Models
Simulation of Grimaud et al. 2014
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Outside of a <functionDefinition>, if a <ci> element is the first element within a MathML <apply>, then the <ci>'s value can only be chosen from the set of identifiers of <functionDefinition>s defined in the SBML model.
Reference: L2V4 Section 4.3.2
The formula 'mod(time + 6, 24)' in the math element of the <assignmentRule> uses 'mod' which is not a function definition id.
Outside of a <functionDefinition>, if a <ci> element is the first element within a MathML <apply>, then the <ci>'s value can only be chosen from the set of identifiers of <functionDefinition>s defined in the SBML model.
Reference: L2V4 Section 4.3.2
The formula 'mod(time + 6 + phase, Tc)' in the math element of the <assignmentRule> uses 'mod' which is not a function definition id.
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="M41">
<annotation>
<rdf:li xmlns:rdf="rdf" rdf:resource="http://identifiers.org/ecyano.model/41/"/>
</annotation>
<listOfCompartments>
<compartment id="Cytosol" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="Ntot" compartment="Cytosol"/>
<species id="Ctot" compartment="Cytosol"/>
<species id="Nf" compartment="Cytosol"/>
<species id="Cnit" compartment="Cytosol" initialConcentration="0"/>
<species id="Nr" compartment="Cytosol" initialConcentration="100"/>
<species id="Cr" compartment="Cytosol" initialConcentration="100"/>
<species id="Cf" compartment="Cytosol" initialConcentration="650"/>
<species id="time" compartment="Cytosol" initialConcentration="0"/>
</listOfSpecies>
<listOfParameters>
<parameter id="phi" constant="false"/>
<parameter id="I_" constant="false"/>
<parameter id="Ir" constant="false"/>
<parameter id="t2" constant="false"/>
<parameter id="phase" value="8" constant="true"/>
<parameter id="Tj" value="0.0001" constant="true"/>
<parameter id="Tc" value="24" constant="true"/>
<parameter id="Tp" value="6" constant="true"/>
<parameter id="theta1" value="1" constant="true"/>
<parameter id="theta0" value="0" constant="true"/>
<parameter id="Kb" value="0.08" constant="true"/>
<parameter id="k_" value="0.27" constant="true"/>
<parameter id="Kil" value="4500" constant="true"/>
<parameter id="Kl" value="55.5" constant="true"/>
<parameter id="lambda6" value="0.88" constant="true"/>
<parameter id="D_" value="0.0083" constant="true"/>
<parameter id="lambda5" value="5200" constant="true"/>
<parameter id="gamma3" value="0.4" constant="true"/>
<parameter id="alpha3" value="0.155" constant="true"/>
<parameter id="alpha1" value="1.9" constant="true"/>
<parameter id="r5" value="0.027" constant="true"/>
<parameter id="r7" value="0.83" constant="true"/>
<parameter id="r4" value="0.00093" constant="true"/>
<parameter id="r3" value="0.023" constant="true"/>
<parameter id="r2" value="0.275" constant="true"/>
<parameter id="r1" value="14.5" constant="true"/>
</listOfParameters>
<listOfRules>
<assignmentRule variable="phi">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> theta0 </ci>
<apply>
<times/>
<apply>
<divide/>
<ci> theta1 </ci>
<cn type="integer"> 2 </cn>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<tanh/>
<apply>
<divide/>
<ci> t2 </ci>
<ci> Tj </ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<tanh/>
<apply>
<divide/>
<apply>
<minus/>
<ci> t2 </ci>
<ci> Tp </ci>
</apply>
<ci> Tj </ci>
</apply>
</apply>
</apply>
</apply>
<cn type="integer"> 1 </cn>
<apply>
<tanh/>
<apply>
<divide/>
<apply>
<minus/>
<ci> t2 </ci>
<ci> Tc </ci>
</apply>
<ci> Tj </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="I_">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<divide/>
<cn type="integer"> 130 </cn>
<cn type="integer"> 3 </cn>
</apply>
<cn type="integer"> 3 </cn>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="Ir">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<cn type="integer"> 130 </cn>
<apply>
<power/>
<apply>
<exp/>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<divide/>
<apply>
<times/>
<apply>
<minus/>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<power/>
<apply>
<minus/>
<apply>
<ci> mod </ci>
<apply>
<plus/>
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
<cn type="integer"> 6 </cn>
</apply>
<cn type="integer"> 24 </cn>
</apply>
<cn type="integer"> 6 </cn>
</apply>
<cn type="integer"> 2 </cn>
</apply>
</apply>
<apply>
<times/>
<cn type="integer"> 2 </cn>
<apply>
<power/>
<cn type="integer"> 2 </cn>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<cn type="integer"> 3 </cn>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="t2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> mod </ci>
<apply>
<plus/>
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
<cn type="integer"> 6 </cn>
<ci> phase </ci>
</apply>
<ci> Tc </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="Ntot">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> Nf </ci>
<ci> Nr </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="Ctot">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> Cf </ci>
<ci> Cr </ci>
<ci> Cnit </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="Nf">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Cf </ci>
<ci> alpha3 </ci>
</apply>
</math>
</assignmentRule>
<rateRule variable="Cnit">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<ci> r4 </ci>
<ci> phi </ci>
<ci> Cf </ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<ci> r7 </ci>
<ci> D_ </ci>
</apply>
<ci> Cnit </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="Nr">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<cn type="integer"> 2 </cn>
<ci> r1 </ci>
<ci> Cnit </ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<apply>
<divide/>
<apply>
<times/>
<ci> alpha3 </ci>
<ci> r3 </ci>
<ci> Cr </ci>
</apply>
<ci> Nf </ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci> lambda6 </ci>
<ci> r1 </ci>
<ci> Cnit </ci>
</apply>
<ci> Nf </ci>
</apply>
<ci> D_ </ci>
</apply>
<ci> Nr </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="Cr">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<times/>
<ci> r2 </ci>
<apply>
<divide/>
<ci> Ir </ci>
<apply>
<plus/>
<ci> Ir </ci>
<ci> Kl </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> I_ </ci>
<ci> I_ </ci>
</apply>
<ci> Kil </ci>
</apply>
</apply>
</apply>
<ci> Cf </ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<apply>
<divide/>
<apply>
<times/>
<apply>
<plus/>
<ci> r3 </ci>
<apply>
<times/>
<ci> r3 </ci>
<ci> gamma3 </ci>
</apply>
</apply>
<ci> Nr </ci>
</apply>
<ci> Nf </ci>
</apply>
<ci> r5 </ci>
<ci> D_ </ci>
</apply>
<ci> Cr </ci>
</apply>
</apply>
<apply>
<times/>
<ci> alpha1 </ci>
<ci> r1 </ci>
<ci> Cnit </ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci> lambda5 </ci>
<ci> r2 </ci>
<apply>
<divide/>
<ci> Ir </ci>
<apply>
<plus/>
<ci> Ir </ci>
<ci> Kl </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> I_ </ci>
<ci> I_ </ci>
</apply>
<ci> Kil </ci>
</apply>
</apply>
</apply>
<ci> Cf </ci>
</apply>
<ci> Cf </ci>
</apply>
<ci> Cnit </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="Cf">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<ci> r3 </ci>
<ci> Cr </ci>
<ci> Nr </ci>
</apply>
<ci> Nf </ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<apply>
<times/>
<ci> r4 </ci>
<ci> phi </ci>
</apply>
<ci> D_ </ci>
</apply>
<ci> Cf </ci>
</apply>
</apply>
<apply>
<times/>
<ci> r7 </ci>
<ci> Cnit </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="time">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn type="integer"> 1 </cn>
</math>
</rateRule>
</listOfRules>
</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