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luciansmithluciansmith
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Create new 'DAE Solver' category; put IDA-like things in it.
IDA solvers are ODE solvers plus algebraic rules, not steady state solvers.
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‎kisao.owl

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@@ -544,13 +544,13 @@
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<dc:creator xml:lang="en">dk</dc:creator>
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<isImplementedIn xml:lang="en">SBML-SAT</isImplementedIn>
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<isImplementedIn xml:lang="en">SUNDIALS</isImplementedIn>
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<isImplementedIn xml:lang="en">libRoadRunner</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/bionetgen</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/jsim</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/opencor</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/pysces</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/vcell</isImplementedIn>
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<isImplementedIn xml:lang="en">libRoadRunner</isImplementedIn>
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<rdfs:label xml:lang="en">CVODE</rdfs:label>
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<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">citeulike:1832863</rdfs:seeAlso>
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<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/doi/10.1145/1089014.1089020</rdfs:seeAlso>
@@ -8720,7 +8720,7 @@ Hierarchical cluster-based partial least squares regression method uses fuzzy C-
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000432 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000432">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000408"/>
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000699"/>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
@@ -11588,10 +11588,10 @@ Levenberg first suggested an improvement to the Newton method in order to make i
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn xml:lang="en">SUNDIALS</isImplementedIn>
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<isImplementedIn xml:lang="en">SciPy</isImplementedIn>
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<isImplementedIn xml:lang="en">libRoadRunner</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/copasi</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/gillespy2</isImplementedIn>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<isImplementedIn xml:lang="en">libRoadRunner</isImplementedIn>
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<rdfs:label xml:lang="en">initial step size</rdfs:label>
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<skos:definition xml:lang="en">Initial time step size.</skos:definition>
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</owl:Class>
@@ -13568,8 +13568,8 @@ Example system of equations:
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000628 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000628">
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<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2012-06-01</dc:creator>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2012-06-01</dc:creator>
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<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
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<rdfs:label xml:lang="en">modelling and simulation algorithm parameter value</rdfs:label>
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<skos:definition xml:lang="en">A value of a parameter of an algorithm</skos:definition>
@@ -13613,8 +13613,8 @@ Example system of equations:
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000631">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000407"/>
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<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-01</dc:creator>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-01</dc:creator>
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<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
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<rdfs:label xml:lang="en">iterative root-finding method</rdfs:label>
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<skos:definition xml:lang="en">Iterative method for finding the root of a function (f(x) = 0).</skos:definition>
@@ -13662,8 +13662,8 @@ This method only involves evaluations of f. This method is suitable for non-stif
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000634">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000820"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-04</dc:created>
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<dc:created xml:lang="en">JRK</dc:created>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-04</dc:created>
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<rdfs:label xml:lang="en">scaled property</rdfs:label>
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</owl:Class>
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@@ -14965,6 +14965,129 @@ This method only involves evaluations of f. This method is suitable for non-stif
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000699 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000699">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
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<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000373"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
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<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000374"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000209"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000211"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000415"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000475"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000476"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000477"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000478"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000479"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000480"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000481"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000543"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000570"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Restriction>
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<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
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<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
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<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000571"/>
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</owl:Restriction>
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</rdfs:subClassOf>
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<dc:created>2024-03-13</dc:created>
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<dc:creator xml:lang="en">lps</dc:creator>
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<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</isOrganizational>
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<rdfs:label>DAE Solver</rdfs:label>
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<skos:altLabel xml:lang="en">differential algebraic equation solver</skos:altLabel>
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<skos:definition xml:lang="en">A DAE solver is the general category of packages such as IDA-like methods [http://identifiers.org/biomodels.kisao/KISAO_0000432] that solve systems of differential algebraic equations (DAEs). DAEs are a superset of ODEs that may additionally contain algebraic equations or &apos;fast&apos; reactions.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000699"/>
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<owl:annotatedProperty rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/>
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<owl:annotatedTarget xml:lang="en">differential algebraic equation solver</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">EXACT</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000800 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000800">
@@ -16457,7 +16580,6 @@ This method only involves evaluations of f. This method is suitable for non-stif
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<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000371"/>
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<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000372"/>
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<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000373"/>
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<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000374"/>
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</owl:members>
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</rdf:Description>
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<rdf:Description>
@@ -16558,5 +16680,5 @@ This method only involves evaluations of f. This method is suitable for non-stif
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<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
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<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->
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