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| ## Examples | ||
| The examples in this folder are encoded in the 0.92 format of the spacial specification. |
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| ## Examples | ||
| The examples in this folder are encoded in the 0.84 format of the spacial specification. |
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" | ||
| level="3" version="1"> | ||
| <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0"> | ||
| <listOfUnitDefinitions> | ||
| <unitDefinition id="substance"> | ||
| <listOfUnits> | ||
| <unit kind="item" exponent="1" scale="0" multiplier="1"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="volume"> | ||
| <listOfUnits> | ||
| <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="area"> | ||
| <listOfUnits> | ||
| <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="molecules"> | ||
| <listOfUnits> | ||
| <unit kind="item" exponent="1" scale="0" multiplier="1"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="umol_um3_litre_1"> | ||
| <listOfUnits> | ||
| <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="um3"> | ||
| <listOfUnits> | ||
| <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="um2"> | ||
| <listOfUnits> | ||
| <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="uM_um3_molecules_1"> | ||
| <listOfUnits> | ||
| <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/> | ||
| <unit kind="item" exponent="-1" scale="0" multiplier="1"/> | ||
| <unit kind="mole" exponent="1" scale="0" multiplier="1"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="uM_s_1"> | ||
| <listOfUnits> | ||
| <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/> | ||
| <unit kind="metre" exponent="-3" scale="0" multiplier="1"/> | ||
| <unit kind="mole" exponent="1" scale="0" multiplier="1"/> | ||
| <unit kind="second" exponent="-1" scale="0" multiplier="1"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="_zero__001_m3_mol_1_s_1"> | ||
| <listOfUnits> | ||
| <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/> | ||
| <unit kind="metre" exponent="3" scale="0" multiplier="1"/> | ||
| <unit kind="mole" exponent="-1" scale="0" multiplier="1"/> | ||
| <unit kind="second" exponent="-1" scale="0" multiplier="1"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="_one__0E_6"> | ||
| <listOfUnits> | ||
| <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="_one_000000_0"> | ||
| <listOfUnits> | ||
| <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="_one_000_0_m_3_mol_s_1"> | ||
| <listOfUnits> | ||
| <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/> | ||
| <unit kind="metre" exponent="-3" scale="0" multiplier="1"/> | ||
| <unit kind="mole" exponent="1" scale="0" multiplier="1"/> | ||
| <unit kind="second" exponent="-1" scale="0" multiplier="1"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| <unitDefinition id="M"> | ||
| <listOfUnits> | ||
| <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/> | ||
| <unit kind="metre" exponent="-3" scale="0" multiplier="1"/> | ||
| <unit kind="mole" exponent="1" scale="0" multiplier="1"/> | ||
| </listOfUnits> | ||
| </unitDefinition> | ||
| </listOfUnitDefinitions> | ||
| <listOfCompartments> | ||
| <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true"/> | ||
| </listOfCompartments> | ||
| <listOfSpecies> | ||
| <species id="species_1" initialConcentration="6" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" /> | ||
| <species id="species_2" initialConcentration="0.1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" /> | ||
| </listOfSpecies> | ||
| <listOfParameters> | ||
| <parameter id="v1" value="0.06" constant="true"/> | ||
| <parameter id="v2" value="0.12" constant="true"/> | ||
| <parameter id="V" value="0.5" constant="true"/> | ||
| <parameter id="Km" value="0.1" constant="true"/> | ||
| <parameter id="k1" value="1" constant="true"/> | ||
| </listOfParameters> | ||
| <listOfReactions> | ||
| <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false"> | ||
| <listOfReactants> | ||
| <speciesReference species="species_1" stoichiometry="1" constant="true"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference species="species_2" stoichiometry="1" constant="true"/> | ||
| </listOfProducts> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <times/> | ||
| <ci> k1 </ci> | ||
| <ci> species_1 </ci> | ||
| <ci> species_2 </ci> | ||
| </apply> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false"> | ||
| <listOfProducts> | ||
| <speciesReference species="species_1" stoichiometry="1" constant="true"/> | ||
| </listOfProducts> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> v2 </ci> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false"> | ||
| <listOfProducts> | ||
| <speciesReference species="species_2" stoichiometry="1" constant="true"/> | ||
| </listOfProducts> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> v1 </ci> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false"> | ||
| <listOfReactants> | ||
| <speciesReference species="species_2" stoichiometry="1" constant="true"/> | ||
| </listOfReactants> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <times/> | ||
| <ci> V </ci> | ||
| <ci> species_2 </ci> | ||
| <apply> | ||
| <divide/> | ||
| <cn> 1 </cn> | ||
| <apply> | ||
| <plus/> | ||
| <ci> Km </ci> | ||
| <ci> species_2 </ci> | ||
| </apply> | ||
| </apply> | ||
| </apply> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| </listOfReactions> | ||
| </model> | ||
| </sbml> |
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