getId(), k); } @@ -1948,7 +1942,7 @@ private ASTNode copyAST(ASTNode node, boolean mergingPossible, FunctionValue fun } copiedAST.putUserObject(TEMP_VALUE, new SpeciesValue(nodeInterpreter, copiedAST, sp, this, symbolHash.get(variable - .getId()), compartmentHash.get(variable.getId()), sp.getCompartment(), hasZeroSpatialDimensions, isAmount[symbolHash.get(variable.getId())])); + .getId()), compartmentHash.get(variable.getId()), hasZeroSpatialDimensions, isAmount[symbolHash.get(variable.getId())])); } else if ((variable instanceof Compartment) || (variable instanceof Parameter)) { copiedAST.putUserObject(TEMP_VALUE, new CompartmentOrParameterValue( @@ -2116,10 +2110,7 @@ public boolean processAssignmentRules(double t, double Y[]) throws DerivativeException { this.currentTime = t; this.astNodeTime += 0.01d; - System.arraycopy(Y, 0, this.Y, 0, Y.length); - boolean changed = processRules(t, null, this.Y, false); - System.arraycopy(this.Y, 0, Y, 0, Y.length); - return changed; + return processRules(t, null, Y, false); } /** @@ -2263,29 +2254,21 @@ public void processInitialAssignments(double time, double[] Y) throws SBMLExcept public boolean processRules(double time, double[] changeRate, double[] Y, boolean initialCalculations) throws SBMLException { boolean changeByAssignmentRules=false; double intermediateASTNodeTime = - astNodeTime; - double oldTime = this.currentTime; if (Y != null) { for (int n = 0; n != nAssignmentRules; n++) { intermediateASTNodeTime = - intermediateASTNodeTime; for (int i = 0; i != nAssignmentRules; i++) { AssignmentRuleValue currentRuleObject = assignmentRulesRoots.get(i); double oldValue = Double.NaN, newValue = Double.NaN; - double[] oldY = new double[Y.length]; - System.arraycopy(Y, 0, oldY, 0, Y.length); int index = currentRuleObject.getIndex(); if(index >= 0) { oldValue = Y[index]; } boolean currentChange = currentRuleObject.processRule(Y, intermediateASTNodeTime, true); - this.currentTime = oldTime; if(index >= 0) { newValue = Y[index]; } - System.arraycopy(oldY, 0, Y, 0, Y.length); - if(index != -1) { - Y[index] = newValue; - } if (currentChange && (!initialCalculations) && (index >= 0) && (compartmentHash.containsValue(index))) { updateSpeciesConcentration(index, Y, oldValue, newValue, false); @@ -2330,13 +2313,13 @@ protected void processVelocities(double[] changeRate, double time) if (hasFastReactions) { if (isProcessingFastReactions == reactionFast[reactionIndex]) { v[reactionIndex] = kineticLawRoots[reactionIndex].compileDouble( - time, 0d); + time); } else { v[reactionIndex] = 0; } } else { v[reactionIndex] = kineticLawRoots[reactionIndex].compileDouble( - time, 0d); + time); } } @@ -2344,7 +2327,7 @@ protected void processVelocities(double[] changeRate, double time) for (int i = 0; i != stoichiometryValues.length; i++) { if ((constantStoichiometry[i] == false) || (stoichiometrySet[i] == false)) { - stoichiometry[i] = stoichiometryValues[i].compileDouble(time); + stoichiometry[i] = stoichiometryValues[i].compileDouble(currentTime); stoichiometrySet[i] = stoichiometryValues[i].getStoichiometrySet(); } double value; @@ -2537,16 +2520,10 @@ public void registerDelayValueHolder(DelayValueHolder dvh) { this.delayValueHolder = dvh; } - - /* - * (non-Javadoc) - * @see org.simulator.math.odes.DelayValueHolder#computeDelayedValue(double, java.lang.String, org.simulator.math.odes.DESystem, double[], int) + /* (non-Javadoc) + * @see org.simulator.math.odes.DelayValueHolder#computeDelayedValue(double, java.lang.String) */ - public double computeDelayedValue(double time, String id, DESystem DES, double[] initialValues, int yIndex) { - if(!delaysIncluded) { - return this.Y[symbolHash.get(id)]; - } - + public double computeDelayedValue(double time, String id) { if ((time < 0d) || ((time >= 0d) && (this.delayValueHolder == null))) { int index = symbolHash.get(id); double oldTime = currentTime; @@ -2569,7 +2546,7 @@ public double computeDelayedValue(double time, String id, DESystem DES, double[] } } if (Double.isNaN(value)) { - value=this.initialValues[index]; + value=initialValues[index]; } this.currentTime=oldTime; return value; @@ -2581,7 +2558,7 @@ else if (this.delayValueHolder == null) { return Double.NaN; } - return this.delayValueHolder.computeDelayedValue(time, id, this, this.initialValues, symbolHash.get(id)); + return this.delayValueHolder.computeDelayedValue(time, id); } /* (non-Javadoc) @@ -2599,15 +2576,8 @@ public boolean getNoDerivatives() { public double compileReaction(int reactionIndex) { astNodeTime+=0.01; double value = kineticLawRoots[reactionIndex].compileDouble( - astNodeTime, 0d); + astNodeTime); return value; } - - /* (non-Javadoc) - * @see org.simulator.math.odes.DESystem#setDelaysIncluded(boolean) - */ - public void setDelaysIncluded(boolean delaysIncluded) { - this.delaysIncluded = delaysIncluded; - } } diff --git a/src/org/simulator/sbml/astnode/ASTNodeInterpreter.java b/src/org/simulator/sbml/astnode/ASTNodeInterpreter.java index 2095c815..9fc2ceb1 100644 --- a/src/org/simulator/sbml/astnode/ASTNodeInterpreter.java +++ b/src/org/simulator/sbml/astnode/ASTNodeInterpreter.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -94,7 +94,7 @@ public final String toString(ASTNode value) { * @param time * @return doubleValue the interpreted double value of the node */ - public double compileDouble(String name, double time, double delay) { + public double compileDouble(String name, double time) { Double funcArg = funcArgs.get(name).doubleValue(); double value; if (funcArg != null) { @@ -111,10 +111,9 @@ public double compileDouble(String name, double time, double delay) { * * @param nsb * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double compileDouble(CallableSBase nsb, double time, double delay) { + public double compileDouble(CallableSBase nsb, double time) { if (nsb instanceof Species) { Species s = (Species) nsb; String id = s.getId(); @@ -145,7 +144,7 @@ else if (s.isSetInitialConcentration() && s.getHasOnlySubstanceUnits()) { Reaction r = (Reaction) nsb; if (r.isSetKineticLaw()) { ((ASTNodeValue) r.getKineticLaw().getMath().getUserObject(SBMLinterpreter.TEMP_VALUE)) - .compileDouble(time, delay); + .compileDouble(time); } } return Double.NaN; @@ -184,9 +183,9 @@ public boolean compileBoolean(CallableSBase nsb, double time) { public double functionDouble(ASTNodeValue rightChild, List variables, ASTNodeValue[] children, int nArguments, double[] values, double time) { for (int i = 0; i < nArguments; i++) { - values[i] = children[i].compileDouble(time, 0d); + values[i] = children[i].compileDouble(time); } - double value = rightChild.compileDouble(time, 0d); + double value = rightChild.compileDouble(time); return value; } @@ -225,10 +224,10 @@ public String compileString(ASTNode child) { public double lambdaDouble(ASTNodeValue[] children, double time) { double d[] = new double[Math.max(0, children.length - 1)]; for (int i = 0; i < children.length - 1; i++) { - d[i++] = children[i].compileDouble(time, 0d); + d[i++] = children[i].compileDouble(time); } // TODO: what happens with d? - return children[children.length - 1].compileDouble(time, 0d); + return children[children.length - 1].compileDouble(time); } /** @@ -240,7 +239,7 @@ public double lambdaDouble(ASTNodeValue[] children, double time) { public boolean lambdaBoolean(ASTNodeValue[] children, double time) { double d[] = new double[Math.max(0, children.length - 1)]; for (int i = 0; i < children.length - 1; i++) { - d[i++] = children[i].compileDouble(time, 0d); + d[i++] = children[i].compileDouble(time); } // TODO: what happens with d? return children[children.length - 1].compileBoolean(time); @@ -251,16 +250,15 @@ public boolean lambdaBoolean(ASTNodeValue[] children, double time) { * * @param children * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double piecewise(ASTNodeValue[] children, double time, double delay) { + public double piecewise(ASTNodeValue[] children, double time) { int i; for (i = 1; i < children.length - 1; i += 2) { if (children[i].compileBoolean(time)) { return (children[i - 1] - .compileDouble(time, delay)); } + .compileDouble(time)); } } - return children[i - 1].compileDouble(time, delay); + return children[i - 1].compileDouble(time); } @@ -268,11 +266,10 @@ public double piecewise(ASTNodeValue[] children, double time, double delay) { * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double log(ASTNodeValue userObject, double time, double delay) { - return Math.log10(userObject.compileDouble(time, delay)); + public double log(ASTNodeValue userObject, double time) { + return Math.log10(userObject.compileDouble(time)); } /** @@ -280,11 +277,10 @@ public double log(ASTNodeValue userObject, double time, double delay) { * @param left * @param right * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double log(ASTNodeValue left, ASTNodeValue right, double time, double delay) { - return Maths.log(right.compileDouble(time, delay), left.compileDouble(time, delay)); + public double log(ASTNodeValue left, ASTNodeValue right, double time) { + return Maths.log(right.compileDouble(time), left.compileDouble(time)); } /** @@ -306,66 +302,60 @@ public double functionDouble(String functionDefinitionName, * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double tanh(ASTNodeValue userObject, double time, double delay) { - return Math.tanh(userObject.compileDouble(time, delay)); + public double tanh(ASTNodeValue userObject, double time) { + return Math.tanh(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double tan(ASTNodeValue userObject, double time, double delay) { - return Math.tan(userObject.compileDouble(time, delay)); + public double tan(ASTNodeValue userObject, double time) { + return Math.tan(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double sinh(ASTNodeValue userObject, double time, double delay) { - return Math.sinh(userObject.compileDouble(time, delay)); + public double sinh(ASTNodeValue userObject, double time) { + return Math.sinh(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double sin(ASTNodeValue userObject, double time, double delay) { - return Math.sin(userObject.compileDouble(time, delay)); + public double sin(ASTNodeValue userObject, double time) { + return Math.sin(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double sech(ASTNodeValue userObject, double time, double delay) { - return Maths.sech(userObject.compileDouble(time, delay)); + public double sech(ASTNodeValue userObject, double time) { + return Maths.sech(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double sec(ASTNodeValue userObject, double time, double delay) { - double argument = userObject.compileDouble(time, delay); + public double sec(ASTNodeValue userObject, double time) { + double argument = userObject.compileDouble(time); return Maths.sec(argument); } @@ -374,11 +364,10 @@ public double sec(ASTNodeValue userObject, double time, double delay) { * @param rootExponent * @param radiant * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double root(ASTNodeValue rootExponent, ASTNodeValue radiant, double time, double delay) { - return root(rootExponent.compileDouble(time, delay), radiant, time, delay); + public double root(ASTNodeValue rootExponent, ASTNodeValue radiant, double time) { + return root(rootExponent.compileDouble(time), radiant, time); } /** @@ -386,143 +375,130 @@ public double root(ASTNodeValue rootExponent, ASTNodeValue radiant, double time, * @param rootExponent * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double root(double rootExponent, ASTNodeValue userObject, double time, double delay) { - return Maths.root(userObject.compileDouble(time, delay), rootExponent); + public double root(double rootExponent, ASTNodeValue userObject, double time) { + return Maths.root(userObject.compileDouble(time), rootExponent); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double ln(ASTNodeValue userObject, double time, double delay) { - return Maths.ln(userObject.compileDouble(time, delay)); + public double ln(ASTNodeValue userObject, double time) { + return Maths.ln(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double floor(ASTNodeValue userObject, double time, double delay) { - return Math.floor(userObject.compileDouble(time, delay)); + public double floor(ASTNodeValue userObject, double time) { + return Math.floor(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double factorial(ASTNodeValue userObject, double time, double delay) { - return Maths.factorial((int) Math.round(userObject.compileDouble(time, delay))); + public double factorial(ASTNodeValue userObject, double time) { + return Maths.factorial((int) Math.round(userObject.compileDouble(time))); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double exp(ASTNodeValue userObject, double time, double delay) { - return Math.exp(userObject.compileDouble(time, delay)); + public double exp(ASTNodeValue userObject, double time) { + return Math.exp(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double csch(ASTNodeValue userObject, double time, double delay) { - return Maths.csch(userObject.compileDouble(time, delay)); + public double csch(ASTNodeValue userObject, double time) { + return Maths.csch(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double csc(ASTNodeValue userObject, double time, double delay) { - return Maths.csc(userObject.compileDouble(time, delay)); + public double csc(ASTNodeValue userObject, double time) { + return Maths.csc(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double coth(ASTNodeValue userObject, double time, double delay) { - return Maths.coth(userObject.compileDouble(time, delay)); + public double coth(ASTNodeValue userObject, double time) { + return Maths.coth(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double cot(ASTNodeValue userObject, double time, double delay) { - return Maths.cot(userObject.compileDouble(time, delay)); + public double cot(ASTNodeValue userObject, double time) { + return Maths.cot(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double cosh(ASTNodeValue userObject, double time, double delay) { - return Math.cosh(userObject.compileDouble(time, delay)); + public double cosh(ASTNodeValue userObject, double time) { + return Math.cosh(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double cos(ASTNodeValue userObject, double time, double delay) { - return Math.cos(userObject.compileDouble(time, delay)); + public double cos(ASTNodeValue userObject, double time) { + return Math.cos(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double ceiling(ASTNodeValue userObject, double time, double delay) { - return Math.ceil(userObject.compileDouble(time, delay)); + public double ceiling(ASTNodeValue userObject, double time) { + return Math.ceil(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arctanh(ASTNodeValue userObject, double time, double delay) { - return Maths.arctanh(userObject.compileDouble(time, delay)); + public double arctanh(ASTNodeValue userObject, double time) { + return Maths.arctanh(userObject.compileDouble(time)); } /** @@ -550,7 +526,7 @@ public boolean functionBoolean(String name, List children) { public boolean functionBoolean(ASTNodeValue rightChild, List variables, ASTNodeValue[] children, double[] values, double time) { for (int i = 0; i < children.length; i++) { - values[i] = children[i].compileDouble(time, 0d); + values[i] = children[i].compileDouble(time); } boolean value = rightChild.compileBoolean(time); return value; @@ -564,7 +540,7 @@ public boolean functionBoolean(ASTNodeValue rightChild, * @return booleanValue the interpreted boolean value of the node */ public boolean lt(ASTNodeValue left, ASTNodeValue right, double time) { - return (left.compileDouble(time, 0d) < right.compileDouble(time, 0d)); + return (left.compileDouble(time) < right.compileDouble(time)); } /** @@ -575,7 +551,7 @@ public boolean lt(ASTNodeValue left, ASTNodeValue right, double time) { * @return booleanValue the interpreted boolean value of the node */ public boolean leq(ASTNodeValue left, ASTNodeValue right, double time) { - return (left.compileDouble(time, 0d) <= right.compileDouble(time, 0d)); + return (left.compileDouble(time) <= right.compileDouble(time)); } /** @@ -586,7 +562,7 @@ public boolean leq(ASTNodeValue left, ASTNodeValue right, double time) { * @return booleanValue the interpreted boolean value of the node */ public boolean neq(ASTNodeValue left, ASTNodeValue right, double time) { - return (left.compileDouble(time, 0d) != right.compileDouble(time, 0d)); + return (left.compileDouble(time) != right.compileDouble(time)); } /** @@ -597,7 +573,7 @@ public boolean neq(ASTNodeValue left, ASTNodeValue right, double time) { * @return booleanValue the interpreted boolean value of the node */ public boolean gt(ASTNodeValue left, ASTNodeValue right, double time) { - return (left.compileDouble(time, 0d) > right.compileDouble(time, 0d)); + return (left.compileDouble(time) > right.compileDouble(time)); } /** @@ -608,7 +584,7 @@ public boolean gt(ASTNodeValue left, ASTNodeValue right, double time) { * @return booleanValue the interpreted boolean value of the node */ public boolean geq(ASTNodeValue left, ASTNodeValue right, double time) { - return (left.compileDouble(time, 0d) >= right.compileDouble(time, 0d)); + return (left.compileDouble(time) >= right.compileDouble(time)); } /** @@ -616,11 +592,10 @@ public boolean geq(ASTNodeValue left, ASTNodeValue right, double time) { * @param left * @param right * @param time - * @return booleanValue the interpreted boolean value of the node */ public boolean eq(ASTNodeValue left, ASTNodeValue right, double time) { - return (left.compileDouble(time, 0d) == right.compileDouble(time, 0d)); + return (left.compileDouble(time) == right.compileDouble(time)); } /** @@ -684,99 +659,90 @@ public boolean and(ASTNodeValue[] children, int size, double time) { * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arctan(ASTNodeValue userObject, double time, double delay) { - return Math.atan(userObject.compileDouble(time, delay)); + public double arctan(ASTNodeValue userObject, double time) { + return Math.atan(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arcsinh(ASTNodeValue userObject, double time, double delay) { - return Maths.arcsinh(userObject.compileDouble(time, delay)); + public double arcsinh(ASTNodeValue userObject, double time) { + return Maths.arcsinh(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arcsin(ASTNodeValue userObject, double time, double delay) { - return Math.asin(userObject.compileDouble(time, delay)); + public double arcsin(ASTNodeValue userObject, double time) { + return Math.asin(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arcsech(ASTNodeValue userObject, double time, double delay) { - return Maths.arcsech(userObject.compileDouble(time, delay)); + public double arcsech(ASTNodeValue userObject, double time) { + return Maths.arcsech(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arcsec(ASTNodeValue userObject, double time, double delay) { - return Maths.arcsec(userObject.compileDouble(time, delay)); + public double arcsec(ASTNodeValue userObject, double time) { + return Maths.arcsec(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arccsch(ASTNodeValue userObject, double time, double delay) { - return Maths.arccsch(userObject.compileDouble(time, delay)); + public double arccsch(ASTNodeValue userObject, double time) { + return Maths.arccsch(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arccsc(ASTNodeValue userObject, double time, double delay) { - return Maths.arccsc(userObject.compileDouble(time, delay)); + public double arccsc(ASTNodeValue userObject, double time) { + return Maths.arccsc(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arccoth(ASTNodeValue userObject, double time, double delay) { - return Maths.arccoth(userObject.compileDouble(time, delay)); + public double arccoth(ASTNodeValue userObject, double time) { + return Maths.arccoth(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arccot(ASTNodeValue userObject, double time, double delay) { - double argument = userObject.compileDouble(time, delay); + public double arccot(ASTNodeValue userObject, double time) { + double argument = userObject.compileDouble(time); return Maths.arccot(argument); } @@ -784,33 +750,30 @@ public double arccot(ASTNodeValue userObject, double time, double delay) { * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arccosh(ASTNodeValue userObject, double time, double delay) { - return Maths.arccosh(userObject.compileDouble(time, delay)); + public double arccosh(ASTNodeValue userObject, double time) { + return Maths.arccosh(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double arccos(ASTNodeValue userObject, double time, double delay) { - return Math.acos(userObject.compileDouble(time, delay)); + public double arccos(ASTNodeValue userObject, double time) { + return Math.acos(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double abs(ASTNodeValue userObject, double time, double delay) { - return Math.abs(userObject.compileDouble(time, delay)); + public double abs(ASTNodeValue userObject, double time) { + return Math.abs(userObject.compileDouble(time)); } /** @@ -826,25 +789,30 @@ public double compile(double mantissa, int exponent, String units) { /** * + * @param delayName * @param x * @param delay * @param timeUnits * @param time * @return doubleValue the interpreted double value of the node */ - public final double delay(ASTNodeValue x, ASTNodeValue delay, + public final double delay(String delayName, ASTNodeValue x, ASTNodeValue delay, String timeUnits, double time) { - double delayTime = delay.compileDouble(time, 0d); - //double valueTime = symbolTime(delayName) - delayTime; - return x.compileDouble(time, delayTime); - //return valueHolder.computeDelayedValue(valueTime, compileString(x), null, null, 0); + //TODO: Delay for arbitrary expressions. + double delayTime = delay.compileDouble(time); + if (delayTime == 0) { + return x.compileDouble(time); + } + double valueTime = symbolTime(delayName) - delayTime; + return valueHolder.computeDelayedValue(valueTime, compileString(x)); } /** * + * @param name * @return doubleValue the interpreted double value of the node */ - public double symbolTime() { + public double symbolTime(String name) { return (valueHolder.getCurrentTime()); } @@ -863,11 +831,10 @@ public double frac(int numerator, int denominator) { * @param left * @param right * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double frac(ASTNodeValue left, ASTNodeValue right, double time, double delay) { - return (left.compileDouble(time, delay) / right.compileDouble(time, delay)); + public double frac(ASTNodeValue left, ASTNodeValue right, double time) { + return (left.compileDouble(time) / right.compileDouble(time)); } /** @@ -875,17 +842,16 @@ public double frac(ASTNodeValue left, ASTNodeValue right, double time, double de * @param children * @param size * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double times(ASTNodeValue[] children, int size, double time, double delay) { + public double times(ASTNodeValue[] children, int size, double time) { if (size == 0) { return (1d); } else { double value = 1d; for (int i = 0; i != size; i++) { - value *= children[i].compileDouble(time, delay); + value *= children[i].compileDouble(time); } return value; } @@ -896,17 +862,16 @@ public double times(ASTNodeValue[] children, int size, double time, double delay * @param children * @param size * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double minus(ASTNodeValue[] children, int size, double time, double delay) { + public double minus(ASTNodeValue[] children, int size, double time) { double value = 0d; if (size > 0) { - value = children[0].compileDouble(time, delay); + value = children[0].compileDouble(time); } for (int i = 1; i < size; i++) { - value -= children[i].compileDouble(time, delay); + value -= children[i].compileDouble(time); } return value; } @@ -916,13 +881,12 @@ public double minus(ASTNodeValue[] children, int size, double time, double delay * @param children * @param size * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double plus(ASTNodeValue[] children, int size, double time, double delay) { + public double plus(ASTNodeValue[] children, int size, double time) { double value = 0d; for (int i = 0; i != size; i++) { - value += children[i].compileDouble(time, delay); + value += children[i].compileDouble(time); } return value; } @@ -932,12 +896,11 @@ public double plus(ASTNodeValue[] children, int size, double time, double delay) * @param left * @param right * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double pow(ASTNodeValue left, ASTNodeValue right, double time, double delay) { - double l = left.compileDouble(time, delay); - double r = right.compileDouble(time, delay); + public double pow(ASTNodeValue left, ASTNodeValue right, double time) { + double l = left.compileDouble(time); + double r = right.compileDouble(time); if(r == 2) { return l * l; } @@ -976,22 +939,20 @@ public double compile(double value, String units) { * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double sqrt(ASTNodeValue userObject, double time, double delay) { - return Math.sqrt(userObject.compileDouble(time, delay)); + public double sqrt(ASTNodeValue userObject, double time) { + return Math.sqrt(userObject.compileDouble(time)); } /** * * @param userObject * @param time - * @param delay * @return doubleValue the interpreted double value of the node */ - public double uMinus(ASTNodeValue userObject, double time, double delay) { - return (-userObject.compileDouble(time, delay)); + public double uMinus(ASTNodeValue userObject, double time) { + return (-userObject.compileDouble(time)); } } diff --git a/src/org/simulator/sbml/astnode/ASTNodeValue.java b/src/org/simulator/sbml/astnode/ASTNodeValue.java index 0c624f35..f8402076 100644 --- a/src/org/simulator/sbml/astnode/ASTNodeValue.java +++ b/src/org/simulator/sbml/astnode/ASTNodeValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -251,7 +251,7 @@ public ASTNode getNode() { */ public Object getValue(double time) { if (isDouble) { - return compileDouble(time, 0d); + return compileDouble(time); } else { return compileBoolean(time); @@ -261,17 +261,16 @@ public Object getValue(double time) { /** * Computes the double value if the time has changed and otherwise returns the already computed value * @param time - * @param delay * @return doubleValue the double value of the node */ - public double compileDouble(double time, double delay) { - if (((this.time==time) && (delay == 0d)) || (isConstant && alreadyProcessed)) { + public double compileDouble(double time) { + if ((this.time==time) || (isConstant && alreadyProcessed)) { return doubleValue; } else { isDouble = true; alreadyProcessed = true; this.time = time; - computeDoubleValue(delay); + computeDoubleValue(); } return doubleValue; } @@ -294,12 +293,12 @@ public boolean compileBoolean(double time) { } return booleanValue; } + /** * Computes the double value of the node. - * @param delay */ - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { switch (nodeType) { /* * Numbers @@ -319,10 +318,10 @@ protected void computeDoubleValue(double delay) { doubleValue = interpreter.frac(numerator, denominator); break; case NAME_TIME: - doubleValue = interpreter.symbolTime(); + doubleValue = interpreter.symbolTime(name); break; case FUNCTION_DELAY: - doubleValue = interpreter.delay(leftChild, + doubleValue = interpreter.delay(name, leftChild, rightChild, units, time); break; /* @@ -346,103 +345,103 @@ protected void computeDoubleValue(double delay) { */ case FUNCTION_LOG: if (numChildren == 2) { - doubleValue = interpreter.log(leftChild, rightChild, time, delay); + doubleValue = interpreter.log(leftChild, rightChild, time); } else { - doubleValue = interpreter.log(rightChild, time, delay); + doubleValue = interpreter.log(rightChild, time); } break; case FUNCTION_ABS: - doubleValue = interpreter.abs(rightChild, time, delay); + doubleValue = interpreter.abs(rightChild, time); break; case FUNCTION_ARCCOS: - doubleValue = interpreter.arccos(leftChild, time, delay); + doubleValue = interpreter.arccos(leftChild, time); break; case FUNCTION_ARCCOSH: - doubleValue = interpreter.arccosh(leftChild, time, delay); + doubleValue = interpreter.arccosh(leftChild, time); break; case FUNCTION_ARCCOT: - doubleValue = interpreter.arccot(leftChild, time, delay); + doubleValue = interpreter.arccot(leftChild, time); break; case FUNCTION_ARCCOTH: - doubleValue = interpreter.arccoth(leftChild, time, delay); + doubleValue = interpreter.arccoth(leftChild, time); break; case FUNCTION_ARCCSC: - doubleValue = interpreter.arccsc(leftChild, time, delay); + doubleValue = interpreter.arccsc(leftChild, time); break; case FUNCTION_ARCCSCH: - doubleValue = interpreter.arccsch(leftChild, time, delay); + doubleValue = interpreter.arccsch(leftChild, time); break; case FUNCTION_ARCSEC: - doubleValue = interpreter.arcsec(leftChild, time, delay); + doubleValue = interpreter.arcsec(leftChild, time); break; case FUNCTION_ARCSECH: - doubleValue = interpreter.arcsech(leftChild, time, delay); + doubleValue = interpreter.arcsech(leftChild, time); break; case FUNCTION_ARCSIN: - doubleValue = interpreter.arcsin(leftChild, time, delay); + doubleValue = interpreter.arcsin(leftChild, time); break; case FUNCTION_ARCSINH: - doubleValue = interpreter.arcsinh(leftChild, time, delay); + doubleValue = interpreter.arcsinh(leftChild, time); break; case FUNCTION_ARCTAN: - doubleValue = interpreter.arctan(leftChild, time, delay); + doubleValue = interpreter.arctan(leftChild, time); break; case FUNCTION_ARCTANH: - doubleValue = interpreter.arctanh(leftChild, time, delay); + doubleValue = interpreter.arctanh(leftChild, time); break; case FUNCTION_CEILING: - doubleValue = interpreter.ceiling(leftChild, time, delay); + doubleValue = interpreter.ceiling(leftChild, time); break; case FUNCTION_COS: - doubleValue = interpreter.cos(leftChild, time, delay); + doubleValue = interpreter.cos(leftChild, time); break; case FUNCTION_COSH: - doubleValue = interpreter.cosh(leftChild, time, delay); + doubleValue = interpreter.cosh(leftChild, time); break; case FUNCTION_COT: - doubleValue = interpreter.cot(leftChild, time, delay); + doubleValue = interpreter.cot(leftChild, time); break; case FUNCTION_COTH: - doubleValue = interpreter.coth(leftChild, time, delay); + doubleValue = interpreter.coth(leftChild, time); break; case FUNCTION_CSC: - doubleValue = interpreter.csc(leftChild, time, delay); + doubleValue = interpreter.csc(leftChild, time); break; case FUNCTION_CSCH: - doubleValue = interpreter.csch(leftChild, time, delay); + doubleValue = interpreter.csch(leftChild, time); break; case FUNCTION_EXP: - doubleValue = interpreter.exp(leftChild, time, delay); + doubleValue = interpreter.exp(leftChild, time); break; case FUNCTION_FACTORIAL: - doubleValue = interpreter.factorial(leftChild, time, delay); + doubleValue = interpreter.factorial(leftChild, time); break; case FUNCTION_FLOOR: - doubleValue = interpreter.floor(leftChild, time, delay); + doubleValue = interpreter.floor(leftChild, time); break; case FUNCTION_LN: - doubleValue = interpreter.ln(leftChild, time, delay); + doubleValue = interpreter.ln(leftChild, time); break; case FUNCTION_SEC: - doubleValue = interpreter.sec(leftChild, time, delay); + doubleValue = interpreter.sec(leftChild, time); break; case FUNCTION_SECH: - doubleValue = interpreter.sech(leftChild, time, delay); + doubleValue = interpreter.sech(leftChild, time); break; case FUNCTION_SIN: - doubleValue = interpreter.sin(leftChild, time, delay); + doubleValue = interpreter.sin(leftChild, time); break; case FUNCTION_SINH: - doubleValue = interpreter.sinh(leftChild, time, delay); + doubleValue = interpreter.sinh(leftChild, time); break; case FUNCTION_TAN: - doubleValue = interpreter.tan(leftChild, time, delay); + doubleValue = interpreter.tan(leftChild, time); break; case FUNCTION_TANH: - doubleValue = interpreter.tanh(leftChild, time, delay); + doubleValue = interpreter.tanh(leftChild, time); break; case FUNCTION_PIECEWISE: - doubleValue = interpreter.piecewise(children, time, delay); + doubleValue = interpreter.piecewise(children, time); break; case LAMBDA: doubleValue = interpreter.lambdaDouble(children, time); diff --git a/src/org/simulator/sbml/astnode/AssignmentRuleValue.java b/src/org/simulator/sbml/astnode/AssignmentRuleValue.java index d9a69ae0..563225e9 100644 --- a/src/org/simulator/sbml/astnode/AssignmentRuleValue.java +++ b/src/org/simulator/sbml/astnode/AssignmentRuleValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -22,105 +22,101 @@ */ package org.simulator.sbml.astnode; + + import java.util.Map; import org.sbml.jsbml.Species; import org.simulator.sbml.SBMLValueHolder; /** - * This class can compute and store the value of an AssignmentRule together with - * the variable of the rule. - * + * This class can compute and store the value of an AssignmentRule together with the variable of the rule. * @author Roland Keller * @version $Rev$ */ -public class AssignmentRuleValue extends RuleValue { - - /** - * The id of the species reference the rule is referring to (if applicable) - */ +public class AssignmentRuleValue extends RuleValue{ + /** + * The id of the species reference the rule is referring to (if applicable) + */ private String speciesReferenceID; - + /** - * The map of the values of the species references that are contained in - * rules + * The map of the values of the species references that are contained in rules */ - private Map stoichiometricCoefHash; + private Map stoichiometricCoefHash; - /** - * - * @param nodeObject - * @param index - */ - public AssignmentRuleValue(ASTNodeValue nodeObject, int index) { - super(nodeObject, index); - } - - /** - * Constructor for rules that refer to a species reference - * @param nodeObject - * @param speciesReferenceID - * @param stoichiometricCoefHash - */ - public AssignmentRuleValue(ASTNodeValue nodeObject, String speciesReferenceID, - Map stoichiometricCoefHash) { - super(nodeObject,-1); - this.speciesReferenceID = speciesReferenceID; - this.stoichiometricCoefHash = stoichiometricCoefHash; - } + + /** + * + * @param nodeObject + * @param index + */ + public AssignmentRuleValue(ASTNodeValue nodeObject, int index) { + super(nodeObject, index); + } - /** - * Constructor for rules that refer to a species - * @param nodeObject - * @param index - * @param sp - * @param compartmentIndex - * @param hasZeroSpatialDimensions - * @param valueHolder - */ - public AssignmentRuleValue(ASTNodeValue nodeObject, int index, - Species sp, int compartmentIndex, boolean hasZeroSpatialDimensions, SBMLValueHolder valueHolder) { - super(nodeObject, index, sp, compartmentIndex, hasZeroSpatialDimensions, valueHolder); - } - - /** - * Processes the rule and saves the new value of the corresponding variable - * in the Y vector if changeY is set to true. - * - * @param Y - * @param time - * @param changeY - * @return Has there been a change in the Y vector caused by the rule? - */ - public boolean processRule(double[] Y, double time, boolean changeY) { - if(index >= 0) { - double oldValue = Y[index]; - processAssignmentVariable(time); - if (changeY) { - Y[index] = value; - } - if (oldValue != value) { - return true; - } - } - else if (speciesReferenceID != null) { - processAssignmentVariable(time); - Double v=stoichiometricCoefHash.get(speciesReferenceID); - stoichiometricCoefHash.put(speciesReferenceID, value); - - if ((v != null) && (v.doubleValue() != value)) { - return true; - } - } - return false; - - } - - /** - * Returns the id of the species reference (if present), null otherwise. - * @return id - */ - public String getSpeciesReferenceID() { - return speciesReferenceID; - } + /** + * Constructor for rules that refer to a species reference + * @param nodeObject + * @param speciesReferenceID + * @param stoichiometricCoefHash + */ + public AssignmentRuleValue(ASTNodeValue nodeObject, String speciesReferenceID, + Map stoichiometricCoefHash) { + super(nodeObject,-1); + this.speciesReferenceID = speciesReferenceID; + this.stoichiometricCoefHash = stoichiometricCoefHash; + } + + /** + * Constructor for rules that refer to a species + * @param nodeObject + * @param index + * @param sp + * @param compartmentIndex + * @param hasZeroSpatialDimensions + * @param valueHolder + */ + public AssignmentRuleValue(ASTNodeValue nodeObject, int index, + Species sp, int compartmentIndex, boolean hasZeroSpatialDimensions, SBMLValueHolder valueHolder) { + super(nodeObject, index, sp, compartmentIndex, hasZeroSpatialDimensions, valueHolder); + } + /** + * Processes the rule and saves the new value of the corresponding variable in the Y vector if changeY is set to true. + * @param Y + * @param time + * @param changeY + * @return Has there been a change in the Y vector caused by the rule? + */ + public boolean processRule(double[] Y, double time, boolean changeY) { + processAssignmentVariable(time); + if(index>=0) { + double oldValue=Y[index]; + if(changeY) { + Y[index] = value; + } + if(oldValue!=value) { + return true; + } + } + else if(speciesReferenceID!=null) { + Double v=stoichiometricCoefHash.get(speciesReferenceID); + stoichiometricCoefHash.put(speciesReferenceID, value); + + if((v!=null) && (v.doubleValue()!=value)) { + return true; + } + } + return false; + + } + + /** + * Returns the id of the species reference (if present), null otherwise. + * @return id + */ + public String getSpeciesReferenceID() { + return speciesReferenceID; + } + } diff --git a/src/org/simulator/sbml/astnode/CompartmentOrParameterValue.java b/src/org/simulator/sbml/astnode/CompartmentOrParameterValue.java index 0e7c6559..8d8c8341 100644 --- a/src/org/simulator/sbml/astnode/CompartmentOrParameterValue.java +++ b/src/org/simulator/sbml/astnode/CompartmentOrParameterValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -79,14 +79,8 @@ public CompartmentOrParameterValue(ASTNodeInterpreter interpreter, ASTNode node, * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ @Override - protected void computeDoubleValue(double delay) { - if(delay == 0) { - doubleValue = valueHolder.getCurrentValueOf(position); - } - else { - double valueTime = interpreter.symbolTime() - delay; - doubleValue = valueHolder.computeDelayedValue(valueTime, id, null, null, 0); - } + protected void computeDoubleValue() { + doubleValue=valueHolder.getCurrentValueOf(position); } } diff --git a/src/org/simulator/sbml/astnode/DivideValue.java b/src/org/simulator/sbml/astnode/DivideValue.java index 53834d19..02a9310f 100644 --- a/src/org/simulator/sbml/astnode/DivideValue.java +++ b/src/org/simulator/sbml/astnode/DivideValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -46,13 +46,13 @@ public DivideValue(ASTNodeInterpreter interpreter, ASTNode node) { * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { if (numChildren != 2) { throw new SBMLException(MessageFormat.format( "Fractions must have one numerator and one denominator, here {0,number,integer} elements are given.", node.getChildCount())); } - doubleValue = interpreter.frac(leftChild, rightChild, time, delay); + doubleValue = interpreter.frac(leftChild, rightChild, time); } } diff --git a/src/org/simulator/sbml/astnode/FunctionValue.java b/src/org/simulator/sbml/astnode/FunctionValue.java index 1daca2b6..c1e72674 100644 --- a/src/org/simulator/sbml/astnode/FunctionValue.java +++ b/src/org/simulator/sbml/astnode/FunctionValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -114,7 +114,7 @@ public FunctionValue(ASTNodeInterpreter interpreter, * @see org.sbml.simulator.math.astnode.ASTNodeObject#computeDoubleValue() */ @Override - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { if (math != null) { doubleValue = interpreter.functionDouble(evaluationBlock, variables, children, numChildren, argumentValues, time); } else { diff --git a/src/org/simulator/sbml/astnode/IntegerValue.java b/src/org/simulator/sbml/astnode/IntegerValue.java index fd4269ce..1381a105 100644 --- a/src/org/simulator/sbml/astnode/IntegerValue.java +++ b/src/org/simulator/sbml/astnode/IntegerValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -43,7 +43,7 @@ public IntegerValue(ASTNodeInterpreter interpreter, ASTNode node) { * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { doubleValue = interpreter.compile(real, units); } diff --git a/src/org/simulator/sbml/astnode/LocalParameterValue.java b/src/org/simulator/sbml/astnode/LocalParameterValue.java index 7bfee12a..2fd8264d 100644 --- a/src/org/simulator/sbml/astnode/LocalParameterValue.java +++ b/src/org/simulator/sbml/astnode/LocalParameterValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -58,7 +58,7 @@ public LocalParameterValue(ASTNodeInterpreter interpreter, ASTNode node, * @see org.simulator.sbml.astnode.ASTNodeValue#compileDouble(double) */ @Override - public double compileDouble(double time, double delay) { + public double compileDouble(double time) { this.time=time; if(alreadyProcessed == false) { doubleValue = lp.getValue(); diff --git a/src/org/simulator/sbml/astnode/MinusValue.java b/src/org/simulator/sbml/astnode/MinusValue.java index 8082bf8b..45d8e51e 100644 --- a/src/org/simulator/sbml/astnode/MinusValue.java +++ b/src/org/simulator/sbml/astnode/MinusValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -43,11 +43,11 @@ public MinusValue(ASTNodeInterpreter interpreter, ASTNode node) { * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { if (numChildren == 1) { - doubleValue = interpreter.uMinus(leftChild, time, delay); + doubleValue = interpreter.uMinus(leftChild, time); } else { - doubleValue = interpreter.minus(children, numChildren, time, delay); + doubleValue = interpreter.minus(children, numChildren, time); } } diff --git a/src/org/simulator/sbml/astnode/NamedValue.java b/src/org/simulator/sbml/astnode/NamedValue.java index be5848d6..045bd19a 100644 --- a/src/org/simulator/sbml/astnode/NamedValue.java +++ b/src/org/simulator/sbml/astnode/NamedValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -56,7 +56,7 @@ public NamedValue(ASTNodeInterpreter interpreter, ASTNode node, FunctionValue fu * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { doubleValue=function.getArgumentValues()[index]; } diff --git a/src/org/simulator/sbml/astnode/PlusValue.java b/src/org/simulator/sbml/astnode/PlusValue.java index 50e06da2..c6aef79a 100755 --- a/src/org/simulator/sbml/astnode/PlusValue.java +++ b/src/org/simulator/sbml/astnode/PlusValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -43,8 +43,8 @@ public PlusValue(ASTNodeInterpreter interpreter, ASTNode node) { * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { - doubleValue = interpreter.plus(children, numChildren, time, delay); + protected void computeDoubleValue() { + doubleValue = interpreter.plus(children, numChildren, time); } } diff --git a/src/org/simulator/sbml/astnode/PowerValue.java b/src/org/simulator/sbml/astnode/PowerValue.java index 61201218..0d842a88 100644 --- a/src/org/simulator/sbml/astnode/PowerValue.java +++ b/src/org/simulator/sbml/astnode/PowerValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -43,8 +43,8 @@ public PowerValue(ASTNodeInterpreter interpreter, ASTNode node) { * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { - doubleValue = interpreter.pow(leftChild, rightChild, time, delay); + protected void computeDoubleValue() { + doubleValue = interpreter.pow(leftChild, rightChild, time); } } diff --git a/src/org/simulator/sbml/astnode/RateRuleValue.java b/src/org/simulator/sbml/astnode/RateRuleValue.java index 1e6ccb85..81c899f5 100644 --- a/src/org/simulator/sbml/astnode/RateRuleValue.java +++ b/src/org/simulator/sbml/astnode/RateRuleValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sbml/astnode/ReactionValue.java b/src/org/simulator/sbml/astnode/ReactionValue.java index 402fa40e..9abc6d94 100644 --- a/src/org/simulator/sbml/astnode/ReactionValue.java +++ b/src/org/simulator/sbml/astnode/ReactionValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -65,10 +65,10 @@ public ReactionValue(ASTNodeInterpreter interpreter, ASTNode node, * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { doubleValue = Double.NaN; if (kineticLawUserObject != null) { - doubleValue = kineticLawUserObject.compileDouble(time, delay); + doubleValue = kineticLawUserObject.compileDouble(time); } } diff --git a/src/org/simulator/sbml/astnode/RootFunctionValue.java b/src/org/simulator/sbml/astnode/RootFunctionValue.java index 254e989d..f454a74f 100644 --- a/src/org/simulator/sbml/astnode/RootFunctionValue.java +++ b/src/org/simulator/sbml/astnode/RootFunctionValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -64,23 +64,23 @@ public RootFunctionValue(ASTNodeInterpreter interpreter, ASTNode node) { * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { if (numChildren == 2) { if (leftChildrenNumeric) { if (leftDoubleValue == 2) { - doubleValue = interpreter.sqrt(rightChild, time, delay); + doubleValue = interpreter.sqrt(rightChild, time); } else { - doubleValue = interpreter.root(leftDoubleValue, rightChild, time, delay); + doubleValue = interpreter.root(leftDoubleValue, rightChild, time); } } else { doubleValue = interpreter.root(leftChild, - rightChild, time, delay); + rightChild, time); } } else if (numChildren == 1) { - doubleValue = interpreter.sqrt(rightChild, time, delay); + doubleValue = interpreter.sqrt(rightChild, time); } else { doubleValue = interpreter.root(leftChild, - rightChild, time, delay); + rightChild, time); } } diff --git a/src/org/simulator/sbml/astnode/RuleValue.java b/src/org/simulator/sbml/astnode/RuleValue.java index 9796953a..4b571d73 100644 --- a/src/org/simulator/sbml/astnode/RuleValue.java +++ b/src/org/simulator/sbml/astnode/RuleValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -121,7 +121,7 @@ public RuleValue(ASTNodeValue nodeObject, int index, * @return value the computed value of the variable */ protected double processAssignmentVariable(double time) { - value = nodeObject.compileDouble(time, 0d); + value = nodeObject.compileDouble(time); if(isSpecies && !hasZeroSpatialDimensions) { double compartmentValue = valueHolder .getCurrentValueOf(compartmentIndex); diff --git a/src/org/simulator/sbml/astnode/SpeciesReferenceValue.java b/src/org/simulator/sbml/astnode/SpeciesReferenceValue.java index 713a1062..61229e59 100644 --- a/src/org/simulator/sbml/astnode/SpeciesReferenceValue.java +++ b/src/org/simulator/sbml/astnode/SpeciesReferenceValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -62,7 +62,7 @@ public SpeciesReferenceValue(ASTNodeInterpreter interpreter, * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { + protected void computeDoubleValue() { doubleValue = valueHolder.getCurrentStoichiometry(id); } } diff --git a/src/org/simulator/sbml/astnode/SpeciesValue.java b/src/org/simulator/sbml/astnode/SpeciesValue.java index 91d9e5da..423db9d2 100644 --- a/src/org/simulator/sbml/astnode/SpeciesValue.java +++ b/src/org/simulator/sbml/astnode/SpeciesValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -33,56 +33,50 @@ * @since 1.0 */ public class SpeciesValue extends ASTNodeValue { - /** - * The corresponding species - */ + /** + * The corresponding species + */ protected Species s; - + /** * The id of the species */ - protected String id; - - /** - * The value holder that stores the current simulation results - */ - protected SBMLValueHolder valueHolder; - - /** - * Is the Y value of the species referring to an amount? - */ - protected boolean isAmount; - - /** - * The hasOnlySubstanceUnits attribute of the species - */ - protected boolean hasOnlySubstanceUnits; - - /** - * Has the species an initial concentration set? - */ - protected boolean isSetInitialConcentration; - - /** - * The position of the species value in the Y vector of the value holder - */ - protected int position; - - /** - * The position of the compartment value of the species in the Y vector of - * the value holder - */ - protected int compartmentPosition; - - /** - * Has the compartment of the species no spatial dimensions? - */ - protected boolean zeroSpatialDimensions; - - /** - * The id of the compartment of the species - */ - private String compartmentID; + protected String id; + + /** + * The value holder that stores the current simulation results + */ + protected SBMLValueHolder valueHolder; + + /** + * Is the Y value of the species referring to an amount? + */ + protected boolean isAmount; + + /** + * The hasOnlySubstanceUnits attribute of the species + */ + protected boolean hasOnlySubstanceUnits; + + /** + * Has the species an initial concentration set? + */ + protected boolean isSetInitialConcentration; + + /** + * The position of the species value in the Y vector of the value holder + */ + protected int position; + + /** + * The position of the compartment value of the species in the Y vector of the value holder + */ + protected int compartmentPosition; + + /** + * Has the compartment of the species no spatial dimensions? + */ + protected boolean zeroSpatialDimensions; /** * @@ -92,12 +86,10 @@ public class SpeciesValue extends ASTNodeValue { * @param valueHolder * @param position * @param compartmentPosition - * @param compartmentID * @param zeroSpatialDimensions - * @param isAmount */ public SpeciesValue(ASTNodeInterpreter interpreter, ASTNode node, - Species s, SBMLValueHolder valueHolder, int position, int compartmentPosition, String compartmentID, boolean zeroSpatialDimensions, boolean isAmount) { + Species s, SBMLValueHolder valueHolder, int position, int compartmentPosition, boolean zeroSpatialDimensions, boolean isAmount) { super(interpreter, node); this.s = s; this.id = s.getId(); @@ -107,7 +99,6 @@ public SpeciesValue(ASTNodeInterpreter interpreter, ASTNode node, this.hasOnlySubstanceUnits = s.getHasOnlySubstanceUnits(); this.position = position; this.compartmentPosition = compartmentPosition; - this.compartmentID = compartmentID; this.zeroSpatialDimensions = zeroSpatialDimensions; } @@ -116,63 +107,30 @@ public SpeciesValue(ASTNodeInterpreter interpreter, ASTNode node, * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ @Override - protected void computeDoubleValue(double delay) { - if(delay == 0) { - if (isAmount && !hasOnlySubstanceUnits) { - double compartmentValue = valueHolder - .getCurrentValueOf(compartmentPosition); - if ((compartmentValue == 0d) || zeroSpatialDimensions) { - doubleValue = valueHolder.getCurrentValueOf(position); - } else { - doubleValue = valueHolder.getCurrentValueOf(position) - / compartmentValue; - - } - } else if (!isAmount && hasOnlySubstanceUnits) { - double compartmentValue = valueHolder - .getCurrentValueOf(compartmentPosition); - if ((compartmentValue == 0d) || zeroSpatialDimensions) { - doubleValue = valueHolder.getCurrentValueOf(position); - } else { - doubleValue = valueHolder.getCurrentValueOf(position) - * compartmentValue; - } - } else { + protected void computeDoubleValue() { + if (isAmount && !hasOnlySubstanceUnits) { + double compartmentValue = valueHolder + .getCurrentValueOf(compartmentPosition); + if ((compartmentValue == 0d) || zeroSpatialDimensions) { doubleValue = valueHolder.getCurrentValueOf(position); + } else { + doubleValue = valueHolder.getCurrentValueOf(position) + / compartmentValue; } - } - else { - double valueTime = interpreter.symbolTime() - delay; - - - if (isAmount && !hasOnlySubstanceUnits) { - double compartmentValue = valueHolder - .computeDelayedValue(valueTime, compartmentID, null, null, 0); - if ((compartmentValue == 0d) || zeroSpatialDimensions) { - doubleValue = valueHolder.computeDelayedValue(valueTime, id, null, null, 0); - } else { - doubleValue = valueHolder.computeDelayedValue(valueTime, id, null, null, 0) - / compartmentValue; - - } - } else if (!isAmount && hasOnlySubstanceUnits) { - double compartmentValue = valueHolder - .computeDelayedValue(valueTime, compartmentID, null, null, 0); - if ((compartmentValue == 0d) || zeroSpatialDimensions) { - doubleValue = valueHolder.computeDelayedValue(valueTime, id, null, null, 0); - } else { - doubleValue = valueHolder.computeDelayedValue(valueTime, id, null, null, 0) - * compartmentValue; - } + } else if (!isAmount && hasOnlySubstanceUnits) { + double compartmentValue = valueHolder + .getCurrentValueOf(compartmentPosition); + if ((compartmentValue == 0d) || zeroSpatialDimensions) { + doubleValue = valueHolder.getCurrentValueOf(position); } else { - doubleValue = valueHolder.computeDelayedValue(valueTime, id, null, null, 0); - + doubleValue = valueHolder.getCurrentValueOf(position) + * compartmentValue; } - } - - - + } else { + doubleValue = valueHolder.getCurrentValueOf(position); + + } } } diff --git a/src/org/simulator/sbml/astnode/StoichiometryValue.java b/src/org/simulator/sbml/astnode/StoichiometryValue.java index bd2f0b92..1e9b49de 100644 --- a/src/org/simulator/sbml/astnode/StoichiometryValue.java +++ b/src/org/simulator/sbml/astnode/StoichiometryValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -136,7 +136,7 @@ private void computeStoichiometricValue() { stoichiometrySet=true; } else { if (isSetStoichiometryMath) { - stoichiometry = stoichiometryMathValue.compileDouble(time, 0d); + stoichiometry = stoichiometryMathValue.compileDouble(time); stoichiometrySet=true; } else if ((!sr.isSetStoichiometry()) && (sr.getLevel() >= 3)) { stoichiometry = 1d; diff --git a/src/org/simulator/sbml/astnode/TimesValue.java b/src/org/simulator/sbml/astnode/TimesValue.java index 75c70180..4102e297 100644 --- a/src/org/simulator/sbml/astnode/TimesValue.java +++ b/src/org/simulator/sbml/astnode/TimesValue.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -44,8 +44,8 @@ public TimesValue(ASTNodeInterpreter interpreter, ASTNode node) { * (non-Javadoc) * @see org.simulator.sbml.astnode.ASTNodeValue#computeDoubleValue() */ - protected void computeDoubleValue(double delay) { - doubleValue = interpreter.times(children, numChildren, time, delay); + protected void computeDoubleValue() { + doubleValue = interpreter.times(children, numChildren, time); } } diff --git a/src/org/simulator/sbml/astnode/package-info.java b/src/org/simulator/sbml/astnode/package-info.java index cda3ecbf..a4dbf030 100644 --- a/src/org/simulator/sbml/astnode/package-info.java +++ b/src/org/simulator/sbml/astnode/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sbml/package-info.java b/src/org/simulator/sbml/package-info.java index 3b4ec401..d20ed168 100755 --- a/src/org/simulator/sbml/package-info.java +++ b/src/org/simulator/sbml/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sedml/ExecutionException.java b/src/org/simulator/sedml/ExecutionException.java index 9aa83d59..ab6c1200 100644 --- a/src/org/simulator/sedml/ExecutionException.java +++ b/src/org/simulator/sedml/ExecutionException.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sedml/MultTableSEDMLWrapper.java b/src/org/simulator/sedml/MultTableSEDMLWrapper.java index 1870182c..c87d8ba6 100644 --- a/src/org/simulator/sedml/MultTableSEDMLWrapper.java +++ b/src/org/simulator/sedml/MultTableSEDMLWrapper.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sedml/SEDMLExecutor.java b/src/org/simulator/sedml/SEDMLExecutor.java index a899947e..ccafe670 100644 --- a/src/org/simulator/sedml/SEDMLExecutor.java +++ b/src/org/simulator/sedml/SEDMLExecutor.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sedml/SEDMLWriter.java b/src/org/simulator/sedml/SEDMLWriter.java index 4c5b0fed..dc843d33 100644 --- a/src/org/simulator/sedml/SEDMLWriter.java +++ b/src/org/simulator/sedml/SEDMLWriter.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sedml/SedMLSBMLSimulatorExecutor.java b/src/org/simulator/sedml/SedMLSBMLSimulatorExecutor.java index 9c311870..f0e77fca 100644 --- a/src/org/simulator/sedml/SedMLSBMLSimulatorExecutor.java +++ b/src/org/simulator/sedml/SedMLSBMLSimulatorExecutor.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA diff --git a/src/org/simulator/sedml/package-info.java b/src/org/simulator/sedml/package-info.java index f2c86c7d..fd3af90b 100755 --- a/src/org/simulator/sedml/package-info.java +++ b/src/org/simulator/sedml/package-info.java @@ -5,7 +5,7 @@ * This file is part of Simulation Core Library, a Java-based library * for efficient numerical simulation of biological models. * - * Copyright (C) 2007-2013 jointly by the following organizations: + * Copyright (C) 2007-2012 jointly by the following organizations: * 1. University of Tuebingen, Germany * 2. Keio University, Japan * 3. Harvard University, USA @@ -31,8 +31,6 @@ *

* Classes for storing and interpreting an SBML model. The most important * class is SBMLinterpreter that can return the current vector of - * derivatives to the solver. - * - * @author Richard Adams + * derivatives to the solver. */ package org.simulator.sedml; diff --git a/src/overview.html b/src/overview.html index 534ce9a4..85ec2175 100644 --- a/src/overview.html +++ b/src/overview.html @@ -133,7 +133,7 @@

Using SED-ML for simulation


-      SEDMLDocument doc = Libsedml.readDocument(f);

+      SEDMLDocument doc = Libsedml.readDocument(f);

       SedML sedml = doc.getSBMLModel();

       Output wanted = sedml.getOutputs().get(0);

       SedMLSBMLSimulatorExecutor exe = new SedMLSBMLSimulatorExecutor(sedml, wanted);

diff --git a/test/org/simulator/SBMLTestSuiteRunner.java b/test/org/simulator/SBMLTestSuiteRunner.java
index 2db3317e..d7d58cfd 100644
--- a/test/org/simulator/SBMLTestSuiteRunner.java
+++ b/test/org/simulator/SBMLTestSuiteRunner.java
@@ -5,7 +5,7 @@
  * This file is part of Simulation Core Library, a Java-based library
  * for efficient numerical simulation of biological models.
  *
- * Copyright (C) 2007-2013 jointly by the following organizations:
+ * Copyright (C) 2007-2012 jointly by the following organizations:
  * 1. University of Tuebingen, Germany
  * 2. Keio University, Japan
  * 3. Harvard University, USA
@@ -371,7 +371,7 @@ public static void testRosenbrockSolver(String file, int from, int to)
 		int errors = 0;
 		int nModels = 0;
 		int correctSimulations = 0;
-		RosenbrockSolver solver = new RosenbrockSolver();
+		AbstractDESSolver solver = new RosenbrockSolver();
 		int[] numberOfModels = new int[6];
 		double[] runningTimes = new double[6];
 		for (int i = 0; i != 6; i++) {
@@ -379,37 +379,9 @@ public static void testRosenbrockSolver(String file, int from, int to)
 			runningTimes[i] = 0d;
 		}
 
-		List modelsWithStrongerTolerance = new LinkedList();
-		modelsWithStrongerTolerance.add(863);
-		modelsWithStrongerTolerance.add(882);
-		modelsWithStrongerTolerance.add(893);
-		modelsWithStrongerTolerance.add(994);
-		modelsWithStrongerTolerance.add(1109);
-		modelsWithStrongerTolerance.add(1121);
-		
-		List modelsWithStrongestTolerance = new LinkedList();
-		modelsWithStrongestTolerance.add(872);
-		modelsWithStrongestTolerance.add(987);
-		modelsWithStrongestTolerance.add(1052);
-		
 		for (int modelnr = from; modelnr <= to; modelnr++) {
-			if((modelnr>=1124) && (modelnr<=1183)) {
-				continue;
-			}
 			System.out.println("model " + modelnr);
-			solver.reset();
-			if(modelsWithStrongestTolerance.contains(modelnr)) {
-				solver.setAbsTol(1E-14);
-				solver.setRelTol(1E-12);
-			}
-			else if (modelsWithStrongerTolerance.contains(modelnr)){
-				solver.setAbsTol(1E-12);
-				solver.setRelTol(1E-8);
-			}
-			else {
-				solver.setAbsTol(1E-12);
-				solver.setRelTol(1E-6);
-			}			
+
 			StringBuilder modelFile = new StringBuilder();
 			modelFile.append(modelnr);
 			while (modelFile.length() < 5)
diff --git a/test/org/simulator/SBMLTestSuiteWrapper.java b/test/org/simulator/SBMLTestSuiteWrapper.java
index bcca8149..10358d46 100644
--- a/test/org/simulator/SBMLTestSuiteWrapper.java
+++ b/test/org/simulator/SBMLTestSuiteWrapper.java
@@ -5,7 +5,7 @@
  * This file is part of Simulation Core Library, a Java-based library
  * for efficient numerical simulation of biological models.
  *
- * Copyright (C) 2007-2013 jointly by the following organizations:
+ * Copyright (C) 2007-2012 jointly by the following organizations:
  * 1. University of Tuebingen, Germany
  * 2. Keio University, Japan
  * 3. Harvard University, USA
@@ -30,8 +30,6 @@
 import java.io.IOException;
 import java.net.URISyntaxException;
 import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
 import java.util.Map;
 import java.util.Properties;
 import java.util.logging.Logger;
@@ -41,6 +39,7 @@
 import org.sbml.jsbml.validator.ModelOverdeterminedException;
 import org.sbml.jsbml.xml.stax.SBMLReader;
 import org.simulator.io.CSVImporter;
+import org.simulator.math.odes.AbstractDESSolver;
 import org.simulator.math.odes.MultiTable;
 import org.simulator.math.odes.RosenbrockSolver;
 
@@ -66,38 +65,9 @@ public class SBMLTestSuiteWrapper {
 	public static void testRosenbrockSolver(String path, int modelnr, String outputPath, int level, int version) 
 			throws FileNotFoundException, IOException, URISyntaxException {
 		String sbmlfile, csvfile, configfile;
-		if((modelnr>=1124) && (modelnr<=1183)) {
-			return;
-		}
-		
-		RosenbrockSolver solver = new RosenbrockSolver();
-
-		List modelsWithStrongerTolerance = new LinkedList();
-		modelsWithStrongerTolerance.add(863);
-		modelsWithStrongerTolerance.add(882);
-		modelsWithStrongerTolerance.add(893);
-		modelsWithStrongerTolerance.add(994);
-		modelsWithStrongerTolerance.add(1109);
-		modelsWithStrongerTolerance.add(1121);
-		
-		List modelsWithStrongestTolerance = new LinkedList();
-		modelsWithStrongestTolerance.add(872);
-		modelsWithStrongestTolerance.add(987);
-		modelsWithStrongestTolerance.add(1052);
-		
-		if(modelsWithStrongestTolerance.contains(modelnr)) {
-			solver.setAbsTol(1E-14);
-			solver.setRelTol(1E-12);
-		}
-		else if (modelsWithStrongerTolerance.contains(modelnr)){
-			solver.setAbsTol(1E-12);
-			solver.setRelTol(1E-8);
-		}
-		else {
-			solver.setAbsTol(1E-12);
-			solver.setRelTol(1E-6);
-		}		
-		
+		AbstractDESSolver solver = new RosenbrockSolver();
+
+
 		StringBuilder fileBuilder = new StringBuilder();
 		fileBuilder.append(modelnr);
 		while (fileBuilder.length() < 5)
@@ -105,7 +75,7 @@ else if (modelsWithStrongerTolerance.contains(modelnr)){
 		String folder = fileBuilder.toString();
 		fileBuilder.append('/');
 		fileBuilder.append(folder);
-		fileBuilder.insert(0, path + "/");
+		fileBuilder.insert(0, path);
 		String modelFile = fileBuilder.toString();
 		csvfile = modelFile + "-results.csv";
 		configfile = modelFile + "-settings.txt";
@@ -113,6 +83,7 @@ else if (modelsWithStrongerTolerance.contains(modelnr)){
 		Properties props = new Properties();
 		props.load(new BufferedReader(new FileReader(configfile)));
 		double duration = Double.valueOf(props.getProperty("duration"));
+		double start = Double.valueOf(props.getProperty("start"));
 
 		int steps = Integer.valueOf(props.getProperty("steps"));
 		Map amountHash = new HashMap();
@@ -169,11 +140,11 @@ else if (modelsWithStrongerTolerance.contains(modelnr)){
 				solution = null;
 			}
 			if(solution != null) {
-				writeMultiTableToFile(outputPath+"/" + folder + ".csv", variables, solution);
+				writeMultiTableToFile(path+"/" + folder + ".csv", variables, solution);
 			}
 		}
 		else {
-			logger.warning("The model "+ modelnr + " does not exist");
+			logger.warning("The model does not exist");
 		}
 	}
 
@@ -207,7 +178,6 @@ private static void writeMultiTableToFile(String outputFile, String[] variables,
 				}
 			}
 		}
-		writer.newLine();
 		writer.close();
 	}
 
@@ -220,14 +190,7 @@ private static void writeMultiTableToFile(String outputFile, String[] variables,
 	 * @throws URISyntaxException
 	 */
 	public static void main(String[] args) throws NumberFormatException, FileNotFoundException, IOException, URISyntaxException {
-		int begin = Integer.valueOf(args[1]);
-		int end = begin;
-		if(args.length > 5) {
-			end = Integer.valueOf(args[5]);
-		}
-		for(int modelnr = begin; modelnr<=end; modelnr++) {
-			testRosenbrockSolver(args[0], modelnr, args[2], Integer.valueOf(args[3]), Integer.valueOf(args[4])); 
-		}
+		testRosenbrockSolver(args[0], Integer.valueOf(args[1]), args[2], Integer.valueOf(args[3]), Integer.valueOf(args[4])); 
 	}
 
 }
diff --git a/test/org/simulator/SimulatorTest.java b/test/org/simulator/SimulatorTest.java
index 88687395..81e68264 100644
--- a/test/org/simulator/SimulatorTest.java
+++ b/test/org/simulator/SimulatorTest.java
@@ -5,7 +5,7 @@
  * This file is part of Simulation Core Library, a Java-based library
  * for efficient numerical simulation of biological models.
  *
- * Copyright (C) 2007-2013 jointly by the following organizations:
+ * Copyright (C) 2007-2012 jointly by the following organizations:
  * 1. University of Tuebingen, Germany
  * 2. Keio University, Japan
  * 3. Harvard University, USA
diff --git a/test/org/simulator/TestBiomodels.java b/test/org/simulator/TestBiomodels.java
index 5f806bd8..373c5ee6 100644
--- a/test/org/simulator/TestBiomodels.java
+++ b/test/org/simulator/TestBiomodels.java
@@ -5,7 +5,7 @@
  * This file is part of Simulation Core Library, a Java-based library
  * for efficient numerical simulation of biological models.
  *
- * Copyright (C) 2007-2013 jointly by the following organizations:
+ * Copyright (C) 2007-2012 jointly by the following organizations:
  * 1. University of Tuebingen, Germany
  * 2. Keio University, Japan
  * 3. Harvard University, USA
@@ -27,9 +27,11 @@
 import java.net.URISyntaxException;
 import java.util.logging.Logger;
 
+import org.apache.commons.math.ode.DerivativeException;
 import org.sbml.jsbml.Model;
+import org.sbml.jsbml.validator.ModelOverdeterminedException;
 import org.sbml.jsbml.xml.stax.SBMLReader;
-import org.simulator.math.odes.AdaptiveStepsizeIntegrator;
+import org.simulator.math.odes.AbstractDESSolver;
 import org.simulator.math.odes.RosenbrockSolver;
 import org.simulator.sbml.SBMLinterpreter;
 
@@ -55,9 +57,7 @@ public static void testBiomodels(String file, int from, int to)
 			throws FileNotFoundException, IOException {
 		int errors = 0;
 		int nModels = 0;
-		AdaptiveStepsizeIntegrator solver = new RosenbrockSolver();
-		solver.setAbsTol(1E-12);
-		solver.setRelTol(1E-6);
+		AbstractDESSolver solver = new RosenbrockSolver();
 
 		for (int modelnr = from; modelnr <= to; modelnr++) {
 			System.out.println("Biomodel " + modelnr);
@@ -84,7 +84,7 @@ public static void testBiomodels(String file, int from, int to)
 
 					if ((solver != null) && (interpreter != null)) {
 						solver.setStepSize(0.1);
-						
+
 						// solve
 						solver.solve(interpreter,
 								interpreter.getInitialValues(), 0, 10);
@@ -94,10 +94,14 @@ public static void testBiomodels(String file, int from, int to)
 							errors++;
 						}
 					}
-				} catch (Exception e) {
+				} catch (DerivativeException e) {
 					logger.warning("Exception in Biomodel " + modelnr);
 					errors++;
-				} 
+				} catch (ModelOverdeterminedException e) {
+					logger.warning("OverdeterminationException in Biomodel "
+							+ modelnr);
+					errors++;
+				}
 			}
 			nModels++;
 		}
diff --git a/test/org/simulator/sedml/SEDMLExecutorTest.java b/test/org/simulator/sedml/SEDMLExecutorTest.java
index 1f89b678..6b5b7738 100644
--- a/test/org/simulator/sedml/SEDMLExecutorTest.java
+++ b/test/org/simulator/sedml/SEDMLExecutorTest.java
@@ -5,7 +5,7 @@
  * This file is part of Simulation Core Library, a Java-based library
  * for efficient numerical simulation of biological models.
  *
- * Copyright (C) 2007-2013 jointly by the following organizations:
+ * Copyright (C) 2007-2012 jointly by the following organizations:
  * 1. University of Tuebingen, Germany
  * 2. Keio University, Japan
  * 3. Harvard University, USA
diff --git a/test/org/simulator/sedml/SEDMLWriterTest.java b/test/org/simulator/sedml/SEDMLWriterTest.java
index 3ace2dec..5ba76c7f 100644
--- a/test/org/simulator/sedml/SEDMLWriterTest.java
+++ b/test/org/simulator/sedml/SEDMLWriterTest.java
@@ -5,7 +5,7 @@
  * This file is part of Simulation Core Library, a Java-based library
  * for efficient numerical simulation of biological models.
  *
- * Copyright (C) 2007-2013 jointly by the following organizations:
+ * Copyright (C) 2007-2012 jointly by the following organizations:
  * 1. University of Tuebingen, Germany
  * 2. Keio University, Japan
  * 3. Harvard University, USA