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Merge pull request #902 from SciML/file_loading_tutorial
Documentation of file loading/saving
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‎docs/pages.jl

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#"model_creation/constraint_equations.md",
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# Events.
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#"model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
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"model_creation/model_file_loading_and_export.md",# Distributed parameters, rates, and initial conditions.
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# Loading and writing models to files.
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"model_creation/model_visualisation.md",
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#"model_creation/network_analysis.md",

‎docs/src/assets/brusselator_sim_SBMLImporter.svg

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‎docs/src/assets/model_files/brusselator.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<!-- Created by COPASI version 4.42 (Build 284) on 2024-01-10 09:22 with libSBML version 5.20.0. -->
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<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
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<model metaid="COPASI0" id="New_Model" name="New Model">
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<annotation>
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<copasi:COPASI xmlns:copasi="http://www.copasi.org/static/sbml">
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<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#COPASI0">
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<dcterms:created>
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<rdf:Description>
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<dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
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</rdf:Description>
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</dcterms:created>
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</rdf:Description>
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</rdf:RDF>
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</copasi:COPASI>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Description rdf:about="#COPASI0">
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<dcterms:created rdf:parseType="Resource">
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<dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
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</dcterms:created>
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<dcterms:modified rdf:parseType="Resource">
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<dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
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</dcterms:modified>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfFunctionDefinitions>
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<functionDefinition id="Constant_flux__irreversible" name="Constant flux (irreversible)">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<lambda>
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<bvar>
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<ci> v </ci>
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</bvar>
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<ci> v </ci>
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</lambda>
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</math>
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</functionDefinition>
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</listOfFunctionDefinitions>
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<listOfUnitDefinitions>
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<unitDefinition id="length" name="length">
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<listOfUnits>
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<unit kind="metre" exponent="1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="area" name="area">
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<listOfUnits>
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<unit kind="metre" exponent="2" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="volume" name="volume">
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<listOfUnits>
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<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="time" name="time">
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<listOfUnits>
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<unit kind="second" exponent="1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="substance" name="substance">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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</listOfUnitDefinitions>
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<listOfCompartments>
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<compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species id="X" name="X" compartment="compartment" hasOnlySubstanceUnits="true" initialAmount="2" boundaryCondition="false" constant="false"/>
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<species id="Y" name="Y" compartment="compartment" hasOnlySubstanceUnits="true" initialAmount="10" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="A" name="A" value="1" constant="true"/>
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<parameter id="B" name="B" value="4" constant="true"/>
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</listOfParameters>
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<listOfReactions>
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<reaction id="r2" name="r2" reversible="false">
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<listOfReactants>
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<speciesReference species="Y" stoichiometry="1"/>
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<speciesReference species="X" stoichiometry="2"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="X" stoichiometry="3"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<ci> k1 </ci>
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<apply>
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<power/>
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<ci> X </ci>
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<cn> 2 </cn>
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</apply>
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<ci> Y </ci>
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</apply>
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</math>
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<listOfParameters>
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<parameter id="k1" name="k1" value="1"/>
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</listOfParameters>
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</kineticLaw>
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</reaction>
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<reaction id="r3" name="r3" reversible="false">
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<listOfReactants>
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<speciesReference species="X" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="Y" stoichiometry="1"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<ci> B </ci>
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<ci> X </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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<reaction id="r4" name="r4" reversible="false">
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<listOfReactants>
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<speciesReference species="X" stoichiometry="1"/>
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</listOfReactants>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<ci> k1 </ci>
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<ci> X </ci>
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</apply>
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</math>
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<listOfParameters>
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<parameter id="k1" name="k1" value="1"/>
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</listOfParameters>
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</kineticLaw>
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</reaction>
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<reaction id="r1" name="r1" reversible="false">
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<listOfProducts>
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<speciesReference species="X" stoichiometry="1"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<apply>
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<ci> Constant_flux__irreversible </ci>
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<ci> A </ci>
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</apply>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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</listOfReactions>
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</model>
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</sbml>

‎docs/src/assets/model_files/repressilator.net

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# Created by BioNetGen 2.3.1
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begin parameters
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1 Na 6.022e23 # Constant
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2 V 1.4e-15 # Constant
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3 c0 1e9 # Constant
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4 c1 224 # Constant
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5 c2 9 # Constant
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6 c3 0.5 # Constant
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7 c4 5e-4 # Constant
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8 c5 0.167 # Constant
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9 c6 ln(2)/120 # Constant
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10 c7 ln(2)/600 # Constant
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11 tF 1e-4 # Constant
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12 rF 1000 # Constant
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13 pF 1000 # Constant
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14 _rateLaw1 (((c0/Na)/V)*tF)/pF # ConstantExpression
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15 _rateLaw2 c1*tF # ConstantExpression
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16 _rateLaw3 (((c0/Na)/V)*tF)/pF # ConstantExpression
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17 _rateLaw4 c2*tF # ConstantExpression
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18 _rateLaw5 c3*rF # ConstantExpression
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19 _rateLaw6 c4*rF # ConstantExpression
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20 _rateLaw7 (c5/rF)*pF # ConstantExpression
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21 _rateLaw8 (((c0/Na)/V)*tF)/pF # ConstantExpression
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22 _rateLaw9 c1*tF # ConstantExpression
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23 _rateLaw10 (((c0/Na)/V)*tF)/pF # ConstantExpression
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24 _rateLaw11 c2*tF # ConstantExpression
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25 _rateLaw12 c3*rF # ConstantExpression
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26 _rateLaw13 c4*rF # ConstantExpression
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27 _rateLaw14 (c5/rF)*pF # ConstantExpression
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28 _rateLaw15 (((c0/Na)/V)*tF)/pF # ConstantExpression
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29 _rateLaw16 c1*tF # ConstantExpression
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30 _rateLaw17 (((c0/Na)/V)*tF)/pF # ConstantExpression
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31 _rateLaw18 c2*tF # ConstantExpression
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32 _rateLaw19 c3*rF # ConstantExpression
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33 _rateLaw20 c4*rF # ConstantExpression
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34 _rateLaw21 (c5/rF)*pF # ConstantExpression
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end parameters
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begin species
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1 Null() 1
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2 gTetR(lac!1,lac!2).pLacI(tet!1).pLacI(tet!2) 1
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3 gCI(tet!1,tet!2).pTetR(cI!1).pTetR(cI!2) 1
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4 gLacI(cI!1,cI!2).pCI(lac!1).pCI(lac!2) 1
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5 mTetR() 3163
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6 mCI() 6819
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7 mLacI() 129
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8 pTetR(cI) 183453
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9 pCI(lac) 2006198
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10 pLacI(tet) 165670
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11 gTetR(lac!1,lac).pLacI(tet!1) 0
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12 gCI(tet!1,tet).pTetR(cI!1) 0
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13 gLacI(cI!1,cI).pCI(lac!1) 0
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14 gTetR(lac,lac) 0
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15 gCI(tet,tet) 0
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16 gLacI(cI,cI) 0
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end species
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begin reactions
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1 2 10,11 2*_rateLaw4 #_reverse__R2
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2 2 2,5 _rateLaw6 #_R4
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3 5 5,8 _rateLaw7 #_R5
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4 1,5 1 c6 #_R6
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5 1,8 1 c7 #_R7
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6 3 8,12 2*_rateLaw11 #_reverse__R9
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7 3 3,6 _rateLaw13 #_R11
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8 6 6,9 _rateLaw14 #_R12
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9 1,6 1 c6 #_R13
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10 1,9 1 c7 #_R14
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11 4 9,13 2*_rateLaw18 #_reverse__R16
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12 4 4,7 _rateLaw20 #_R18
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13 7 7,10 _rateLaw21 #_R19
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14 1,7 1 c6 #_R20
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15 1,10 1 c7 #_R21
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16 11 10,14 _rateLaw2 #_reverse__R1
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17 10,11 2 _rateLaw3 #_R2
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18 11 5,11 _rateLaw6 #_R4
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19 12 8,15 _rateLaw9 #_reverse__R8
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20 8,12 3 _rateLaw10 #_R9
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21 12 6,12 _rateLaw13 #_R11
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22 13 9,16 _rateLaw16 #_reverse__R15
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23 9,13 4 _rateLaw17 #_R16
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24 13 7,13 _rateLaw20 #_R18
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25 10,14 11 2*_rateLaw1 #_R1
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26 14 5,14 _rateLaw5 #_R3
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27 8,15 12 2*_rateLaw8 #_R8
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28 15 6,15 _rateLaw12 #_R10
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29 9,16 13 2*_rateLaw15 #_R15
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30 16 7,16 _rateLaw19 #_R17
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end reactions
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begin groups
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1 pTetR 8
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2 pCI 9
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3 pLacI 10
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4 NULL 1
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end groups

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