Models
Simulation of Clark et al. 2014 (in progress)
The SBML file representing the requested model is shown below. Click "SBML download" to save the file into your client file system. The SBML file can be used for further analysis of the model by using third party tools.
SBML download
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="M36">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.model/36/"/>
</annotation>
<listOfCompartments>
<compartment id="cyt" size="1">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/9/"/>
</annotation>
</compartment>
<compartment id="carb" size="1">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/7/"/>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species id="CO2_cyt" compartment="cyt">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/56/"/>
</annotation>
</species>
<species id="HCO3_cyt" compartment="cyt">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/68/"/>
</annotation>
</species>
<species id="CO2_carb" compartment="carb">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/56/"/>
</annotation>
</species>
<species id="HCO3_carb" compartment="carb">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/68/"/>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter id="v1" value="2e-18" constant="true"/>
<parameter id="v2" constant="false"/>
<parameter id="K1" constant="true"/>
<parameter id="k2" constant="false"/>
<parameter id="k3" constant="false"/>
<parameter id="K4" constant="true"/>
<parameter id="K5" constant="true"/>
<parameter id="kH" constant="false"/>
<parameter id="kW" constant="true"/>
<parameter id="pH_ext" value="8.2" constant="true"/>
<parameter id="pH_cyt" value="8" constant="true"/>
<parameter id="pH_carb" value="8" constant="true"/>
<parameter id="fast" value="100" constant="true">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/1065/"/>
</annotation>
</parameter>
<parameter id="O2_carb" constant="true"/>
<parameter id="CO2_ext" constant="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/56/"/>
</annotation>
</parameter>
<parameter id="HCO3_ext" constant="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.entity/68/"/>
</annotation>
</parameter>
<parameter id="OH_cyt" constant="false"/>
<parameter id="OH_ext" constant="false"/>
<parameter id="PCO2" value="0.0004" constant="true"/>
<parameter id="OH_carb" constant="false"/>
<parameter id="Temperature" value="38" constant="true"/>
<parameter id="IonicStrength" value="0.1" constant="true"/>
<parameter id="K6" constant="false"/>
<parameter id="k7" constant="true"/>
<parameter id="Nsites" value="13400" constant="true"/>
<parameter id="Vcarb" constant="true"/>
<parameter id="Vcell" constant="true"/>
<parameter id="CO2_fixation_rate" constant="false"/>
<parameter id="factorCo2dehyd" value="1" constant="true"/>
<parameter id="factorHCO3dehyd" value="1" constant="true"/>
<parameter id="rate3" constant="false"/>
<parameter id="rate2" constant="false"/>
<parameter id="rate6" constant="false"/>
<parameter id="rate1" constant="false"/>
<parameter id="rate4" constant="false"/>
<parameter id="rate5" constant="false"/>
<parameter id="rate7" constant="false"/>
<parameter id="rate8" constant="false"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="K1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 2.2 </cn>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<cn type="integer"> 4 </cn>
</apply>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="K4">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 1.9 </cn>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<cn type="integer"> 4 </cn>
</apply>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="K5">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 1.3 </cn>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<cn type="integer"> 3 </cn>
</apply>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="kW">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<cn type="integer"> 14 </cn>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="O2_carb">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> 4 </cn>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<cn type="integer"> 4 </cn>
</apply>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="k7">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 1.9 </cn>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<cn type="integer"> 23 </cn>
</apply>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="Vcarb">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 1.7 </cn>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<cn type="integer"> 17 </cn>
</apply>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="Vcell">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn> 5.2 </cn>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<cn type="integer"> 16 </cn>
</apply>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="CO2_cyt">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> CO2_ext </ci>
</math>
</initialAssignment>
<initialAssignment symbol="HCO3_cyt">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<divide/>
<ci> k2 </ci>
<ci> k3 </ci>
</apply>
<ci> CO2_cyt </ci>
<ci> OH_cyt </ci>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="CO2_carb">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> CO2_cyt </ci>
</math>
</initialAssignment>
<initialAssignment symbol="HCO3_carb">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<divide/>
<ci> k2 </ci>
<ci> k3 </ci>
</apply>
<ci> CO2_carb </ci>
<ci> OH_carb </ci>
</apply>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfRules>
<assignmentRule variable="v2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> k7 </ci>
<ci> Nsites </ci>
</apply>
<ci> Vcarb </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="k2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<cn type="integer"> 12100 </cn>
<apply>
<times/>
<cn type="integer"> 1156 </cn>
<apply>
<minus/>
<ci> Temperature </ci>
<cn type="integer"> 25 </cn>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="k3">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<cn type="e-notation"> 6 <sep/> -5 </cn>
<apply>
<times/>
<cn type="e-notation"> 6 <sep/> -5 </cn>
<apply>
<minus/>
<ci> Temperature </ci>
<cn type="integer"> 25 </cn>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="kH">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<apply>
<plus/>
<cn> 1.5 </cn>
<apply>
<times/>
<cn> 0.01 </cn>
<apply>
<minus/>
<ci> Temperature </ci>
<cn type="integer"> 25 </cn>
</apply>
</apply>
<apply>
<times/>
<cn> 0.1 </cn>
<ci> IonicStrength </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="CO2_ext">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kH </ci>
<ci> PCO2 </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="HCO3_ext">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<divide/>
<ci> k2 </ci>
<ci> k3 </ci>
</apply>
<ci> CO2_ext </ci>
<ci> OH_ext </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="OH_cyt">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> kW </ci>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<ci> pH_cyt </ci>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="OH_ext">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> kW </ci>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<ci> pH_ext </ci>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="OH_carb">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> kW </ci>
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<ci> pH_carb </ci>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="K6">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<power/>
<cn type="integer"> 10 </cn>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<plus/>
<cn> 6.4 </cn>
<apply>
<times/>
<cn> 0.0001 </cn>
<apply>
<power/>
<ci> Temperature </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</apply>
<apply>
<times/>
<cn> 0.01 </cn>
<ci> Temperature </ci>
</apply>
</apply>
<apply>
<times/>
<cn> 1.7 </cn>
<apply>
<power/>
<ci> IonicStrength </ci>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</apply>
<apply>
<times/>
<cn> 1.9 </cn>
<ci> IonicStrength </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="CO2_fixation_rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> v2 </ci>
<ci> CO2_carb </ci>
</apply>
<apply>
<plus/>
<ci> CO2_carb </ci>
<apply>
<times/>
<ci> K4 </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<divide/>
<ci> O2_carb </ci>
<ci> K5 </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="rate3">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k3 </ci>
<ci> HCO3_cyt </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="rate2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k2 </ci>
<ci> CO2_cyt </ci>
<ci> OH_cyt </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="rate6">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> fast </ci>
<apply>
<minus/>
<ci> CO2_ext </ci>
<ci> CO2_cyt </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="rate1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<divide/>
<apply>
<times/>
<ci> v1 </ci>
<ci> HCO3_ext </ci>
</apply>
<apply>
<plus/>
<ci> K1 </ci>
<ci> HCO3_ext </ci>
</apply>
</apply>
<ci> Vcell </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="rate4">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> factorCo2dehyd </ci>
<ci> fast </ci>
<ci> k2 </ci>
<ci> OH_carb </ci>
<ci> CO2_carb </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="rate5">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> factorHCO3dehyd </ci>
<ci> fast </ci>
<ci> k3 </ci>
<ci> HCO3_carb </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="rate7">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<ci> fast </ci>
<ci> HCO3_cyt </ci>
</apply>
<apply>
<times/>
<ci> fast </ci>
<ci> HCO3_carb </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="rate8">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> v2 </ci>
<ci> CO2_carb </ci>
</apply>
<apply>
<plus/>
<ci> CO2_carb </ci>
<apply>
<times/>
<ci> K4 </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<divide/>
<ci> O2_carb </ci>
<ci> K5 </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
</listOfRules>
<listOfReactions>
<reaction id="R734" name="HCO3 Membrane Transport" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/579/"/>
</annotation>
<listOfProducts>
<speciesReference species="HCO3_cyt" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<divide/>
<apply>
<times/>
<ci> v1 </ci>
<ci> HCO3_ext </ci>
</apply>
<apply>
<plus/>
<ci> K1 </ci>
<ci> HCO3_ext </ci>
</apply>
</apply>
<ci> Vcell </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R749" name="CO2 Fixation" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/689/"/>
</annotation>
<listOfReactants>
<speciesReference species="CO2_carb" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> v2 </ci>
<ci> CO2_carb </ci>
</apply>
<apply>
<plus/>
<ci> CO2_carb </ci>
<apply>
<times/>
<ci> K4 </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<divide/>
<ci> O2_carb </ci>
<ci> K5 </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R740" name="CO2 Hydration cyt" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/687/"/>
</annotation>
<listOfReactants>
<speciesReference species="CO2_cyt" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="HCO3_cyt" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k2 </ci>
<ci> CO2_cyt </ci>
<ci> OH_cyt </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R741" name="HCO3 Dehydration cyt" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/687/"/>
</annotation>
<listOfReactants>
<speciesReference species="HCO3_cyt" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="CO2_cyt" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k3 </ci>
<ci> HCO3_cyt </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R742" name="CO2 Hydration carb" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/687/"/>
</annotation>
<listOfReactants>
<speciesReference species="CO2_carb" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="HCO3_carb" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> factorCo2dehyd </ci>
<ci> fast </ci>
<ci> k2 </ci>
<ci> OH_carb </ci>
<ci> CO2_carb </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R743" name="HCO3 Dehydration carb" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/687/"/>
</annotation>
<listOfReactants>
<speciesReference species="HCO3_carb" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="CO2_carb" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> factorHCO3dehyd </ci>
<ci> fast </ci>
<ci> k3 </ci>
<ci> HCO3_carb </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R744" name="CO2 membrane transport in" reversible="false">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/576/"/>
</annotation>
<listOfProducts>
<speciesReference species="CO2_cyt" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> fast </ci>
<apply>
<minus/>
<ci> CO2_ext </ci>
<ci> CO2_cyt </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="R746" name="HCO3 carboxysome transport in" reversible="true">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.rule/615/"/>
</annotation>
<listOfReactants>
<speciesReference species="HCO3_cyt" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="HCO3_carb" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<ci> fast </ci>
<ci> HCO3_cyt </ci>
</apply>
<apply>
<times/>
<ci> fast </ci>
<ci> HCO3_carb </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI