-
Notifications
You must be signed in to change notification settings - Fork 3
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
toy model created in BioUML and simulation results
- Loading branch information
axec
committed
Nov 17, 2015
1 parent
7582188
commit 1cba588
Showing
6 changed files
with
210 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| <?xml version="1.0" encoding="UTF-8" standalone="no"?> | ||
| <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:required="true" level="3" version="1"> | ||
| <model id="Top_level" name="Top level"> | ||
| <listOfCompartments> | ||
| <compartment constant="false" id="default" name="Top_level" size="1" spatialDimensions="3"/> | ||
| </listOfCompartments> | ||
| <listOfSpecies> | ||
| <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="false" id="C" initialAmount="100.0"> | ||
| <comp:listOfReplacedElements> | ||
| <comp:replacedElement comp:portRef="C_port" comp:submodelRef="kinetik" metaid="CONNECTION0019"/> | ||
| <comp:replacedElement comp:portRef="C_port" comp:submodelRef="fba_update" metaid="CONNECTION0020"/> | ||
| </comp:listOfReplacedElements> | ||
| </species> | ||
| <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="false" id="Dummy" initialAmount="0.0"/> | ||
| </listOfSpecies> | ||
| <listOfParameters> | ||
| <parameter constant="false" id="boundary" value="0.0"> | ||
| <comp:listOfReplacedElements> | ||
| <comp:replacedElement comp:portRef="r1_port_1" comp:submodelRef="fba" metaid="CONNECTION0017"/> | ||
| </comp:listOfReplacedElements> | ||
| </parameter> | ||
| <parameter constant="false" id="k" value="0.0"/> | ||
| <parameter constant="false" id="k_R4" value="0.0"/> | ||
| <parameter constant="false" id="kf" value="0.0"/> | ||
| <parameter constant="false" id="p" value="0.0"> | ||
| <comp:listOfReplacedElements> | ||
| <comp:replacedElement comp:portRef="p_port" comp:submodelRef="fba_update" metaid="CONNECTION0030"/> | ||
| </comp:listOfReplacedElements> | ||
| </parameter> | ||
| <parameter constant="false" id="unknown" value="0.0"/> | ||
| </listOfParameters> | ||
| <listOfRules> | ||
| <assignmentRule metaid="equation_1" variable="p"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci>R000008</ci> | ||
| </math> | ||
| </assignmentRule> | ||
| <rateRule metaid="equation_2" variable="boundary"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <sin/> | ||
| <csymbol definitionURL="http://www.sbml.org/sbml/symbols/time" encoding="text">time</csymbol> | ||
| </apply> | ||
| </math> | ||
| </rateRule> | ||
| </listOfRules> | ||
| <listOfReactions> | ||
| <reaction fast="false" id="R000008" name="Dummy ->" reversible="false"> | ||
| <listOfReactants> | ||
| <speciesReference constant="false" species="Dummy" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <cn>0.0</cn> | ||
| </math> | ||
| </kineticLaw> | ||
| <comp:replacedBy comp:portRef="R3_port" comp:submodelRef="fba" metaid="CONNECTION0021"/> | ||
| </reaction> | ||
| </listOfReactions> | ||
| <comp:listOfSubmodels> | ||
| <comp:submodel comp:id="fba" comp:modelRef="fba"/> | ||
| <comp:submodel comp:id="fba_update" comp:modelRef="fba_update"/> | ||
| <comp:submodel comp:id="kinetik" comp:modelRef="kinetik"/> | ||
| </comp:listOfSubmodels> | ||
| </model> | ||
| <comp:listOfExternalModelDefinitions> | ||
| <comp:externalModelDefinition comp:id="fba" comp:source="fba.xml"/> | ||
| <comp:externalModelDefinition comp:id="fba_update" comp:source="fba_update.xml"/> | ||
| <comp:externalModelDefinition comp:id="kinetik" comp:source="kinetik.xml"/> | ||
| </comp:listOfExternalModelDefinitions> | ||
| </sbml> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| <?xml version="1.0" encoding="UTF-8" standalone="no"?> | ||
| <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" comp:required="true" fbc:required="false" level="3" version="1"> | ||
| <model fbc:strict="false" id="fba" name="fba"> | ||
| <listOfCompartments> | ||
| <compartment constant="true" id="Cell" name="Cell" size="1.0" spatialDimensions="3"/> | ||
| </listOfCompartments> | ||
| <listOfSpecies> | ||
| <species boundaryCondition="true" compartment="Cell" constant="false" fbc:charge="" fbc:chemicalFormula="" hasOnlySubstanceUnits="true" id="A" initialAmount="0.0"/> | ||
| <species boundaryCondition="false" compartment="Cell" constant="false" fbc:charge="" fbc:chemicalFormula="" hasOnlySubstanceUnits="true" id="B1" initialAmount="0.0"/> | ||
| <species boundaryCondition="false" compartment="Cell" constant="false" fbc:charge="" fbc:chemicalFormula="" hasOnlySubstanceUnits="true" id="B2" initialAmount="0.0"/> | ||
| <species boundaryCondition="true" compartment="Cell" constant="false" fbc:charge="" fbc:chemicalFormula="" hasOnlySubstanceUnits="true" id="C" initialAmount="0.0"/> | ||
| </listOfSpecies> | ||
| <listOfParameters> | ||
| <parameter constant="false" id="lb" value="0.0"/> | ||
| <parameter constant="false" id="r1" value="0.0"/> | ||
| <parameter constant="false" id="ub" value="1000.0"/> | ||
| <parameter constant="false" id="unknown" value="0.0"/> | ||
| </listOfParameters> | ||
| <listOfReactions> | ||
| <reaction fast="false" fbc:lowerFluxBound="lb" fbc:upperFluxBound="r1" id="R1" name="" reversible="false"> | ||
| <listOfReactants> | ||
| <speciesReference constant="false" species="A" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="false" species="B1" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <cn>0.0</cn> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| <reaction fast="false" fbc:lowerFluxBound="lb" fbc:upperFluxBound="ub" id="R2" name="" reversible="false"> | ||
| <listOfReactants> | ||
| <speciesReference constant="false" species="B1" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="false" species="B2" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <cn>0.0</cn> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| <reaction fast="false" fbc:lowerFluxBound="lb" fbc:upperFluxBound="ub" id="R3" name="" reversible="false"> | ||
| <listOfReactants> | ||
| <speciesReference constant="false" species="B2" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="false" species="C" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <cn>0.0</cn> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| </listOfReactions> | ||
| <comp:listOfPorts> | ||
| <comp:port comp:id="R3_port" comp:idRef="R3" sboTerm="SBO:0000599"/> | ||
| <comp:port comp:id="r1_port_1" comp:idRef="r1" sboTerm="SBO:0000599"/> | ||
| </comp:listOfPorts> | ||
| <fbc:listOfObjectives fbc:activeObjective="maxR3"> | ||
| <fbc:objective fbc:id="maxR3" fbc:type="maximize"> | ||
| <fbc:listOfFluxObjectives> | ||
| <fbc:fluxObjective fbc:coefficient="1.0" fbc:reaction="R3"/> | ||
| </fbc:listOfFluxObjectives> | ||
| </fbc:objective> | ||
| </fbc:listOfObjectives> | ||
| </model> | ||
| </sbml> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| <?xml version="1.0" encoding="UTF-8" standalone="no"?> | ||
| <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:required="true" level="3" version="1"> | ||
| <model id="fba_update" name="fba_update"> | ||
| <listOfCompartments> | ||
| <compartment constant="false" id="default" name="fba_update" size="1" spatialDimensions="3"/> | ||
| </listOfCompartments> | ||
| <listOfSpecies> | ||
| <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="false" id="C" initialAmount="100.0"/> | ||
| </listOfSpecies> | ||
| <listOfParameters> | ||
| <parameter constant="false" id="p" value="0.1"/> | ||
| </listOfParameters> | ||
| <listOfReactions> | ||
| <reaction fast="false" id="R000002" name="-> C" reversible="false"> | ||
| <listOfProducts> | ||
| <speciesReference constant="false" species="C" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci>p</ci> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| </listOfReactions> | ||
| <comp:listOfPorts> | ||
| <comp:port comp:id="C_port" comp:idRef="C" sboTerm="SBO:0000599"/> | ||
| <comp:port comp:id="p_port" comp:idRef="p" sboTerm="SBO:0000599"/> | ||
| </comp:listOfPorts> | ||
| </model> | ||
| </sbml> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| <?xml version="1.0" encoding="UTF-8" standalone="no"?> | ||
| <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:required="true" level="3" version="1"> | ||
| <model id="kinetik" name="kinetic"> | ||
| <listOfCompartments> | ||
| <compartment constant="false" id="default" name="kinetik" size="1" spatialDimensions="3"/> | ||
| </listOfCompartments> | ||
| <listOfSpecies> | ||
| <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="true" id="C" initialAmount="100.0"/> | ||
| <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="false" id="D" initialAmount="0.0"/> | ||
| </listOfSpecies> | ||
| <listOfParameters> | ||
| <parameter constant="false" id="k_R4" value="1.0"/> | ||
| </listOfParameters> | ||
| <listOfReactions> | ||
| <reaction fast="false" id="R000005" name="C -> D" reversible="false"> | ||
| <listOfReactants> | ||
| <speciesReference constant="false" species="C" stoichiometry="1"/> | ||
| </listOfReactants> | ||
| <listOfProducts> | ||
| <speciesReference constant="false" species="D" stoichiometry="1"/> | ||
| </listOfProducts> | ||
| <kineticLaw> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <times/> | ||
| <ci>k_R4</ci> | ||
| <ci>C</ci> | ||
| </apply> | ||
| </math> | ||
| </kineticLaw> | ||
| </reaction> | ||
| </listOfReactions> | ||
| <comp:listOfPorts> | ||
| <comp:port comp:id="C_port" comp:idRef="C" sboTerm="SBO:0000599"/> | ||
| </comp:listOfPorts> | ||
| </model> | ||
| </sbml> |
Binary file added
BIN
+12.1 KB
wholecell-integration/ilya/toy_model/simulation_results/Ilya model simulated in BioUML.txt
Binary file not shown.
Binary file added
BIN
+3.77 KB
wholecell-integration/ilya/toy_model/simulation_results/Leandro model result in BioUML.txt
Binary file not shown.