diff --git a/biosimulator_processes/processes/comparator_process.py b/biosimulator_processes/processes/comparator_process.py index d2af75b1b..4e56bb601 100644 --- a/biosimulator_processes/processes/comparator_process.py +++ b/biosimulator_processes/processes/comparator_process.py @@ -6,8 +6,22 @@ from biosimulator_processes.data_model.compare_data_model import ComparisonResults, SimulatorResult, IntervalResult -def mean_squared_error(true_values: np.ndarray, predicted_values: np.ndarray): - return np.mean((predicted_values - true_values) ** 2) +def mean_squared_error(data: Union[List[float, np.ndarray]]) -> np.ndarray[float]: + """Takes in an array of data which represents the results of a composition for a species/param + at a given interval, averages the values, and then scores each item in the data array with an MSE value + calculated against the average, returning the MSE scores as an array. + + Args: + data:`Union[List[float, np.ndarray[float]]]`: An array of data which represents the results + of a composition for a species/param. + + Returns: + `np.ndarray[float]`: An array of MSE scores for each item in `data`. + """ + if isinstance(data, list): + data = np.array(data) + data_average = np.mean(data) + return (data - data_average) ** 2 class CompareResults(Step): diff --git a/composer-notebooks/amici_process_composer.ipynb b/composer-notebooks/amici_process_composer.ipynb index f25630a5c..b3ae9763b 100644 --- a/composer-notebooks/amici_process_composer.ipynb +++ b/composer-notebooks/amici_process_composer.ipynb @@ -11,19 +11,6 @@ }, "collapsed": false }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CobraProcess registered successfully.\n", - "CopasiProcess registered successfully.\n", - "SmoldynProcess not available. Error: \n", - "PLEASE NOTE: Smoldyn is not correctly installed on your system which prevents you from using the SmoldynProcess. Please refer to the README for further information on installing Smoldyn.\n", - "TelluriumProcess registered successfully.\n" - ] - } - ], "source": [ "import sys\n", "\n", @@ -40,7 +27,8 @@ "from biosimulator_processes.data_model.compare_data_model import ODEComparisonDocument, DocumentFactory\n", "from biosimulator_processes import CORE\n", "from process_bigraph import Composite, pp" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -53,41 +41,6 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'copasi_0': {'_type': 'process',\n", - " 'address': 'local:copasi',\n", - " 'config': {'model': {'model_source': '../biosimulator_processes/model_files/sbml/BIOMD0000000630_url.xml'}},\n", - " 'inputs': {'floating_species_concentrations': ['floating_species_concentrations_store'],\n", - " 'model_parameters': ['model_parameters_store'],\n", - " 'time': ['time_store'],\n", - " 'reactions': ['reactions_store']},\n", - " 'outputs': {'floating_species_concentrations': ['floating_species_concentrations_store'],\n", - " 'time': ['time_store']}},\n", - " 'amici_1': {'_type': 'process',\n", - " 'address': 'local:amici',\n", - " 'config': {'model': {'model_source': '../biosimulator_processes/model_files/sbml/BIOMD0000000630_url.xml'}},\n", - " 'inputs': {'floating_species_concentrations': ['floating_species_concentrations_store'],\n", - " 'model_parameters': ['model_parameters_store'],\n", - " 'time': ['time_store'],\n", - " 'reactions': ['reactions_store']},\n", - " 'outputs': {'floating_species_concentrations': ['floating_species_concentrations_store'],\n", - " 'time': ['time_store']}},\n", - " 'emitter': {'_type': 'step',\n", - " 'address': 'local:ram-emitter',\n", - " 'config': {'emit': {'floating_species_concentrations': 'tree[float]',\n", - " 'time': 'float'}},\n", - " 'inputs': {'floating_species_concentrations': ['floating_species_concentrations_store'],\n", - " 'time': ['time_store']}}}" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "#### Step 1: Define the document to be read by the Composite, which is implemented by the Process.\n", "biomodel_id = 'BIOMD0000000630'\n", @@ -104,7 +57,8 @@ " model_filepath=model_fp)\n", "\n", "comparison_document.composite" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -117,7 +71,6 @@ }, "collapsed": false }, - "outputs": [], "source": [ "# Amici Model from compiled module\n", "sbml_importer = amici.SbmlImporter(model_fp)\n", @@ -133,7 +86,8 @@ "compiled_model = model_module.getModel()\n", "# instantiate solver\n", "method = compiled_model.getSolver()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -146,7 +100,6 @@ }, "collapsed": false }, - "outputs": [], "source": [ "# From load sbml model module \n", "sbml_reader = libsbml.SBMLReader()\n", @@ -155,7 +108,8 @@ "species_objects_list = sbml_model.getListOfSpecies()\n", "floating_species_list = [s.getId() for s in species_objects_list]\n", "floating_species_initial = dict(zip(floating_species_list, [s.getInitialConcentration() for s in species_objects_list]))" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -168,24 +122,11 @@ }, "collapsed": false }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "0.0\n", - "0.0\n", - "0.0\n", - "0.0\n", - "0.0\n", - "0.0\n" - ] - } - ], "source": [ "for s in species_objects_list:\n", " print(s.getInitialAmount())" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -198,21 +139,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "['species_1', 'species_2', 'species_3', 'species_4', 'species_5', 'species_6']" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "[s.getId() for s in species_objects_list]" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -225,26 +155,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'plasminogen': 0.01,\n", - " 'plasmin': 0.0,\n", - " 'single intact chain urokinase-type plasminogen activator': 0.002,\n", - " 'two-chain urokinase-type plasminogen activator': 0.0,\n", - " 'x': 0.0,\n", - " 'x-plasmin': 0.0}" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "floating_species_initial" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -257,26 +171,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'species_1': 0.01,\n", - " 'species_2': 0.0,\n", - " 'species_3': 0.002,\n", - " 'species_4': 0.0,\n", - " 'species_5': 0.0,\n", - " 'species_6': 0.0}" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "dict(zip(floating_species_list, [s.getInitialConcentration() for s in species_objects_list]))" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -289,26 +187,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'species_1': 0.01,\n", - " 'species_2': 0.0,\n", - " 'species_3': 0.002,\n", - " 'species_4': 0.0,\n", - " 'species_5': 0.0,\n", - " 'species_6': 0.0}" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "floating_species_initial" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -321,10 +203,10 @@ }, "collapsed": false }, - "outputs": [], "source": [ "species_objects_list = sbml_model.getListOfSpecies()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -337,31 +219,12 @@ }, "collapsed": false }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "species_1\n", - "0 0.01\n", - "species_2\n", - "1 0.0\n", - "species_3\n", - "2 0.002\n", - "species_4\n", - "3 0.0\n", - "species_5\n", - "4 0.0\n", - "species_6\n", - "5 0.0\n" - ] - } - ], "source": [ "for i, s in enumerate(species_objects_list):\n", " print(s.getId())\n", " print(i, s.getInitialConcentration())" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -374,192 +237,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "['__bool__',\n", - " '__class__',\n", - " '__deepcopy__',\n", - " '__delattr__',\n", - " '__deref__',\n", - " '__dict__',\n", - " '__dir__',\n", - " '__doc__',\n", - " '__eq__',\n", - " '__format__',\n", - " '__ge__',\n", - " '__getattribute__',\n", - " '__gt__',\n", - 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" 'set_steadystate_mask',\n", - " 'state_independent_events_',\n", - " 'swap',\n", - " 't0',\n", - " 'this',\n", - " 'thisown',\n", - " 'ubw']" - ] - }, - "execution_count": 25, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "dir(model)" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -572,21 +253,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "(0.084, 0.032, 2.0, 0.035, 40.0, 0.9, 0.016, 0.0, 0.02, 0.0032, 0.01, 0.01)" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "model.getParameters()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -599,21 +269,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11)" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "model.getParameterList()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -626,32 +285,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "('parameter_1',\n", - " 'parameter_2',\n", - " 'parameter_13',\n", - " 'reaction_1_k1',\n", - " 'reaction_2_parameter_8',\n", - " 'reaction_3_k1',\n", - " 'reaction_8_k2',\n", - " 'reaction_8_k1',\n", - " 'reaction_9_k1',\n", - " 'reaction_12_v',\n", - " 'reaction_13_v',\n", - " 'reaction_14_v')" - ] - }, - "execution_count": 28, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "model.getParameterIds()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -660,10 +297,10 @@ "metadata": { "collapsed": false }, - "outputs": [], "source": [ "model_parameters_list = model.getP" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -676,409 +313,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "['__class__',\n", - " '__delattr__',\n", - " '__dict__',\n", - " '__dir__',\n", - " '__doc__',\n", - " '__eq__',\n", - " '__format__',\n", - " '__ge__',\n", - " '__getattribute__',\n", - " '__gt__',\n", - 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" 'getNumSpeciesTypes',\n", - " 'getNumSpeciesWithBoundaryCondition',\n", - " 'getNumUnitDefinitions',\n", - " 'getPackageCoreVersion',\n", - " 'getPackageName',\n", - " 'getPackageVersion',\n", - " 'getParameter',\n", - " 'getParentSBMLObject',\n", - " 'getPlugin',\n", - " 'getPrefix',\n", - " 'getRateRule',\n", - " 'getRateRuleByVariable',\n", - " 'getReaction',\n", - " 'getResourceBiologicalQualifier',\n", - " 'getResourceModelQualifier',\n", - " 'getRule',\n", - " 'getRuleByVariable',\n", - " 'getSBMLDocument',\n", - " 'getSBMLNamespaces',\n", - " 'getSBOTerm',\n", - " 'getSBOTermAsURL',\n", - " 'getSBOTermID',\n", - " 'getSpecies',\n", - " 'getSpeciesReference',\n", - " 'getSpeciesType',\n", - " 'getSubstanceUnits',\n", - " 'getTimeUnits',\n", - " 'getTypeCode',\n", - " 'getURI',\n", - " 'getUnitDefinition',\n", - " 'getVersion',\n", - " 'getVolumeUnits',\n", - " 'hasNonstandardIdentifierBeginningWith',\n", - " 'hasOptionalAttributes',\n", - " 'hasOptionalElements',\n", - " 'hasRequiredAttributes',\n", - " 'hasRequiredElements',\n", - " 'hasValidLevelVersionNamespaceCombination',\n", - " 'id',\n", - " 'id_attribute',\n", - " 'initial_assignments',\n", - " 'isPackageEnabled',\n", - " 'isPackageURIEnabled',\n", - " 'isPkgEnabled',\n", - " 'isPkgURIEnabled',\n", - " 'isPopulatedAllElementIdList',\n", - " 'isPopulatedAllElementMetaIdList',\n", - " 'isPopulatedListFormulaUnitsData',\n", - " 'isSetAnnotation',\n", - " 'isSetAreaUnits',\n", - " 'isSetConversionFactor',\n", - " 'isSetCreatedDate',\n", - " 'isSetExtentUnits',\n", - " 'isSetId',\n", - " 'isSetIdAttribute',\n", - " 'isSetLengthUnits',\n", - " 'isSetMetaId',\n", - " 'isSetModelHistory',\n", - " 'isSetModifiedDate',\n", - " 'isSetName',\n", - " 'isSetNotes',\n", - " 'isSetSBOTerm',\n", - " 'isSetSubstanceUnits',\n", - " 'isSetTimeUnits',\n", - " 'isSetUserData',\n", - " 'isSetVolumeUnits',\n", - " 'length_units',\n", - " 'level',\n", - " 'line',\n", - " 'matchesRequiredSBMLNamespacesForAddition',\n", - " 'matchesSBMLNamespaces',\n", - " 'meta_id',\n", - " 'model',\n", - " 'multiplyAssignmentsToSIdByFunction',\n", - " 'name',\n", - " 'namespaces',\n", - " 'notes',\n", - " 'notes_string',\n", - " 'num_compartment_types',\n", - " 'num_compartments',\n", - " 'num_constraints',\n", - " 'num_cv_terms',\n", - " 'num_disabled_plugins',\n", - " 'num_events',\n", - " 'num_function_definitions',\n", - " 'num_initial_assignments',\n", - " 'num_modified_dates',\n", - " 'num_parameters',\n", - " 'num_plugins',\n", - " 'num_reactions',\n", - " 'num_rules',\n", - " 'num_species',\n", - " 'num_species_types',\n", - " 'num_species_with_boundary_condition',\n", - " 'num_unit_definitions',\n", - " 'package_core_version',\n", - " 'package_name',\n", - " 'package_version',\n", - " 'parameters',\n", - " 'populateAllElementIdList',\n", - " 'populateAllElementMetaIdList',\n", - " 'populateListFormulaUnitsData',\n", - " 'prefix',\n", - " 'prependStringToAllIdentifiers',\n", - " 'reactions',\n", - " 'read',\n", - " 'removeCompartment',\n", - " 'removeCompartmentType',\n", - " 'removeCompartmentTypes',\n", - " 'removeConstraint',\n", - " 'removeDuplicateAnnotations',\n", - " 'removeEvent',\n", - " 'removeFromParentAndDelete',\n", - " 'removeFunctionDefinition',\n", - " 'removeInitialAssignment',\n", - " 'removeListFormulaUnitsData',\n", - " 'removeParameter',\n", - " 'removeParameterRuleUnits',\n", - " 'removeReaction',\n", - " 'removeRule',\n", - " 'removeRuleByVariable',\n", - " 'removeSpecies',\n", - " 'removeSpeciesType',\n", - " 'removeSpeciesTypes',\n", - " 'removeTopLevelAnnotationElement',\n", - " 'removeUnitDefinition',\n", - " 'renameAllIds',\n", - " 'renameIDs',\n", - " 'renameMetaIdRefs',\n", - " 'renameSIdRefs',\n", - " 'renameUnitSIdRefs',\n", - " 'replaceSIDWithFunction',\n", - " 'replaceTopLevelAnnotationElement',\n", - " 'rules',\n", - " 'sbml_namespaces',\n", - " 'sbml_namespaces_and_own',\n", - " 'sbo_term',\n", - " 'sbo_term_as_url',\n", - " 'sbo_term_id',\n", - " 'setAnnotation',\n", - " 'setAreaUnits',\n", - " 'setConversionFactor',\n", - " 'setCreatedDate',\n", - " 'setExtentUnits',\n", - " 'setId',\n", - " 'setIdAttribute',\n", - " 'setLengthUnits',\n", - " 'setMetaId',\n", - " 'setModelHistory',\n", - " 'setName',\n", - " 'setNamespaces',\n", - " 'setNotes',\n", - " 'setSBMLNamespacesAndOwn',\n", - " 'setSBOTerm',\n", - " 'setSpatialDimensions',\n", - " 'setSpeciesReferenceConstantValueAndStoichiometry',\n", - " 'setSubstanceUnits',\n", - " 'setTimeUnits',\n", - " 'setVolumeUnits',\n", - " 'spatial_dimensions',\n", - " 'species',\n", - " 'species_reference_constant_value_and_stoichiometry',\n", - " 'species_types',\n", - " 'substance_units',\n", - " 'this',\n", - " 'thisown',\n", - " 'time_units',\n", - " 'toSBML',\n", - " 'toXMLNode',\n", - " 'transformIdentifiers',\n", - " 'type_code',\n", - " 'unit_definitions',\n", - " 'unsetAnnotation',\n", - " 'unsetAreaUnits',\n", - " 'unsetCVTerms',\n", - " 'unsetConversionFactor',\n", - " 'unsetCreatedDate',\n", - " 'unsetExtentUnits',\n", - " 'unsetId',\n", - " 'unsetIdAttribute',\n", - " 'unsetLengthUnits',\n", - " 'unsetMetaId',\n", - " 'unsetModelHistory',\n", - " 'unsetModifiedDates',\n", - " 'unsetName',\n", - " 'unsetNotes',\n", - " 'unsetSBOTerm',\n", - " 'unsetSubstanceUnits',\n", - " 'unsetTimeUnits',\n", - " 'unsetUserData',\n", - " 'unsetVolumeUnits',\n", - " 'updateSBMLNamespace',\n", - " 'uri',\n", - " 'version',\n", - " 'volume_units',\n", - " 'write',\n", - " 'writeExtensionElements']" - ] - }, - "execution_count": 29, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "dir(sbml_model)" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1091,10 +329,10 @@ }, "collapsed": false }, - "outputs": [], "source": [ "model_parameter_objects = sbml_model.getListOfParameters()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1107,21 +345,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 37, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "model_parameter_objects" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1134,29 +361,13 @@ }, "collapsed": false }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__metaclass__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__swig_destroy__', '__weakref__', 'addCVTerm', 'addModifiedDate', 'all_elements', 'all_elements_from_plugins', 'annotation', 'annotation_string', 'appendAnnotation', 'appendNotes', 'calculating_units', 'checkCompatibility', 'checkMathMLNamespace', 'clone', 'column', 'connectToChild', 'connectToParent', 'constant', 'containsUndeclaredUnits', 'cv_terms', 'deleteDisabledPlugins', 'derived_unit_definition', 'disablePackage', 'divideAssignmentsToSIdByFunction', 'element_name', 'enablePackage', 'enablePackageInternal', 'getAncestorOfType', 'getAnnotation', 'getAnnotationString', 'getCVTerm', 'getCVTerms', 'getColumn', 'getConstant', 'getCreatedDate', 'getDerivedUnitDefinition', 'getDisabledPlugin', 'getElementByMetaId', 'getElementBySId', 'getElementFromPluginsByMetaId', 'getElementFromPluginsBySId', 'getElementName', 'getId', 'getIdAttribute', 'getLevel', 'getLine', 'getListOfAllElements', 'getListOfAllElementsFromPlugins', 'getMetaId', 'getModel', 'getModelHistory', 'getModifiedDate', 'getName', 'getNamespaces', 'getNotes', 'getNotesString', 'getNumCVTerms', 'getNumDisabledPlugins', 'getNumModifiedDates', 'getNumPlugins', 'getPackageCoreVersion', 'getPackageName', 'getPackageVersion', 'getParentSBMLObject', 'getPlugin', 'getPrefix', 'getResourceBiologicalQualifier', 'getResourceModelQualifier', 'getSBMLDocument', 'getSBMLNamespaces', 'getSBOTerm', 'getSBOTermAsURL', 'getSBOTermID', 'getTypeCode', 'getURI', 'getUnits', 'getValue', 'getVersion', 'hasNonstandardIdentifierBeginningWith', 'hasOptionalAttributes', 'hasOptionalElements', 'hasRequiredAttributes', 'hasRequiredElements', 'hasValidLevelVersionNamespaceCombination', 'id', 'id_attribute', 'initDefaults', 'isPackageEnabled', 'isPackageURIEnabled', 'isPkgEnabled', 'isPkgURIEnabled', 'isSetAnnotation', 'isSetConstant', 'isSetCreatedDate', 'isSetId', 'isSetIdAttribute', 'isSetMetaId', 'isSetModelHistory', 'isSetModifiedDate', 'isSetName', 'isSetNotes', 'isSetSBOTerm', 'isSetUnits', 'isSetUserData', 'isSetValue', 'level', 'line', 'matchesRequiredSBMLNamespacesForAddition', 'matchesSBMLNamespaces', 'meta_id', 'model', 'multiplyAssignmentsToSIdByFunction', 'name', 'namespaces', 'notes', 'notes_string', 'num_cv_terms', 'num_disabled_plugins', 'num_modified_dates', 'num_plugins', 'package_core_version', 'package_name', 'package_version', 'prefix', 'prependStringToAllIdentifiers', 'read', 'removeDuplicateAnnotations', 'removeFromParentAndDelete', 'removeTopLevelAnnotationElement', 'renameMetaIdRefs', 'renameSIdRefs', 'renameUnitSIdRefs', 'replaceSIDWithFunction', 'replaceTopLevelAnnotationElement', 'sbml_namespaces', 'sbml_namespaces_and_own', 'sbo_term', 'sbo_term_as_url', 'sbo_term_id', 'setAnnotation', 'setCalculatingUnits', 'setConstant', 'setCreatedDate', 'setId', 'setIdAttribute', 'setMetaId', 'setModelHistory', 'setName', 'setNamespaces', 'setNotes', 'setSBMLNamespacesAndOwn', 'setSBOTerm', 'setUnits', 'setValue', 'this', 'thisown', 'toSBML', 'toXMLNode', 'transformIdentifiers', 'type_code', 'units', 'unsetAnnotation', 'unsetCVTerms', 'unsetConstant', 'unsetCreatedDate', 'unsetId', 'unsetIdAttribute', 'unsetMetaId', 'unsetModelHistory', 'unsetModifiedDates', 'unsetName', 'unsetNotes', 'unsetSBOTerm', 'unsetUnits', 'unsetUserData', 'unsetValue', 'updateSBMLNamespace', 'uri', 'value', 'version', 'write', 'writeExtensionElements']\n", - "0.084\n", - "degradation constant 1\n", - "['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__metaclass__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__swig_destroy__', '__weakref__', 'addCVTerm', 'addModifiedDate', 'all_elements', 'all_elements_from_plugins', 'annotation', 'annotation_string', 'appendAnnotation', 'appendNotes', 'calculating_units', 'checkCompatibility', 'checkMathMLNamespace', 'clone', 'column', 'connectToChild', 'connectToParent', 'constant', 'containsUndeclaredUnits', 'cv_terms', 'deleteDisabledPlugins', 'derived_unit_definition', 'disablePackage', 'divideAssignmentsToSIdByFunction', 'element_name', 'enablePackage', 'enablePackageInternal', 'getAncestorOfType', 'getAnnotation', 'getAnnotationString', 'getCVTerm', 'getCVTerms', 'getColumn', 'getConstant', 'getCreatedDate', 'getDerivedUnitDefinition', 'getDisabledPlugin', 'getElementByMetaId', 'getElementBySId', 'getElementFromPluginsByMetaId', 'getElementFromPluginsBySId', 'getElementName', 'getId', 'getIdAttribute', 'getLevel', 'getLine', 'getListOfAllElements', 'getListOfAllElementsFromPlugins', 'getMetaId', 'getModel', 'getModelHistory', 'getModifiedDate', 'getName', 'getNamespaces', 'getNotes', 'getNotesString', 'getNumCVTerms', 'getNumDisabledPlugins', 'getNumModifiedDates', 'getNumPlugins', 'getPackageCoreVersion', 'getPackageName', 'getPackageVersion', 'getParentSBMLObject', 'getPlugin', 'getPrefix', 'getResourceBiologicalQualifier', 'getResourceModelQualifier', 'getSBMLDocument', 'getSBMLNamespaces', 'getSBOTerm', 'getSBOTermAsURL', 'getSBOTermID', 'getTypeCode', 'getURI', 'getUnits', 'getValue', 'getVersion', 'hasNonstandardIdentifierBeginningWith', 'hasOptionalAttributes', 'hasOptionalElements', 'hasRequiredAttributes', 'hasRequiredElements', 'hasValidLevelVersionNamespaceCombination', 'id', 'id_attribute', 'initDefaults', 'isPackageEnabled', 'isPackageURIEnabled', 'isPkgEnabled', 'isPkgURIEnabled', 'isSetAnnotation', 'isSetConstant', 'isSetCreatedDate', 'isSetId', 'isSetIdAttribute', 'isSetMetaId', 'isSetModelHistory', 'isSetModifiedDate', 'isSetName', 'isSetNotes', 'isSetSBOTerm', 'isSetUnits', 'isSetUserData', 'isSetValue', 'level', 'line', 'matchesRequiredSBMLNamespacesForAddition', 'matchesSBMLNamespaces', 'meta_id', 'model', 'multiplyAssignmentsToSIdByFunction', 'name', 'namespaces', 'notes', 'notes_string', 'num_cv_terms', 'num_disabled_plugins', 'num_modified_dates', 'num_plugins', 'package_core_version', 'package_name', 'package_version', 'prefix', 'prependStringToAllIdentifiers', 'read', 'removeDuplicateAnnotations', 'removeFromParentAndDelete', 'removeTopLevelAnnotationElement', 'renameMetaIdRefs', 'renameSIdRefs', 'renameUnitSIdRefs', 'replaceSIDWithFunction', 'replaceTopLevelAnnotationElement', 'sbml_namespaces', 'sbml_namespaces_and_own', 'sbo_term', 'sbo_term_as_url', 'sbo_term_id', 'setAnnotation', 'setCalculatingUnits', 'setConstant', 'setCreatedDate', 'setId', 'setIdAttribute', 'setMetaId', 'setModelHistory', 'setName', 'setNamespaces', 'setNotes', 'setSBMLNamespacesAndOwn', 'setSBOTerm', 'setUnits', 'setValue', 'this', 'thisown', 'toSBML', 'toXMLNode', 'transformIdentifiers', 'type_code', 'units', 'unsetAnnotation', 'unsetCVTerms', 'unsetConstant', 'unsetCreatedDate', 'unsetId', 'unsetIdAttribute', 'unsetMetaId', 'unsetModelHistory', 'unsetModifiedDates', 'unsetName', 'unsetNotes', 'unsetSBOTerm', 'unsetUnits', 'unsetUserData', 'unsetValue', 'updateSBMLNamespace', 'uri', 'value', 'version', 'write', 'writeExtensionElements']\n", - "0.032\n", - "degradation constant 2\n", - "['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__metaclass__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__swig_destroy__', '__weakref__', 'addCVTerm', 'addModifiedDate', 'all_elements', 'all_elements_from_plugins', 'annotation', 'annotation_string', 'appendAnnotation', 'appendNotes', 'calculating_units', 'checkCompatibility', 'checkMathMLNamespace', 'clone', 'column', 'connectToChild', 'connectToParent', 'constant', 'containsUndeclaredUnits', 'cv_terms', 'deleteDisabledPlugins', 'derived_unit_definition', 'disablePackage', 'divideAssignmentsToSIdByFunction', 'element_name', 'enablePackage', 'enablePackageInternal', 'getAncestorOfType', 'getAnnotation', 'getAnnotationString', 'getCVTerm', 'getCVTerms', 'getColumn', 'getConstant', 'getCreatedDate', 'getDerivedUnitDefinition', 'getDisabledPlugin', 'getElementByMetaId', 'getElementBySId', 'getElementFromPluginsByMetaId', 'getElementFromPluginsBySId', 'getElementName', 'getId', 'getIdAttribute', 'getLevel', 'getLine', 'getListOfAllElements', 'getListOfAllElementsFromPlugins', 'getMetaId', 'getModel', 'getModelHistory', 'getModifiedDate', 'getName', 'getNamespaces', 'getNotes', 'getNotesString', 'getNumCVTerms', 'getNumDisabledPlugins', 'getNumModifiedDates', 'getNumPlugins', 'getPackageCoreVersion', 'getPackageName', 'getPackageVersion', 'getParentSBMLObject', 'getPlugin', 'getPrefix', 'getResourceBiologicalQualifier', 'getResourceModelQualifier', 'getSBMLDocument', 'getSBMLNamespaces', 'getSBOTerm', 'getSBOTermAsURL', 'getSBOTermID', 'getTypeCode', 'getURI', 'getUnits', 'getValue', 'getVersion', 'hasNonstandardIdentifierBeginningWith', 'hasOptionalAttributes', 'hasOptionalElements', 'hasRequiredAttributes', 'hasRequiredElements', 'hasValidLevelVersionNamespaceCombination', 'id', 'id_attribute', 'initDefaults', 'isPackageEnabled', 'isPackageURIEnabled', 'isPkgEnabled', 'isPkgURIEnabled', 'isSetAnnotation', 'isSetConstant', 'isSetCreatedDate', 'isSetId', 'isSetIdAttribute', 'isSetMetaId', 'isSetModelHistory', 'isSetModifiedDate', 'isSetName', 'isSetNotes', 'isSetSBOTerm', 'isSetUnits', 'isSetUserData', 'isSetValue', 'level', 'line', 'matchesRequiredSBMLNamespacesForAddition', 'matchesSBMLNamespaces', 'meta_id', 'model', 'multiplyAssignmentsToSIdByFunction', 'name', 'namespaces', 'notes', 'notes_string', 'num_cv_terms', 'num_disabled_plugins', 'num_modified_dates', 'num_plugins', 'package_core_version', 'package_name', 'package_version', 'prefix', 'prependStringToAllIdentifiers', 'read', 'removeDuplicateAnnotations', 'removeFromParentAndDelete', 'removeTopLevelAnnotationElement', 'renameMetaIdRefs', 'renameSIdRefs', 'renameUnitSIdRefs', 'replaceSIDWithFunction', 'replaceTopLevelAnnotationElement', 'sbml_namespaces', 'sbml_namespaces_and_own', 'sbo_term', 'sbo_term_as_url', 'sbo_term_id', 'setAnnotation', 'setCalculatingUnits', 'setConstant', 'setCreatedDate', 'setId', 'setIdAttribute', 'setMetaId', 'setModelHistory', 'setName', 'setNamespaces', 'setNotes', 'setSBMLNamespacesAndOwn', 'setSBOTerm', 'setUnits', 'setValue', 'this', 'thisown', 'toSBML', 'toXMLNode', 'transformIdentifiers', 'type_code', 'units', 'unsetAnnotation', 'unsetCVTerms', 'unsetConstant', 'unsetCreatedDate', 'unsetId', 'unsetIdAttribute', 'unsetMetaId', 'unsetModelHistory', 'unsetModifiedDates', 'unsetName', 'unsetNotes', 'unsetSBOTerm', 'unsetUnits', 'unsetUserData', 'unsetValue', 'updateSBMLNamespace', 'uri', 'value', 'version', 'write', 'writeExtensionElements']\n", - "2.0\n", - "hill cooperativity\n" - ] - } - ], "source": [ "for m in model_parameter_objects:\n", " print(dir(m))\n", " print(m.getValue())\n", " print(m.getName())" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1165,12 +376,12 @@ "metadata": { "collapsed": false }, - "outputs": [], "source": [ "model_parameter_objects = sbml_model.getListOfParameters()\n", "model_parameters_list = [param.getName() for param in model_parameter_objects]\n", "model_parameters_values = [param.getValue() for param in model_parameter_objects]" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1183,409 +394,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "['__class__',\n", - " '__delattr__',\n", - " '__dict__',\n", - " '__dir__',\n", - " '__doc__',\n", - " '__eq__',\n", - " '__format__',\n", - " '__ge__',\n", - " '__getattribute__',\n", - " '__gt__',\n", - " '__hash__',\n", - " '__init__',\n", - " '__init_subclass__',\n", - " '__le__',\n", - " '__lt__',\n", - " '__metaclass__',\n", - " '__module__',\n", - " '__ne__',\n", - " '__new__',\n", - " '__parent_ref__',\n", - " '__reduce__',\n", - " '__reduce_ex__',\n", - " '__repr__',\n", - " '__setattr__',\n", - " '__sizeof__',\n", - " '__str__',\n", - " '__subclasshook__',\n", - " '__swig_destroy__',\n", - " '__weakref__',\n", - " 'addCVTerm',\n", - " 'addCompartment',\n", - " 'addCompartmentType',\n", - " 'addConstantAttribute',\n", - " 'addConstraint',\n", - " 'addDefinitionsForDefaultUnits',\n", - " 'addEvent',\n", - " 'addFunctionDefinition',\n", - " 'addInitialAssignment',\n", - " 'addModifiedDate',\n", - " 'addModifiers',\n", - " 'addParameter',\n", - " 'addReaction',\n", - " 'addRule',\n", - " 'addSpecies',\n", - " 'addSpeciesType',\n", - " 'addUnitDefinition',\n", - " 'all_element_id_list',\n", - " 'all_element_meta_id_list',\n", - " 'all_elements',\n", - " 'all_elements_from_plugins',\n", - " 'annotation',\n", - " 'annotation_string',\n", - " 'appendAnnotation',\n", - " 'appendFrom',\n", - " 'appendNotes',\n", - " 'area_units',\n", - " 'assignRequiredValues',\n", - " 'checkCompatibility',\n", - " 'checkMathMLNamespace',\n", - " 'clearAllElementIdList',\n", - " 'clearAllElementMetaIdList',\n", - " 'clone',\n", - " 'column',\n", - " 'compartment_types',\n", - " 'compartments',\n", - " 'connectToChild',\n", - " 'connectToParent',\n", - " 'constraints',\n", - " 'containsUndeclaredUnits',\n", - " 'conversion_factor',\n", - " 'convertFromL3V2',\n", - " 'convertL1ToL2',\n", - " 'convertL1ToL3',\n", - " 'convertL2ToL1',\n", - " 'convertL2ToL3',\n", - " 'convertL3ToL1',\n", - " 'convertL3ToL2',\n", - " 'convertParametersToLocals',\n", - " 'convertStoichiometryMath',\n", - " 'createAlgebraicRule',\n", - " 'createAssignmentRule',\n", - " 'createCompartment',\n", - " 'createCompartmentType',\n", - " 'createConstraint',\n", - " 'createDelay',\n", - " 'createEvent',\n", - " 'createEventAssignment',\n", - " 'createFunctionDefinition',\n", - " 'createInitialAssignment',\n", - " 'createKineticLaw',\n", - " 'createKineticLawLocalParameter',\n", - " 'createKineticLawParameter',\n", - " 'createModifier',\n", - " 'createParameter',\n", - " 'createProduct',\n", - " 'createRateRule',\n", - " 'createReactant',\n", - " 'createReaction',\n", - " 'createSpecies',\n", - " 'createSpeciesType',\n", - " 'createTrigger',\n", - " 'createUnit',\n", - " 'createUnitDefinition',\n", - " 'cv_terms',\n", - " 'dealWithDefaultValues',\n", - " 'dealWithEvents',\n", - " 'dealWithFast',\n", - " 'dealWithL3Fast',\n", - " 'dealWithModelUnits',\n", - " 'dealWithStoichiometry',\n", - " 'deleteDisabledPlugins',\n", - " 'derived_unit_definition',\n", - " 'disablePackage',\n", - " 'divideAssignmentsToSIdByFunction',\n", - " 'element_name',\n", - " 'enablePackage',\n", - " 'enablePackageInternal',\n", - " 'events',\n", - " 'extent_units',\n", - " 'function_definitions',\n", - " 'getAllElementIdList',\n", - " 'getAllElementMetaIdList',\n", - " 'getAncestorOfType',\n", - " 'getAnnotation',\n", - " 'getAnnotationString',\n", - " 'getAreaUnits',\n", - " 'getAssignmentRule',\n", - " 'getAssignmentRuleByVariable',\n", - " 'getCVTerm',\n", - " 'getCVTerms',\n", - " 'getColumn',\n", - " 'getCompartment',\n", - " 'getCompartmentType',\n", - " 'getConstraint',\n", - " 'getConversionFactor',\n", - " 'getCreatedDate',\n", - " 'getDerivedUnitDefinition',\n", - " 'getDisabledPlugin',\n", - " 'getElementByMetaId',\n", - " 'getElementBySId',\n", - " 'getElementFromPluginsByMetaId',\n", - " 'getElementFromPluginsBySId',\n", - " 'getElementName',\n", - " 'getEvent',\n", - " 'getExtentUnits',\n", - " 'getFormulaUnitsDataForAssignment',\n", - " 'getFormulaUnitsDataForVariable',\n", - " 'getFunctionDefinition',\n", - " 'getId',\n", - " 'getIdAttribute',\n", - " 'getInitialAssignment',\n", - " 'getInitialAssignmentBySymbol',\n", - " 'getLengthUnits',\n", - " 'getLevel',\n", - " 'getLine',\n", - " 'getListOfAllElements',\n", - " 'getListOfAllElementsFromPlugins',\n", - " 'getListOfCompartmentTypes',\n", - " 'getListOfCompartments',\n", - " 'getListOfConstraints',\n", - " 'getListOfEvents',\n", - " 'getListOfFunctionDefinitions',\n", - " 'getListOfInitialAssignments',\n", - " 'getListOfParameters',\n", - " 'getListOfReactions',\n", - " 'getListOfRules',\n", - " 'getListOfSpecies',\n", - " 'getListOfSpeciesTypes',\n", - " 'getListOfUnitDefinitions',\n", - " 'getMetaId',\n", - " 'getModel',\n", - " 'getModelHistory',\n", - " 'getModifiedDate',\n", - " 'getModifierSpeciesReference',\n", - " 'getName',\n", - " 'getNamespaces',\n", - " 'getNotes',\n", - " 'getNotesString',\n", - " 'getNumCVTerms',\n", - " 'getNumCompartmentTypes',\n", - " 'getNumCompartments',\n", - " 'getNumConstraints',\n", - " 'getNumDisabledPlugins',\n", - " 'getNumEvents',\n", - " 'getNumFunctionDefinitions',\n", - " 'getNumInitialAssignments',\n", - " 'getNumModifiedDates',\n", - " 'getNumParameters',\n", - " 'getNumPlugins',\n", - " 'getNumReactions',\n", - " 'getNumRules',\n", - " 'getNumSpecies',\n", - " 'getNumSpeciesTypes',\n", - " 'getNumSpeciesWithBoundaryCondition',\n", - " 'getNumUnitDefinitions',\n", - " 'getPackageCoreVersion',\n", - " 'getPackageName',\n", - " 'getPackageVersion',\n", - " 'getParameter',\n", - " 'getParentSBMLObject',\n", - " 'getPlugin',\n", - " 'getPrefix',\n", - " 'getRateRule',\n", - " 'getRateRuleByVariable',\n", - " 'getReaction',\n", - " 'getResourceBiologicalQualifier',\n", - " 'getResourceModelQualifier',\n", - " 'getRule',\n", - " 'getRuleByVariable',\n", - " 'getSBMLDocument',\n", - " 'getSBMLNamespaces',\n", - " 'getSBOTerm',\n", - " 'getSBOTermAsURL',\n", - " 'getSBOTermID',\n", - " 'getSpecies',\n", - " 'getSpeciesReference',\n", - " 'getSpeciesType',\n", - " 'getSubstanceUnits',\n", - " 'getTimeUnits',\n", - " 'getTypeCode',\n", - " 'getURI',\n", - " 'getUnitDefinition',\n", - " 'getVersion',\n", - " 'getVolumeUnits',\n", - " 'hasNonstandardIdentifierBeginningWith',\n", - " 'hasOptionalAttributes',\n", - " 'hasOptionalElements',\n", - " 'hasRequiredAttributes',\n", - " 'hasRequiredElements',\n", - " 'hasValidLevelVersionNamespaceCombination',\n", - " 'id',\n", - " 'id_attribute',\n", - " 'initial_assignments',\n", - " 'isPackageEnabled',\n", - " 'isPackageURIEnabled',\n", - " 'isPkgEnabled',\n", - " 'isPkgURIEnabled',\n", - " 'isPopulatedAllElementIdList',\n", - " 'isPopulatedAllElementMetaIdList',\n", - " 'isPopulatedListFormulaUnitsData',\n", - " 'isSetAnnotation',\n", - " 'isSetAreaUnits',\n", - " 'isSetConversionFactor',\n", - " 'isSetCreatedDate',\n", - " 'isSetExtentUnits',\n", - " 'isSetId',\n", - " 'isSetIdAttribute',\n", - " 'isSetLengthUnits',\n", - " 'isSetMetaId',\n", - " 'isSetModelHistory',\n", - " 'isSetModifiedDate',\n", - " 'isSetName',\n", - " 'isSetNotes',\n", - " 'isSetSBOTerm',\n", - " 'isSetSubstanceUnits',\n", - " 'isSetTimeUnits',\n", - " 'isSetUserData',\n", - " 'isSetVolumeUnits',\n", - " 'length_units',\n", - " 'level',\n", - " 'line',\n", - " 'matchesRequiredSBMLNamespacesForAddition',\n", - " 'matchesSBMLNamespaces',\n", - " 'meta_id',\n", - " 'model',\n", - " 'multiplyAssignmentsToSIdByFunction',\n", - " 'name',\n", - " 'namespaces',\n", - " 'notes',\n", - " 'notes_string',\n", - " 'num_compartment_types',\n", - " 'num_compartments',\n", - " 'num_constraints',\n", - " 'num_cv_terms',\n", - " 'num_disabled_plugins',\n", - " 'num_events',\n", - " 'num_function_definitions',\n", - " 'num_initial_assignments',\n", - " 'num_modified_dates',\n", - " 'num_parameters',\n", - " 'num_plugins',\n", - " 'num_reactions',\n", - " 'num_rules',\n", - " 'num_species',\n", - " 'num_species_types',\n", - " 'num_species_with_boundary_condition',\n", - " 'num_unit_definitions',\n", - " 'package_core_version',\n", - " 'package_name',\n", - " 'package_version',\n", - " 'parameters',\n", - " 'populateAllElementIdList',\n", - " 'populateAllElementMetaIdList',\n", - " 'populateListFormulaUnitsData',\n", - " 'prefix',\n", - " 'prependStringToAllIdentifiers',\n", - " 'reactions',\n", - " 'read',\n", - " 'removeCompartment',\n", - " 'removeCompartmentType',\n", - " 'removeCompartmentTypes',\n", - " 'removeConstraint',\n", - " 'removeDuplicateAnnotations',\n", - " 'removeEvent',\n", - " 'removeFromParentAndDelete',\n", - " 'removeFunctionDefinition',\n", - " 'removeInitialAssignment',\n", - " 'removeListFormulaUnitsData',\n", - " 'removeParameter',\n", - " 'removeParameterRuleUnits',\n", - " 'removeReaction',\n", - " 'removeRule',\n", - " 'removeRuleByVariable',\n", - " 'removeSpecies',\n", - " 'removeSpeciesType',\n", - " 'removeSpeciesTypes',\n", - " 'removeTopLevelAnnotationElement',\n", - " 'removeUnitDefinition',\n", - " 'renameAllIds',\n", - " 'renameIDs',\n", - " 'renameMetaIdRefs',\n", - " 'renameSIdRefs',\n", - " 'renameUnitSIdRefs',\n", - " 'replaceSIDWithFunction',\n", - " 'replaceTopLevelAnnotationElement',\n", - " 'rules',\n", - " 'sbml_namespaces',\n", - " 'sbml_namespaces_and_own',\n", - " 'sbo_term',\n", - " 'sbo_term_as_url',\n", - " 'sbo_term_id',\n", - " 'setAnnotation',\n", - " 'setAreaUnits',\n", - " 'setConversionFactor',\n", - " 'setCreatedDate',\n", - " 'setExtentUnits',\n", - " 'setId',\n", - " 'setIdAttribute',\n", - " 'setLengthUnits',\n", - " 'setMetaId',\n", - " 'setModelHistory',\n", - " 'setName',\n", - " 'setNamespaces',\n", - " 'setNotes',\n", - " 'setSBMLNamespacesAndOwn',\n", - " 'setSBOTerm',\n", - " 'setSpatialDimensions',\n", - " 'setSpeciesReferenceConstantValueAndStoichiometry',\n", - " 'setSubstanceUnits',\n", - " 'setTimeUnits',\n", - " 'setVolumeUnits',\n", - " 'spatial_dimensions',\n", - " 'species',\n", - " 'species_reference_constant_value_and_stoichiometry',\n", - " 'species_types',\n", - " 'substance_units',\n", - " 'this',\n", - " 'thisown',\n", - " 'time_units',\n", - " 'toSBML',\n", - " 'toXMLNode',\n", - " 'transformIdentifiers',\n", - " 'type_code',\n", - " 'unit_definitions',\n", - " 'unsetAnnotation',\n", - " 'unsetAreaUnits',\n", - " 'unsetCVTerms',\n", - " 'unsetConversionFactor',\n", - " 'unsetCreatedDate',\n", - " 'unsetExtentUnits',\n", - " 'unsetId',\n", - " 'unsetIdAttribute',\n", - " 'unsetLengthUnits',\n", - " 'unsetMetaId',\n", - " 'unsetModelHistory',\n", - " 'unsetModifiedDates',\n", - " 'unsetName',\n", - " 'unsetNotes',\n", - " 'unsetSBOTerm',\n", - " 'unsetSubstanceUnits',\n", - " 'unsetTimeUnits',\n", - " 'unsetUserData',\n", - " 'unsetVolumeUnits',\n", - " 'updateSBMLNamespace',\n", - " 'uri',\n", - " 'version',\n", - " 'volume_units',\n", - " 'write',\n", - " 'writeExtensionElements']" - ] - }, - "execution_count": 39, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "dir(sbml_model)" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1598,37 +410,13 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "['cleavage of plasminogen',\n", - " 'activation of urokinase-type plasminogen activator',\n", - " 'activation of plasmin',\n", - " 'degradation of single intact chain urokinase-type plasminogen activator',\n", - " 'degradation of plasminogen',\n", - " 'degradation of plasmin',\n", - " 'degradation of two-chain urokinase type plasminogen activator',\n", - " 'reversible plasmin bonding x',\n", - " 'catalytic reaction of x-plasmin',\n", - " 'degradation of x',\n", - " 'degradation of x-plasmin',\n", - " 'synthesis of single intact chain urokinase-type plasminogen activator',\n", - " 'synthesis of plasminogen',\n", - " 'synthesis of x']" - ] - }, - "execution_count": 50, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "reaction_objects = sbml_model.reactions\n", "reaction_list = [reaction.getName() for reaction in reaction_objects]\n", "\n", "reaction_list" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1641,255 +429,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "['__class__',\n", - " '__delattr__',\n", - " '__dict__',\n", - " '__dir__',\n", - " '__doc__',\n", - " '__eq__',\n", - " '__format__',\n", - " '__ge__',\n", - " '__getattribute__',\n", - " '__gt__',\n", - " '__hash__',\n", - " '__init__',\n", - " '__init_subclass__',\n", - " '__le__',\n", - " '__lt__',\n", - " '__metaclass__',\n", - " '__module__',\n", - " '__ne__',\n", - " '__new__',\n", - " '__reduce__',\n", - " '__reduce_ex__',\n", - " '__repr__',\n", - " '__setattr__',\n", - " '__sizeof__',\n", - " '__str__',\n", - " '__subclasshook__',\n", - " '__swig_destroy__',\n", - " '__weakref__',\n", - " 'addCVTerm',\n", - " 'addModifiedDate',\n", - " 'addModifier',\n", - " 'addProduct',\n", - " 'addReactant',\n", - " 'all_elements',\n", - " 'all_elements_from_plugins',\n", - " 'annotation',\n", - " 'annotation_string',\n", - " 'appendAnnotation',\n", - " 'appendNotes',\n", - " 'checkCompatibility',\n", - " 'checkMathMLNamespace',\n", - " 'clone',\n", - " 'column',\n", - " 'compartment',\n", - " 'connectToChild',\n", - " 'connectToParent',\n", - " 'containsUndeclaredUnits',\n", - " 'createKineticLaw',\n", - " 'createModifier',\n", - " 'createProduct',\n", - " 'createReactant',\n", - " 'cv_terms',\n", - " 'deleteDisabledPlugins',\n", - " 'derived_unit_definition',\n", - " 'disablePackage',\n", - " 'divideAssignmentsToSIdByFunction',\n", - " 'element_name',\n", - " 'enablePackage',\n", - " 'enablePackageInternal',\n", - " 'fast',\n", - " 'getAncestorOfType',\n", - " 'getAnnotation',\n", - " 'getAnnotationString',\n", - " 'getCVTerm',\n", - " 'getCVTerms',\n", - " 'getColumn',\n", - " 'getCompartment',\n", - " 'getCreatedDate',\n", - " 'getDerivedUnitDefinition',\n", - " 'getDisabledPlugin',\n", - " 'getElementByMetaId',\n", - " 'getElementBySId',\n", - " 'getElementFromPluginsByMetaId',\n", - " 'getElementFromPluginsBySId',\n", - " 'getElementName',\n", - " 'getFast',\n", - " 'getId',\n", - " 'getIdAttribute',\n", - " 'getKineticLaw',\n", - " 'getLevel',\n", - " 'getLine',\n", - " 'getListOfAllElements',\n", - " 'getListOfAllElementsFromPlugins',\n", - " 'getListOfModifiers',\n", - " 'getListOfProducts',\n", - " 'getListOfReactants',\n", - " 'getMetaId',\n", - " 'getModel',\n", - " 'getModelHistory',\n", - " 'getModifiedDate',\n", - " 'getModifier',\n", - " 'getName',\n", - " 'getNamespaces',\n", - " 'getNotes',\n", - " 'getNotesString',\n", - " 'getNumCVTerms',\n", - " 'getNumDisabledPlugins',\n", - " 'getNumModifiedDates',\n", - " 'getNumModifiers',\n", - " 'getNumPlugins',\n", - " 'getNumProducts',\n", - " 'getNumReactants',\n", - " 'getPackageCoreVersion',\n", - " 'getPackageName',\n", - " 'getPackageVersion',\n", - " 'getParentSBMLObject',\n", - " 'getPlugin',\n", - " 'getPrefix',\n", - " 'getProduct',\n", - " 'getReactant',\n", - " 'getResourceBiologicalQualifier',\n", - " 'getResourceModelQualifier',\n", - " 'getReversible',\n", - " 'getSBMLDocument',\n", - " 'getSBMLNamespaces',\n", - " 'getSBOTerm',\n", - " 'getSBOTermAsURL',\n", - " 'getSBOTermID',\n", - " 'getTypeCode',\n", - " 'getURI',\n", - " 'getVersion',\n", - " 'hasNonstandardIdentifierBeginningWith',\n", - " 'hasOptionalAttributes',\n", - " 'hasOptionalElements',\n", - " 'hasRequiredAttributes',\n", - " 'hasRequiredElements',\n", - " 'hasValidLevelVersionNamespaceCombination',\n", - " 'id',\n", - " 'id_attribute',\n", - " 'initDefaults',\n", - " 'isPackageEnabled',\n", - " 'isPackageURIEnabled',\n", - " 'isPkgEnabled',\n", - " 'isPkgURIEnabled',\n", - " 'isSetAnnotation',\n", - " 'isSetCompartment',\n", - " 'isSetCreatedDate',\n", - " 'isSetFast',\n", - " 'isSetId',\n", - " 'isSetIdAttribute',\n", - " 'isSetKineticLaw',\n", - " 'isSetMetaId',\n", - " 'isSetModelHistory',\n", - " 'isSetModifiedDate',\n", - " 'isSetName',\n", - " 'isSetNotes',\n", - " 'isSetReversible',\n", - " 'isSetSBOTerm',\n", - " 'isSetUserData',\n", - " 'level',\n", - " 'line',\n", - " 'matchesRequiredSBMLNamespacesForAddition',\n", - " 'matchesSBMLNamespaces',\n", - " 'meta_id',\n", - " 'model',\n", - " 'modifiers',\n", - " 'multiplyAssignmentsToSIdByFunction',\n", - " 'name',\n", - " 'namespaces',\n", - " 'notes',\n", - " 'notes_string',\n", - " 'num_cv_terms',\n", - " 'num_disabled_plugins',\n", - " 'num_modified_dates',\n", - " 'num_modifiers',\n", - " 'num_plugins',\n", - " 'num_products',\n", - " 'num_reactants',\n", - " 'package_core_version',\n", - " 'package_name',\n", - " 'package_version',\n", - " 'prefix',\n", - " 'prependStringToAllIdentifiers',\n", - " 'products',\n", - " 'reactants',\n", - " 'read',\n", - " 'removeDuplicateAnnotations',\n", - " 'removeFromParentAndDelete',\n", - " 'removeModifier',\n", - " 'removeProduct',\n", - " 'removeReactant',\n", - " 'removeTopLevelAnnotationElement',\n", - " 'renameMetaIdRefs',\n", - " 'renameSIdRefs',\n", - " 'renameUnitSIdRefs',\n", - " 'replaceSIDWithFunction',\n", - " 'replaceTopLevelAnnotationElement',\n", - " 'reversible',\n", - " 'sbml_namespaces',\n", - " 'sbml_namespaces_and_own',\n", - " 'sbo_term',\n", - " 'sbo_term_as_url',\n", - " 'sbo_term_id',\n", - " 'setAnnotation',\n", - " 'setCompartment',\n", - " 'setCreatedDate',\n", - " 'setFast',\n", - " 'setId',\n", - " 'setIdAttribute',\n", - " 'setKineticLaw',\n", - " 'setMetaId',\n", - " 'setModelHistory',\n", - " 'setName',\n", - " 'setNamespaces',\n", - " 'setNotes',\n", - " 'setReversible',\n", - " 'setSBMLNamespacesAndOwn',\n", - " 'setSBOTerm',\n", - " 'this',\n", - " 'thisown',\n", - " 'toSBML',\n", - " 'toXMLNode',\n", - " 'transformIdentifiers',\n", - " 'type_code',\n", - " 'unsetAnnotation',\n", - " 'unsetCVTerms',\n", - " 'unsetCompartment',\n", - " 'unsetCreatedDate',\n", - " 'unsetFast',\n", - " 'unsetId',\n", - " 'unsetIdAttribute',\n", - " 'unsetKineticLaw',\n", - " 'unsetMetaId',\n", - " 'unsetModelHistory',\n", - " 'unsetModifiedDates',\n", - " 'unsetName',\n", - " 'unsetNotes',\n", - " 'unsetReversible',\n", - " 'unsetSBOTerm',\n", - " 'unsetUserData',\n", - " 'updateSBMLNamespace',\n", - " 'uri',\n", - " 'version',\n", - " 'write',\n", - " 'writeExtensionElements']" - ] - }, - "execution_count": 45, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "dir(reaction_objects[0])" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1902,23 +445,10 @@ }, "collapsed": false }, - "outputs": [ - { - "ename": "TypeError", - "evalue": "Wrong number or type of arguments for overloaded function 'Reaction_getProduct'.\n Possible C/C++ prototypes are:\n Reaction::getProduct(unsigned int) const\n Reaction::getProduct(unsigned int)\n Reaction::getProduct(std::string const &) const\n Reaction::getProduct(std::string const &)\n", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m/var/folders/5d/d79js_zj5b7dwk7h0sr8m23c0000gn/T/ipykernel_66466/3781945296.py\u001b[0m in \u001b[0;36m?\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mreaction_objects\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgetProduct\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-ECOqdsTs-py3.10/lib/python3.10/site-packages/libsbml/__init__.py\u001b[0m in \u001b[0;36m?\u001b[0;34m(self, *args)\u001b[0m\n\u001b[1;32m 32429\u001b[0m \u001b[0mReturns\u001b[0m \u001b[0ma\u001b[0m \u001b[0mSpeciesReference\u001b[0m \u001b[0mobject\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0;34m'None'\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mno\u001b[0m \u001b[0mspecies\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mthe\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 32430\u001b[0m \u001b[0mgiven\u001b[0m \u001b[0midentifier\u001b[0m \u001b[0;34m'species'\u001b[0m \u001b[0mappears\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0ma\u001b[0m \u001b[0mproduct\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mthis\u001b[0m \u001b[0mReaction\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 32431\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 32432\u001b[0m \"\"\"\n\u001b[0;32m> 32433\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0m_libsbml\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mReaction_getProduct\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;31mTypeError\u001b[0m: Wrong number or type of arguments for overloaded function 'Reaction_getProduct'.\n Possible C/C++ prototypes are:\n Reaction::getProduct(unsigned int) const\n Reaction::getProduct(unsigned int)\n Reaction::getProduct(std::string const &) const\n Reaction::getProduct(std::string const &)\n" - ] - } - ], "source": [ "reaction_objects[0].getProduct()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -1931,409 +461,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "['__class__',\n", - " '__delattr__',\n", - " '__dict__',\n", - " '__dir__',\n", - " '__doc__',\n", - " '__eq__',\n", - " '__format__',\n", - " '__ge__',\n", - " '__getattribute__',\n", - " '__gt__',\n", - " '__hash__',\n", - " '__init__',\n", - " '__init_subclass__',\n", - " '__le__',\n", - " '__lt__',\n", - " '__metaclass__',\n", - " '__module__',\n", - " '__ne__',\n", - " '__new__',\n", - " '__parent_ref__',\n", - " '__reduce__',\n", - " '__reduce_ex__',\n", - " '__repr__',\n", - " '__setattr__',\n", - " '__sizeof__',\n", - " '__str__',\n", - " '__subclasshook__',\n", - " '__swig_destroy__',\n", - " '__weakref__',\n", - " 'addCVTerm',\n", - " 'addCompartment',\n", - " 'addCompartmentType',\n", - " 'addConstantAttribute',\n", - " 'addConstraint',\n", - " 'addDefinitionsForDefaultUnits',\n", - " 'addEvent',\n", - " 'addFunctionDefinition',\n", - " 'addInitialAssignment',\n", - " 'addModifiedDate',\n", - " 'addModifiers',\n", - " 'addParameter',\n", - " 'addReaction',\n", - " 'addRule',\n", - " 'addSpecies',\n", - " 'addSpeciesType',\n", - " 'addUnitDefinition',\n", - " 'all_element_id_list',\n", - " 'all_element_meta_id_list',\n", - " 'all_elements',\n", - " 'all_elements_from_plugins',\n", - " 'annotation',\n", - " 'annotation_string',\n", - " 'appendAnnotation',\n", - " 'appendFrom',\n", - " 'appendNotes',\n", - " 'area_units',\n", - " 'assignRequiredValues',\n", - " 'checkCompatibility',\n", - " 'checkMathMLNamespace',\n", - " 'clearAllElementIdList',\n", - " 'clearAllElementMetaIdList',\n", - " 'clone',\n", - " 'column',\n", - " 'compartment_types',\n", - " 'compartments',\n", - " 'connectToChild',\n", - " 'connectToParent',\n", - " 'constraints',\n", - " 'containsUndeclaredUnits',\n", - " 'conversion_factor',\n", - " 'convertFromL3V2',\n", - " 'convertL1ToL2',\n", - " 'convertL1ToL3',\n", - " 'convertL2ToL1',\n", - " 'convertL2ToL3',\n", - " 'convertL3ToL1',\n", - " 'convertL3ToL2',\n", - " 'convertParametersToLocals',\n", - " 'convertStoichiometryMath',\n", - " 'createAlgebraicRule',\n", - " 'createAssignmentRule',\n", - " 'createCompartment',\n", - " 'createCompartmentType',\n", - " 'createConstraint',\n", - " 'createDelay',\n", - " 'createEvent',\n", - " 'createEventAssignment',\n", - " 'createFunctionDefinition',\n", - " 'createInitialAssignment',\n", - " 'createKineticLaw',\n", - " 'createKineticLawLocalParameter',\n", - " 'createKineticLawParameter',\n", - " 'createModifier',\n", - " 'createParameter',\n", - " 'createProduct',\n", - " 'createRateRule',\n", - " 'createReactant',\n", - " 'createReaction',\n", - " 'createSpecies',\n", - " 'createSpeciesType',\n", - " 'createTrigger',\n", - " 'createUnit',\n", - " 'createUnitDefinition',\n", - " 'cv_terms',\n", - " 'dealWithDefaultValues',\n", - " 'dealWithEvents',\n", - " 'dealWithFast',\n", - " 'dealWithL3Fast',\n", - " 'dealWithModelUnits',\n", - " 'dealWithStoichiometry',\n", - " 'deleteDisabledPlugins',\n", - " 'derived_unit_definition',\n", - " 'disablePackage',\n", - " 'divideAssignmentsToSIdByFunction',\n", - " 'element_name',\n", - " 'enablePackage',\n", - " 'enablePackageInternal',\n", - " 'events',\n", - " 'extent_units',\n", - " 'function_definitions',\n", - " 'getAllElementIdList',\n", - " 'getAllElementMetaIdList',\n", - " 'getAncestorOfType',\n", - " 'getAnnotation',\n", - " 'getAnnotationString',\n", - " 'getAreaUnits',\n", - " 'getAssignmentRule',\n", - " 'getAssignmentRuleByVariable',\n", - " 'getCVTerm',\n", - " 'getCVTerms',\n", - " 'getColumn',\n", - " 'getCompartment',\n", - " 'getCompartmentType',\n", - " 'getConstraint',\n", - " 'getConversionFactor',\n", - " 'getCreatedDate',\n", - " 'getDerivedUnitDefinition',\n", - " 'getDisabledPlugin',\n", - " 'getElementByMetaId',\n", - " 'getElementBySId',\n", - " 'getElementFromPluginsByMetaId',\n", - " 'getElementFromPluginsBySId',\n", - " 'getElementName',\n", - " 'getEvent',\n", - " 'getExtentUnits',\n", - " 'getFormulaUnitsDataForAssignment',\n", - " 'getFormulaUnitsDataForVariable',\n", - " 'getFunctionDefinition',\n", - " 'getId',\n", - " 'getIdAttribute',\n", - " 'getInitialAssignment',\n", - " 'getInitialAssignmentBySymbol',\n", - " 'getLengthUnits',\n", - " 'getLevel',\n", - " 'getLine',\n", - " 'getListOfAllElements',\n", - " 'getListOfAllElementsFromPlugins',\n", - " 'getListOfCompartmentTypes',\n", - " 'getListOfCompartments',\n", - " 'getListOfConstraints',\n", - " 'getListOfEvents',\n", - " 'getListOfFunctionDefinitions',\n", - " 'getListOfInitialAssignments',\n", - " 'getListOfParameters',\n", - " 'getListOfReactions',\n", - " 'getListOfRules',\n", - " 'getListOfSpecies',\n", - " 'getListOfSpeciesTypes',\n", - " 'getListOfUnitDefinitions',\n", - " 'getMetaId',\n", - " 'getModel',\n", - " 'getModelHistory',\n", - " 'getModifiedDate',\n", - " 'getModifierSpeciesReference',\n", - " 'getName',\n", - " 'getNamespaces',\n", - " 'getNotes',\n", - " 'getNotesString',\n", - " 'getNumCVTerms',\n", - " 'getNumCompartmentTypes',\n", - " 'getNumCompartments',\n", - " 'getNumConstraints',\n", - " 'getNumDisabledPlugins',\n", - " 'getNumEvents',\n", - " 'getNumFunctionDefinitions',\n", - " 'getNumInitialAssignments',\n", - " 'getNumModifiedDates',\n", - " 'getNumParameters',\n", - " 'getNumPlugins',\n", - " 'getNumReactions',\n", - " 'getNumRules',\n", - " 'getNumSpecies',\n", - " 'getNumSpeciesTypes',\n", - " 'getNumSpeciesWithBoundaryCondition',\n", - " 'getNumUnitDefinitions',\n", - " 'getPackageCoreVersion',\n", - " 'getPackageName',\n", - " 'getPackageVersion',\n", - " 'getParameter',\n", - " 'getParentSBMLObject',\n", - " 'getPlugin',\n", - " 'getPrefix',\n", - " 'getRateRule',\n", - " 'getRateRuleByVariable',\n", - " 'getReaction',\n", - " 'getResourceBiologicalQualifier',\n", - " 'getResourceModelQualifier',\n", - " 'getRule',\n", - " 'getRuleByVariable',\n", - " 'getSBMLDocument',\n", - " 'getSBMLNamespaces',\n", - " 'getSBOTerm',\n", - " 'getSBOTermAsURL',\n", - " 'getSBOTermID',\n", - " 'getSpecies',\n", - " 'getSpeciesReference',\n", - " 'getSpeciesType',\n", - " 'getSubstanceUnits',\n", - " 'getTimeUnits',\n", - " 'getTypeCode',\n", - " 'getURI',\n", - " 'getUnitDefinition',\n", - " 'getVersion',\n", - " 'getVolumeUnits',\n", - " 'hasNonstandardIdentifierBeginningWith',\n", - " 'hasOptionalAttributes',\n", - " 'hasOptionalElements',\n", - " 'hasRequiredAttributes',\n", - " 'hasRequiredElements',\n", - " 'hasValidLevelVersionNamespaceCombination',\n", - " 'id',\n", - " 'id_attribute',\n", - " 'initial_assignments',\n", - " 'isPackageEnabled',\n", - " 'isPackageURIEnabled',\n", - " 'isPkgEnabled',\n", - " 'isPkgURIEnabled',\n", - " 'isPopulatedAllElementIdList',\n", - " 'isPopulatedAllElementMetaIdList',\n", - " 'isPopulatedListFormulaUnitsData',\n", - " 'isSetAnnotation',\n", - " 'isSetAreaUnits',\n", - " 'isSetConversionFactor',\n", - " 'isSetCreatedDate',\n", - " 'isSetExtentUnits',\n", - " 'isSetId',\n", - " 'isSetIdAttribute',\n", - " 'isSetLengthUnits',\n", - " 'isSetMetaId',\n", - " 'isSetModelHistory',\n", - " 'isSetModifiedDate',\n", - " 'isSetName',\n", - " 'isSetNotes',\n", - " 'isSetSBOTerm',\n", - " 'isSetSubstanceUnits',\n", - " 'isSetTimeUnits',\n", - " 'isSetUserData',\n", - " 'isSetVolumeUnits',\n", - " 'length_units',\n", - " 'level',\n", - " 'line',\n", - " 'matchesRequiredSBMLNamespacesForAddition',\n", - " 'matchesSBMLNamespaces',\n", - " 'meta_id',\n", - " 'model',\n", - " 'multiplyAssignmentsToSIdByFunction',\n", - " 'name',\n", - " 'namespaces',\n", - " 'notes',\n", - " 'notes_string',\n", - " 'num_compartment_types',\n", - " 'num_compartments',\n", - " 'num_constraints',\n", - " 'num_cv_terms',\n", - " 'num_disabled_plugins',\n", - " 'num_events',\n", - " 'num_function_definitions',\n", - " 'num_initial_assignments',\n", - " 'num_modified_dates',\n", - " 'num_parameters',\n", - " 'num_plugins',\n", - " 'num_reactions',\n", - " 'num_rules',\n", - " 'num_species',\n", - " 'num_species_types',\n", - " 'num_species_with_boundary_condition',\n", - " 'num_unit_definitions',\n", - " 'package_core_version',\n", - " 'package_name',\n", - " 'package_version',\n", - " 'parameters',\n", - " 'populateAllElementIdList',\n", - " 'populateAllElementMetaIdList',\n", - " 'populateListFormulaUnitsData',\n", - " 'prefix',\n", - " 'prependStringToAllIdentifiers',\n", - " 'reactions',\n", - " 'read',\n", - " 'removeCompartment',\n", - " 'removeCompartmentType',\n", - " 'removeCompartmentTypes',\n", - " 'removeConstraint',\n", - " 'removeDuplicateAnnotations',\n", - " 'removeEvent',\n", - " 'removeFromParentAndDelete',\n", - " 'removeFunctionDefinition',\n", - " 'removeInitialAssignment',\n", - " 'removeListFormulaUnitsData',\n", - " 'removeParameter',\n", - " 'removeParameterRuleUnits',\n", - " 'removeReaction',\n", - " 'removeRule',\n", - " 'removeRuleByVariable',\n", - " 'removeSpecies',\n", - " 'removeSpeciesType',\n", - " 'removeSpeciesTypes',\n", - " 'removeTopLevelAnnotationElement',\n", - " 'removeUnitDefinition',\n", - " 'renameAllIds',\n", - " 'renameIDs',\n", - " 'renameMetaIdRefs',\n", - " 'renameSIdRefs',\n", - " 'renameUnitSIdRefs',\n", - " 'replaceSIDWithFunction',\n", - " 'replaceTopLevelAnnotationElement',\n", - " 'rules',\n", - " 'sbml_namespaces',\n", - " 'sbml_namespaces_and_own',\n", - " 'sbo_term',\n", - " 'sbo_term_as_url',\n", - " 'sbo_term_id',\n", - " 'setAnnotation',\n", - " 'setAreaUnits',\n", - " 'setConversionFactor',\n", - " 'setCreatedDate',\n", - " 'setExtentUnits',\n", - " 'setId',\n", - " 'setIdAttribute',\n", - " 'setLengthUnits',\n", - " 'setMetaId',\n", - " 'setModelHistory',\n", - " 'setName',\n", - " 'setNamespaces',\n", - " 'setNotes',\n", - " 'setSBMLNamespacesAndOwn',\n", - " 'setSBOTerm',\n", - " 'setSpatialDimensions',\n", - " 'setSpeciesReferenceConstantValueAndStoichiometry',\n", - " 'setSubstanceUnits',\n", - " 'setTimeUnits',\n", - " 'setVolumeUnits',\n", - " 'spatial_dimensions',\n", - " 'species',\n", - " 'species_reference_constant_value_and_stoichiometry',\n", - " 'species_types',\n", - " 'substance_units',\n", - " 'this',\n", - " 'thisown',\n", - " 'time_units',\n", - " 'toSBML',\n", - " 'toXMLNode',\n", - " 'transformIdentifiers',\n", - " 'type_code',\n", - " 'unit_definitions',\n", - " 'unsetAnnotation',\n", - " 'unsetAreaUnits',\n", - " 'unsetCVTerms',\n", - " 'unsetConversionFactor',\n", - " 'unsetCreatedDate',\n", - " 'unsetExtentUnits',\n", - " 'unsetId',\n", - " 'unsetIdAttribute',\n", - " 'unsetLengthUnits',\n", - " 'unsetMetaId',\n", - " 'unsetModelHistory',\n", - " 'unsetModifiedDates',\n", - " 'unsetName',\n", - " 'unsetNotes',\n", - " 'unsetSBOTerm',\n", - " 'unsetSubstanceUnits',\n", - " 'unsetTimeUnits',\n", - " 'unsetUserData',\n", - " 'unsetVolumeUnits',\n", - " 'updateSBMLNamespace',\n", - " 'uri',\n", - " 'version',\n", - " 'volume_units',\n", - " 'write',\n", - " 'writeExtensionElements']" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "dir(sbml_model)" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2346,32 +477,6 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'simple_amici': {'_type': 'process',\n", - " 'address': 'local:copasi',\n", - " 'config': {'model': {'model_source': '../biosimulator_processes/model_files/sbml/BIOMD0000000630_url.xml'}},\n", - " 'inputs': {'floating_species_concentrations': ['floating_species_concentrations_store'],\n", - " 'model_parameters': ['model_parameters_store'],\n", - " 'time': ['time_store'],\n", - " 'reactions': ['reactions_store']},\n", - " 'outputs': {'floating_species_concentrations': ['floating_species_concentrations_store'],\n", - " 'time': ['time_store']}},\n", - " 'emitter': {'emitter': {'_type': 'step',\n", - " 'address': 'local:ram-emitter',\n", - " 'config': {'emit': {'floating_species_concentrations': 'tree[float]',\n", - " 'time': 'float'}},\n", - " 'inputs': {'floating_species_concentrations': ['floating_species_concentrations_store'],\n", - " 'time': ['time_store']}}}}" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "from biosimulator_processes.processes.amici_process import AmiciProcess\n", "\n", @@ -2383,7 +488,8 @@ " sbml_model_fp=model_fp)\n", "\n", "amici_process_document" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2396,10 +502,10 @@ }, "collapsed": false }, - "outputs": [], "source": [ "amici_process_config = amici_process_document[process_id]['config']" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2412,21 +518,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'model': {'model_source': '../biosimulator_processes/model_files/sbml/BIOMD0000000630_url.xml'}}" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "amici_process_config" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2439,20 +534,12 @@ }, "collapsed": false }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "found a filepath\n" - ] - } - ], "source": [ "amici_workflow = Composite(\n", " config={'state': amici_process_document},\n", " core=CORE)" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2465,10 +552,10 @@ }, "collapsed": false }, - "outputs": [], "source": [ "amici_process: AmiciProcess = amici_workflow.state[process_id]['instance']" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2481,30 +568,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'time': 0.0,\n", - " 'model_parameters': {'degradation constant 1': 0.084,\n", - " 'degradation constant 2': 0.032,\n", - " 'hill cooperativity': 2.0},\n", - " 'floating_species_concentrations': {'plasminogen': 6022140760000000.0,\n", - " 'plasmin': 0.0,\n", - " 'single intact chain urokinase-type plasminogen activator': 1204428152000000.0,\n", - " 'two-chain urokinase-type plasminogen activator': 0.0,\n", - " 'x': 0.0,\n", - " 'x-plasmin': 0.0}}" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "amici_process.initial_state()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2517,34 +584,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "['cleavage of plasminogen',\n", - " 'activation of urokinase-type plasminogen activator',\n", - " 'activation of plasmin',\n", - " 'degradation of single intact chain urokinase-type plasminogen activator',\n", - " 'degradation of plasminogen',\n", - " 'degradation of plasmin',\n", - " 'degradation of two-chain urokinase type plasminogen activator',\n", - " 'reversible plasmin bonding x',\n", - " 'catalytic reaction of x-plasmin',\n", - " 'degradation of x',\n", - " 'degradation of x-plasmin',\n", - " 'synthesis of single intact chain urokinase-type plasminogen activator',\n", - " 'synthesis of plasminogen',\n", - " 'synthesis of x']" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "amici_process.reaction_list" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2557,30 +600,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "{'time': 0.0,\n", - " 'model_parameters': {'degradation constant 1': 0.084,\n", - " 'degradation constant 2': 0.032,\n", - " 'hill cooperativity': 2.0},\n", - " 'floating_species_concentrations': {'plasminogen': 6022140760000000.0,\n", - " 'plasmin': 0.0,\n", - " 'single intact chain urokinase-type plasminogen activator': 1204428152000000.0,\n", - " 'two-chain urokinase-type plasminogen activator': 0.0,\n", - " 'x': 0.0,\n", - " 'x-plasmin': 0.0}}" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "amici_process.initial_state()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2593,15 +616,6 @@ }, "collapsed": false }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "found a filepath\n" - ] - } - ], "source": [ "# Let's compare that against copasi process\n", "from biosimulator_processes.processes.copasi_process import CopasiProcess\n", @@ -2609,7 +623,8 @@ "\n", "copasi_process: CopasiProcess = CopasiProcess(\n", " config=comparison_document.composite['copasi_0']['config'])" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2622,21 +637,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "True" - ] - }, - "execution_count": 32, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "copasi_process.outputs() == amici_process.outputs()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2649,21 +653,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "True" - ] - }, - "execution_count": 33, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "amici_process.initial_state() == copasi_process.initial_state()" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2676,21 +669,10 @@ }, "collapsed": false }, - "outputs": [ - { - "data": { - "text/plain": [ - "True" - ] - }, - "execution_count": 34, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "copasi_process.reaction_list == amici_process.reaction_list" - ] + ], + "outputs": [] }, { "cell_type": "code", @@ -2699,8 +681,8 @@ "metadata": { "collapsed": false }, - "outputs": [], - "source": [] + "source": [], + "outputs": [] } ], "metadata": { diff --git a/demos/comparison_api_demo.ipynb b/demos/comparison_api_demo.ipynb index a53a34dd9..8be089e00 100644 --- a/demos/comparison_api_demo.ipynb +++ b/demos/comparison_api_demo.ipynb @@ -46,6 +46,41 @@ }, "id": "159305ff5f3dc676" }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2024-05-09T17:19:29.172101Z", + "start_time": "2024-05-09T17:19:29.168073Z" + } + }, + "cell_type": "code", + "source": [ + "import numpy as np \n", + "\n", + "y = np.array([0.5, 1.0, 0.75, 0.60, 0.66])\n", + "\n", + "average_y = np.mean(y)\n", + "\n", + "# Calculate the MSE for each value in y with respect to the average\n", + "mse_scores = (y - average_y) ** 2\n", + "\n", + "mse_scores, average_y" + ], + "id": "521b15f5cec33415", + "outputs": [ + { + "data": { + "text/plain": [ + "(array([0.040804, 0.088804, 0.002304, 0.010404, 0.001764]), 0.7020000000000001)" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "execution_count": 18 + }, { "cell_type": "code", "execution_count": 2, diff --git a/demos/compositions.ipynb b/demos/compositions.ipynb index 27bceaf9e..687f16227 100644 --- a/demos/compositions.ipynb +++ b/demos/compositions.ipynb @@ -3,7 +3,6 @@ { "cell_type": "code", "execution_count": 1, - "outputs": [], "source": [ "import sys\n", "\n", @@ -20,24 +19,12 @@ "start_time": "2024-05-01T08:45:09.646937Z" } }, - "id": "24fc5d62890368dd" + "id": "24fc5d62890368dd", + "outputs": [] }, { "cell_type": "code", "execution_count": 2, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CobraProcess registered successfully.\n", - "CopasiProcess registered successfully.\n", - "SmoldynProcess not available. Error: \n", - "PLEASE NOTE: Smoldyn is not correctly installed on your system which prevents you from using the SmoldynProcess. Please refer to the README for further information on installing Smoldyn.\n", - "TelluriumProcess registered successfully.\n" - ] - } - ], "source": [ "from biosimulator_processes.compare import ComparisonDocument\n", "from biosimulator_processes import CORE\n", @@ -50,7 +37,8 @@ "start_time": "2024-05-01T08:45:10.281028Z" } }, - "id": "1dc1ba69e5acc44" + "id": "1dc1ba69e5acc44", + "outputs": [] }, { "cell_type": "markdown", @@ -65,7 +53,6 @@ { "cell_type": "code", "execution_count": 3, - "outputs": [], "source": [ "simulators = ['copasi', 'tellurium'] # , 'amici']\n", "duration = 30\n", @@ -82,45 +69,12 @@ "start_time": "2024-05-01T06:59:32.976561Z" } }, - "id": "d9fce82a600bb9af" + "id": "d9fce82a600bb9af", + "outputs": [] }, { "cell_type": "code", "execution_count": 4, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{ 'processes': { 'copasi_0': { '_type': 'process',\n", - " 'address': 'local:copasi',\n", - " 'config': { 'model': { 'model_source': '../biosimulator_processes/model_files/sbml/Caravagna2010.xml'}},\n", - " 'inputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'model_parameters': [ 'model_parameters_store'],\n", - " 'reactions': ['reactions_store'],\n", - " 'time': ['time_store']},\n", - " 'outputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'time': ['time_store']}},\n", - " 'duration': 30,\n", - " 'emitter': { '_type': 'step',\n", - " 'address': 'local:ram-emitter',\n", - " 'config': { 'emit': { 'floating_species_concentrations': 'tree[float]',\n", - " 'time': 'float'}},\n", - " 'inputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'time': ['time_store']}},\n", - " 'num_steps': 200,\n", - " 'tellurium_1': { '_type': 'process',\n", - " 'address': 'local:tellurium',\n", - " 'config': { 'model': { 'model_source': '../biosimulator_processes/model_files/sbml/Caravagna2010.xml'}},\n", - " 'inputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'model_parameters': [ 'model_parameters_store'],\n", - " 'reactions': ['reactions_store'],\n", - " 'time': ['time_store']},\n", - " 'outputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'time': ['time_store']}}}}\n" - ] - } - ], "source": [ "pp(comparison.composite)" ], @@ -131,7 +85,8 @@ "start_time": "2024-05-01T06:59:32.981251Z" } }, - "id": "57a94e90c5c2ba41" + "id": "57a94e90c5c2ba41", + "outputs": [] }, { "cell_type": "markdown", @@ -146,7 +101,6 @@ { "cell_type": "code", "execution_count": 5, - "outputs": [], "source": [ "from biosimulator_processes.compare import ComparisonDocument\n", "\n", @@ -190,45 +144,12 @@ "start_time": "2024-05-01T06:59:32.986334Z" } }, - "id": "3cc9032bbca74784" + "id": "3cc9032bbca74784", + "outputs": [] }, { "cell_type": "code", "execution_count": 6, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{ 'processes': { 'copasi_0': { '_type': 'process',\n", - " 'address': 'local:copasi',\n", - " 'config': { 'model': { 'model_source': '../biosimulator_processes/model_files/sbml/BIOMD0000000630_url.xml'}},\n", - " 'inputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'model_parameters': [ 'model_parameters_store'],\n", - " 'reactions': ['reactions_store'],\n", - " 'time': ['time_store']},\n", - " 'outputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'time': ['time_store']}},\n", - " 'copasi_1': { '_type': 'process',\n", - " 'address': 'local:copasi',\n", - " 'config': { 'model': { 'model_source': '../biosimulator_processes/model_files/sbml/BIOMD0000000630_url.xml'}},\n", - " 'inputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'model_parameters': [ 'model_parameters_store'],\n", - " 'reactions': ['reactions_store'],\n", - " 'time': ['time_store']},\n", - " 'outputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'time': ['time_store']}},\n", - " 'duration': 30,\n", - " 'emitter': { '_type': 'step',\n", - " 'address': 'local:ram-emitter',\n", - " 'config': { 'emit': { 'floating_species_concentrations': 'tree[float]',\n", - " 'time': 'float'}},\n", - " 'inputs': { 'floating_species_concentrations': [ 'floating_species_concentrations_store'],\n", - " 'time': ['time_store']}},\n", - " 'num_steps': 50}}\n" - ] - } - ], "source": [ "pp(ode_comparison_document.composite)" ], @@ -239,21 +160,12 @@ "start_time": "2024-05-01T06:59:33.496658Z" } }, - "id": "5f99df92f1acbf52" + "id": "5f99df92f1acbf52", + "outputs": [] }, { "cell_type": "code", "execution_count": 7, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "found a filepath\n", - "found a filepath\n" - ] - } - ], "source": [ "ode_comparison_workflow = Composite(config={'state': ode_comparison_document.composite}, core=CORE)" ], @@ -264,12 +176,12 @@ "start_time": "2024-05-01T06:59:34.257050Z" } }, - "id": "9c44bd491ad5ddb0" + "id": "9c44bd491ad5ddb0", + "outputs": [] }, { "cell_type": "code", "execution_count": 8, - "outputs": [], "source": [ "ode_comparison_workflow.run(duration)\n", "ode_comparison_results = ode_comparison_workflow.gather_results()" @@ -281,21 +193,12 @@ "start_time": "2024-05-01T06:59:34.946595Z" } }, - "id": "a52b1903520045a0" + "id": "a52b1903520045a0", + "outputs": [] }, { "cell_type": "code", "execution_count": 9, - "outputs": [ - { - "data": { - "text/plain": "{}" - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "ode_comparison_results" ], @@ -306,12 +209,12 @@ "start_time": "2024-05-01T06:59:35.539397Z" } }, - "id": "806d60012d71a2eb" + "id": "806d60012d71a2eb", + "outputs": [] }, { "cell_type": "code", "execution_count": 9, - "outputs": [], "source": [], "metadata": { "collapsed": false, @@ -320,12 +223,12 @@ "start_time": "2024-05-01T06:56:28.160529Z" } }, - "id": "da55f1556e28363f" + "id": "da55f1556e28363f", + "outputs": [] }, { "cell_type": "code", "execution_count": 9, - "outputs": [], "source": [], "metadata": { "collapsed": false, @@ -334,12 +237,12 @@ "start_time": "2024-05-01T06:56:28.163347Z" } }, - "id": "3330d11b7b80252b" + "id": "3330d11b7b80252b", + "outputs": [] }, { "cell_type": "code", "execution_count": 10, - "outputs": [], "source": [ "import tellurium as te\n", "\n", @@ -352,21 +255,12 @@ "start_time": "2024-05-01T06:56:28.167336Z" } }, - "id": "5f07a08ac835b2b5" + "id": "5f07a08ac835b2b5", + "outputs": [] }, { "cell_type": "code", "execution_count": 11, - "outputs": [ - { - "data": { - "text/plain": "['_ExtendedRoadRunner__getSBML',\n '_RoadRunner__simulateOld',\n '_RoadRunner__simulateOptions',\n '__class__',\n '__delattr__',\n '__dict__',\n '__dir__',\n '__doc__',\n '__eq__',\n '__format__',\n '__ge__',\n '__getattr__',\n '__getattribute__',\n '__getitem__',\n '__getstate__',\n '__gt__',\n '__hash__',\n '__init__',\n '__init_subclass__',\n '__le__',\n '__len__',\n '__lt__',\n '__module__',\n '__ne__',\n '__new__',\n '__reduce__',\n '__reduce_ex__',\n '__repr__',\n '__setattr__',\n '__setitem__',\n '__setstate__',\n '__sizeof__',\n '__str__',\n '__subclasshook__',\n '__swig_destroy__',\n '__weakref__',\n '_addCompartment',\n '_addParameter',\n '_addReaction',\n '_addSpeciesAmount',\n '_addSpeciesConcentration',\n '_diffstep_getter',\n '_diffstep_stter',\n '_getConservedMoietyAnalysis',\n '_getDependentFloatingSpeciesIds',\n '_getIds',\n '_getIndependentFloatingSpeciesIds',\n '_getModel',\n '_getSelections',\n '_getSteadyStateSelections',\n '_getValue',\n '_load',\n '_makeProperties',\n '_model_functions',\n '_new_init',\n '_properties',\n '_setConservedMoietyAnalysis',\n '_setConservedMoietyAnalysisProxy',\n '_setSelections',\n '_setSimulateOptionsTimes',\n '_setSteadyStateSelections',\n '_simulate',\n '_steadyStateThresh_getter',\n '_steadyStateThresh_setter',\n '_swig_init',\n 'addAssignmentRule',\n 'addCompartment',\n 'addDelay',\n 'addEvent',\n 'addEventAssignment',\n 'addInitialAssignment',\n 'addParameter',\n 'addPriority',\n 'addRateRule',\n 'addReaction',\n 'addSpecies',\n 'addSpeciesAmount',\n 'addSpeciesConcentration',\n 'addTrigger',\n 'bs',\n 'clearModel',\n 'compartment_1',\n 'conservedMoietyAnalysis',\n 'createSelection',\n 'diffstep',\n 'draw',\n 'dv',\n 'exportToAntimony',\n 'exportToCellML',\n 'exportToMatlab',\n 'exportToSBML',\n 'fjac',\n 'fs',\n 'getAntimony',\n 'getAssignmentRuleIds',\n 'getAvailableIntegrators',\n 'getBoundarySpeciesAmounts',\n 'getBoundarySpeciesAmountsNamedArray',\n 'getBoundarySpeciesConcentrationIds',\n 'getBoundarySpeciesConcentrations',\n 'getBoundarySpeciesConcentrationsNamedArray',\n 'getBoundarySpeciesIds',\n 'getCC',\n 'getCellML',\n 'getCompartmentIds',\n 'getCompartmentVolumes',\n 'getCompiler',\n 'getConservationMatrix',\n 'getConservedMoietyIds',\n 'getConservedMoietyValues',\n 'getCurrentAntimony',\n 'getCurrentCellML',\n 'getCurrentMatlab',\n 'getCurrentSBML',\n 'getCurrentTime',\n 'getDependentFloatingSpeciesAmountsNamedArray',\n 'getDependentFloatingSpeciesAmountsV',\n 'getDependentFloatingSpeciesConcentrationsNamedArray',\n 'getDependentFloatingSpeciesConcentrationsV',\n 'getDependentFloatingSpeciesIds',\n 'getDependentRatesOfChange',\n 'getDependentRatesOfChangeNamedArray',\n 'getDiffStepSize',\n 'getEE',\n 'getEigenValueIds',\n 'getExistingIntegratorNames',\n 'getExistingSensitivitySolverNames',\n 'getExistingSteadyStateSolverNames',\n 'getExtendedStoichiometryMatrix',\n 'getExtendedVersionInfo',\n 'getFloatingSpeciesAmounts',\n 'getFloatingSpeciesAmountsNamedArray',\n 'getFloatingSpeciesConcentrationIds',\n 'getFloatingSpeciesConcentrations',\n 'getFloatingSpeciesConcentrationsNamedArray',\n 'getFloatingSpeciesIds',\n 'getFloatingSpeciesInitialConcentrationIds',\n 'getFluxThreshold',\n 'getFrequencyResponse',\n 'getFullEigenValues',\n 'getFullEigenValuesNamedArray',\n 'getFullJacobian',\n 'getFullStoichiometryMatrix',\n 'getGlobalParameterByName',\n 'getGlobalParameterIds',\n 'getGlobalParameterValues',\n 'getHasOnlySubstanceUnits',\n 'getIds',\n 'getIndependentFloatingSpeciesAmountsNamedArray',\n 'getIndependentFloatingSpeciesAmountsV',\n 'getIndependentFloatingSpeciesConcentrationsNamedArray',\n 'getIndependentFloatingSpeciesConcentrationsV',\n 'getIndependentFloatingSpeciesIds',\n 'getIndependentRatesOfChange',\n 'getIndependentRatesOfChangeNamedArray',\n 'getInfo',\n 'getInitialAssignmentIds',\n 'getInstanceCount',\n 'getInstanceID',\n 'getIntegrator',\n 'getIntegratorByName',\n 'getKMatrix',\n 'getKineticLaw',\n 'getL0Matrix',\n 'getLinkMatrix',\n 'getMatlab',\n 'getModel',\n 'getModelId',\n 'getModelName',\n 'getNrMatrix',\n 'getNumBoundarySpecies',\n 'getNumCompartments',\n 'getNumConservedMoieties',\n 'getNumDepFloatingSpecies',\n 'getNumEvents',\n 'getNumFloatingSpecies',\n 'getNumGlobalParameters',\n 'getNumIndFloatingSpecies',\n 'getNumRateRules',\n 'getNumReactions',\n 'getNumberOfDependentSpecies',\n 'getNumberOfIndependentSpecies',\n 'getParamPromotedSBML',\n 'getRateRuleIds',\n 'getRatesOfChange',\n 'getRatesOfChangeNamedArray',\n 'getReactionIds',\n 'getReactionRates',\n 'getReducedEigenValues',\n 'getReducedEigenValuesNamedArray',\n 'getReducedJacobian',\n 'getReducedStoichiometryMatrix',\n 'getRegisteredIntegratorNames',\n 'getRegisteredSensitivitySolverNames',\n 'getRegisteredSteadyStateSolverNames',\n 'getSBML',\n 'getScaledConcentrationControlCoefficientMatrix',\n 'getScaledElasticityMatrix',\n 'getScaledFloatingSpeciesElasticity',\n 'getScaledFluxControlCoefficientMatrix',\n 'getSeed',\n 'getSelectedValues',\n 'getSensitivitySolver',\n 'getSensitivitySolverByName',\n 'getSimulationData',\n 'getSteadyStateSelectionStrings',\n 'getSteadyStateSolver',\n 'getSteadyStateSolverByName',\n 'getSteadyStateThreshold',\n 'getSteadyStateValues',\n 'getSteadyStateValuesNamedArray',\n 'getSupportedIdTypes',\n 'getUnscaledConcentrationControlCoefficientMatrix',\n 'getUnscaledElasticityMatrix',\n 'getUnscaledFluxControlCoefficientMatrix',\n 'getUnscaledParameterElasticity',\n 'getUnscaledSpeciesElasticity',\n 'getValue',\n 'getuCC',\n 'getuEE',\n 'gillespie',\n 'integrator',\n 'integratorExists',\n 'internalOneStep',\n 'isModelLoaded',\n 'items',\n 'iteritems',\n 'iterkeys',\n 'itervalues',\n 'keys',\n 'load',\n 'loadState',\n 'loadStateS',\n 'makeIntegrator',\n 'makeSensitivitySolver',\n 'makeSteadyStateSolver',\n 'mcaSteadyState',\n 'model',\n 'oneStep',\n 'options',\n 'parameter_1',\n 'parameter_13',\n 'parameter_2',\n 'plot',\n 'plotLegend',\n 'ps',\n 'reaction_1',\n 'reaction_10',\n 'reaction_11',\n 'reaction_12',\n 'reaction_13',\n 'reaction_14',\n 'reaction_2',\n 'reaction_3',\n 'reaction_4',\n 'reaction_5',\n 'reaction_6',\n 'reaction_7',\n 'reaction_8',\n 'reaction_9',\n 'regenerateModel',\n 'registerSolvers',\n 'removeCompartment',\n 'removeEvent',\n 'removeEventAssignments',\n 'removeInitialAssignment',\n 'removeParameter',\n 'removeReaction',\n 'removeRules',\n 'removeSpecies',\n 'reset',\n 'resetAll',\n 'resetParameter',\n 'resetSelectionLists',\n 'resetToOrigin',\n 'rs',\n 'rv',\n 'saveState',\n 'saveStateS',\n 'seed',\n 'selections',\n 'sensitivitySolverExists',\n 'setBoundary',\n 'setConstant',\n 'setDiffStepSize',\n 'setFluxThreshold',\n 'setGlobalParameterByName',\n 'setHasOnlySubstanceUnits',\n 'setInitAmount',\n 'setInitConcentration',\n 'setIntegrator',\n 'setIntegratorSetting',\n 'setKineticLaw',\n 'setModelId',\n 'setModelName',\n 'setOptions',\n 'setPersistent',\n 'setReversible',\n 'setSeed',\n 'setSensitivitySolver',\n 'setSteadyStateSolver',\n 'setSteadyStateThreshold',\n 'setTriggerInitialValue',\n 'setValue',\n 'setValues',\n 'show',\n 'showPlot',\n 'simulate',\n 'sm',\n 'species_1',\n 'species_1_amt',\n 'species_1_conc',\n 'species_2',\n 'species_2_amt',\n 'species_2_conc',\n 'species_3',\n 'species_3_amt',\n 'species_3_conc',\n 'species_4',\n 'species_4_amt',\n 'species_4_conc',\n 'species_5',\n 'species_5_amt',\n 'species_5_conc',\n 'species_6',\n 'species_6_amt',\n 'species_6_conc',\n 'steadyState',\n 'steadyStateNamedArray',\n 'steadyStateSelections',\n 'steadyStateSolver',\n 'steadyStateSolverExists',\n 'steadyStateThresh',\n 'sv',\n 'this',\n 'thisown',\n 'timeCourseSelections',\n 'timeSeriesSensitivities',\n 'validateCurrentSBML',\n 'values',\n 'vs']" - }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "dir(simulator)" ], @@ -377,21 +271,12 @@ "start_time": "2024-05-01T06:56:28.963005Z" } }, - "id": "f4fd7072004772cb" + "id": "f4fd7072004772cb", + "outputs": [] }, { "cell_type": "code", "execution_count": 12, - "outputs": [ - { - "data": { - "text/plain": "array([7.00e-07, 0.00e+00, 0.00e+00, 1.68e-04, 3.20e-04, 0.00e+00,\n 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 0.00e+00, 3.20e-03,\n 1.00e-02, 1.00e-02])" - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "simulator.getReactionRates()" ], @@ -402,21 +287,12 @@ "start_time": "2024-05-01T06:56:28.967766Z" } }, - "id": "e92d5b185840048f" + "id": "e92d5b185840048f", + "outputs": [] }, { "cell_type": "code", "execution_count": 13, - "outputs": [ - { - "data": { - "text/plain": "['reaction_1',\n 'reaction_2',\n 'reaction_3',\n 'reaction_4',\n 'reaction_5',\n 'reaction_6',\n 'reaction_7',\n 'reaction_8',\n 'reaction_9',\n 'reaction_10',\n 'reaction_11',\n 'reaction_12',\n 'reaction_13',\n 'reaction_14']" - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "simulator.getReactionIds()" ], @@ -427,7 +303,8 @@ "start_time": "2024-05-01T06:56:28.971951Z" } }, - "id": "278ae59c7dedfc33" + "id": "278ae59c7dedfc33", + "outputs": [] }, { "cell_type": "markdown", @@ -440,20 +317,6 @@ { "cell_type": "code", "execution_count": 14, - "outputs": [ - { - "ename": "RuntimeError", - "evalue": "No such solver called \"stochastic\". Available options are \"cvode\", \"gillespie\", \"rk4\", \"rk45\", \"euler\"", - "output_type": "error", - "traceback": [ - "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", - "\u001B[0;31mRuntimeError\u001B[0m Traceback (most recent call last)", - "Cell \u001B[0;32mIn[14], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m \u001B[43msimulator\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mintegrator\u001B[49m \u001B[38;5;241m=\u001B[39m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mstochastic\u001B[39m\u001B[38;5;124m'\u001B[39m\n", - "File \u001B[0;32m~/Library/Caches/pypoetry/virtualenvs/biosimulator-processes-ECOqdsTs-py3.10/lib/python3.10/site-packages/roadrunner/roadrunner.py:2867\u001B[0m, in \u001B[0;36mRoadRunner.setIntegrator\u001B[0;34m(self, name)\u001B[0m\n\u001B[1;32m 2865\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m \u001B[38;5;21msetIntegrator\u001B[39m(\u001B[38;5;28mself\u001B[39m, name: \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mstd::string const &\u001B[39m\u001B[38;5;124m\"\u001B[39m) \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m>\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mvoid\u001B[39m\u001B[38;5;124m\"\u001B[39m:\n\u001B[1;32m 2866\u001B[0m \u001B[38;5;250m \u001B[39m\u001B[38;5;124mr\u001B[39m\u001B[38;5;124;03m\"\"\"set the current Integrator to :param name;:\"\"\"\u001B[39;00m\n\u001B[0;32m-> 2867\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43m_roadrunner\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mRoadRunner_setIntegrator\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mname\u001B[49m\u001B[43m)\u001B[49m\n", - "\u001B[0;31mRuntimeError\u001B[0m: No such solver called \"stochastic\". Available options are \"cvode\", \"gillespie\", \"rk4\", \"rk45\", \"euler\"" - ] - } - ], "source": [ "simulator.integrator = 'stochastic'" ], @@ -464,12 +327,12 @@ "start_time": "2024-05-01T06:56:28.975565Z" } }, - "id": "3692858d8548cbee" + "id": "3692858d8548cbee", + "outputs": [] }, { "cell_type": "code", "execution_count": null, - "outputs": [], "source": [ "simulator.integrator" ], @@ -480,12 +343,12 @@ "start_time": "2024-05-01T06:56:29.394793Z" } }, - "id": "f688e9553786d36e" + "id": "f688e9553786d36e", + "outputs": [] }, { "cell_type": "code", "execution_count": null, - "outputs": [], "source": [ "simulator.getIds()" ], @@ -495,21 +358,12 @@ "start_time": "2024-05-01T06:56:29.397421Z" } }, - "id": "850c62b4ab027800" + "id": "850c62b4ab027800", + "outputs": [] }, { "cell_type": "code", "execution_count": 11, - "outputs": [ - { - "data": { - "text/plain": "type" - }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [], "metadata": { "collapsed": false, @@ -518,21 +372,12 @@ "start_time": "2024-05-01T08:34:23.547556Z" } }, - "id": "66b8d04c5b4d6d38" + "id": "66b8d04c5b4d6d38", + "outputs": [] }, { "cell_type": "code", "execution_count": 6, - "outputs": [ - { - "data": { - "text/plain": "numpy.ndarray" - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "import numpy as np \n", "type(np.random.rand(3, 4))" @@ -544,134 +389,12 @@ "start_time": "2024-05-01T16:16:16.843628Z" } }, - "id": "665d11516a211ac8" + "id": "665d11516a211ac8", + "outputs": [] }, { "cell_type": "code", "execution_count": 2, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Generation 0\n", - "Best fitness: 0.02801479563046072\n", - "Generation 1\n", - "Best fitness: 0.02801479563046072\n", - "Generation 2\n", - "Best fitness: 0.02801479563046072\n", - "Generation 3\n", - "Best fitness: 0.02801479563046072\n", - "Generation 4\n", - "Best fitness: 0.02801479563046072\n", - "Generation 5\n", - "Best fitness: 0.006007810411500336\n", - "Generation 6\n", - "Best fitness: 0.006007810411500336\n", - "Generation 7\n", - "Best fitness: 0.006007810411500336\n", - "Generation 8\n", - "Best fitness: 0.0007575817243439253\n", - "Generation 9\n", - "Best fitness: 6.63345185392128e-05\n", - "Generation 10\n", - "Best fitness: 4.4860689358605654e-05\n", - "Generation 11\n", - "Best fitness: 3.97414125982154e-05\n", - "Generation 12\n", - "Best fitness: 1.7883422972375662e-05\n", - "Generation 13\n", - "Best fitness: 1.5526645734675881e-06\n", - "Generation 14\n", - "Best fitness: 1.5526645734675881e-06\n", - "Generation 15\n", - "Best fitness: 1.925006692937714e-07\n", - "Generation 16\n", - "Best fitness: 1.925006692937714e-07\n", - "Generation 17\n", - "Best fitness: 3.75755874193473e-08\n", - "Generation 18\n", - "Best fitness: 3.75755874193473e-08\n", - "Generation 19\n", - "Best fitness: 2.2750193617859793e-08\n", - "Generation 20\n", - "Best fitness: 3.442072293857734e-09\n", - "Generation 21\n", - "Best fitness: 3.442072293857734e-09\n", - "Generation 22\n", - "Best fitness: 1.479702693707452e-09\n", - "Generation 23\n", - "Best fitness: 8.82388606626705e-11\n", - "Generation 24\n", - "Best fitness: 1.3380296870479924e-11\n", - "Generation 25\n", - "Best fitness: 1.3380296870479924e-11\n", - "Generation 26\n", - "Best fitness: 9.421019520061691e-12\n", - "Generation 27\n", - "Best fitness: 9.421019520061691e-12\n", - "Generation 28\n", - "Best fitness: 1.0754730439543891e-12\n", - "Generation 29\n", - "Best fitness: 9.72333324966712e-13\n", - "Generation 30\n", - "Best fitness: 9.72333324966712e-13\n", - "Generation 31\n", - "Best fitness: 3.93574062229618e-13\n", - "Generation 32\n", - "Best fitness: 4.5852210917018965e-14\n", - "Generation 33\n", - "Best fitness: 9.992007221626409e-15\n", - "Generation 34\n", - "Best fitness: 9.992007221626409e-15\n", - "Generation 35\n", - "Best fitness: 2.4424906541753444e-15\n", - "Generation 36\n", - "Best fitness: 2.3314683517128287e-15\n", - "Generation 37\n", - "Best fitness: 3.3306690738754696e-16\n", - "Generation 38\n", - "Best fitness: 1.1102230246251565e-16\n", - "Generation 39\n", - "Best fitness: 1.1102230246251565e-16\n", - "Generation 40\n", - "Best fitness: 1.1102230246251565e-16\n", - "Generation 41\n", - "Best fitness: 0.0\n", - "Generation 42\n", - "Best fitness: 0.0\n", - "Generation 43\n", - "Best fitness: 0.0\n", - "Generation 44\n", - "Best fitness: 0.0\n", - "Generation 45\n", - "Best fitness: 0.0\n", - "Generation 46\n", - "Best fitness: 0.0\n", - "Generation 47\n", - "Best fitness: 0.0\n", - "Generation 48\n", - "Best fitness: 0.0\n", - "Generation 49\n", - "Best fitness: 0.0\n", - "Generation 50\n", - "Best fitness: 0.0\n", - "Generation 51\n", - "Best fitness: 0.0\n", - "Generation 52\n", - "Best fitness: 0.0\n", - "Generation 53\n", - "Best fitness: 0.0\n", - "Generation 54\n", - "Best fitness: 0.0\n", - "Generation 55\n", - "Best fitness: 0.0\n", - "Stopping: No improvement in 40 generations.\n", - "The winning value: 0.5742081442947241\n", - "Best output closest to winning value with dynamic stopping: BestOutput(value=0.5742081442947241, generation=55, index=0, winning_value=0.5742081442947241)\n" - ] - } - ], "source": [ "import numpy as np\n", "from dataclasses import dataclass\n", @@ -792,17 +515,18 @@ "start_time": "2024-05-01T17:26:10.084506Z" } }, - "id": "e6938f543d913ac" + "id": "e6938f543d913ac", + "outputs": [] }, { "cell_type": "code", "execution_count": null, - "outputs": [], "source": [], "metadata": { "collapsed": false }, - "id": "21fcf6952f0ba30" + "id": "21fcf6952f0ba30", + "outputs": [] } ], "metadata": { diff --git a/poetry.lock b/poetry.lock index 5e94c2628..8d5ae5cf3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "aiobotocore" @@ -5872,4 +5872,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.10" -content-hash = "a4b0f01522ab5bbe93cf3e0f637f166025c6f97457c1b9a9beab05468d6784f3" +content-hash = "5073dbbf25a0c02c52426728bcddfa50f865d744424afb5a2639cdc5d12c110b" diff --git a/pyproject.toml b/pyproject.toml index 16311fd8b..1d48beee4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ numpy = "*" # "^1.26.4" copasi-basico = "*" cobra = "*" tellurium = "*" -amici = "^0.24.0" +amici = "*" smoldyn = ">=2.72" python-libsbml = "^5.20.2" docker = ">=7.0"