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BIOMD0000000005.xml
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BIOMD0000000005.xml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" metaid="_000000" level="2" version="4">
<model metaid="_000001" id="Tyson1991CellModel_6" name="Tyson1991_CellCycle_6var">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>
This a model from the article:
<br/>
<strong> Modeling the cell division cycle: cdc2 and cyclin interactions.
</strong>
<br/>
Tyson JJ
<em>Proc. Natl. Acad. Sci. U.S.A.</em>1991; 88(16); 7328-32
<a href="http://www.ncbi.nlm.nih.gov/pubmed/1831270">1831270</a>,
<br/>
<strong>Abstract:</strong>
<br/>
The proteins cdc2 and cyclin form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. A mathematical model for the interactions of cdc2 and cyclin is constructed. Simulation and analysis of the model show that the control system can operate in three modes: as a steady state with high maturation promoting factor activity, as a spontaneous oscillator, or as an excitable switch. We associate the steady state with metaphase arrest in unfertilized eggs, the spontaneous oscillations with rapid division cycles in early embryos, and the excitable switch with growth-controlled division cycles typical of nonembryonic cells.
</p>
<p>This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.<br/>For more information see the <a href="http://www.ebi.ac.uk/biomodels/legal.html" target="_blank">terms of use</a>.<br/>To cite BioModels Database, please use <a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16381960" target="_blank">Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.</a>
</p>
</body>
</notes>
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<speciesReference species="Y"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pM"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> CP </ci>
<ci> k3 </ci>
<ci> Y </ci>
</apply>
</math>
<listOfParameters>
<parameter metaid="_840217" id="k3" value="200"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="_000014" id="Reaction5" name="deactivation of cdc2 kinase" reversible="false">
<annotation>
<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/">
<rdf:Description rdf:about="#_000014">
<bqbiol:hasVersion>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:reactome:REACT_6327"/>
<rdf:li rdf:resource="urn:miriam:reactome:REACT_3178"/>
</rdf:Bag>
</bqbiol:hasVersion>
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:ec-code:2.7.10.2"/>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0045736"/>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006468"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="M"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="pM"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> k5notP </ci>
<ci> M </ci>
</apply>
</math>
<listOfParameters>
<parameter metaid="_840219" id="k5notP" value="0"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="_000015" id="Reaction6" name="cyclin biosynthesis" reversible="false">
<annotation>
<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/">
<rdf:Description rdf:about="#_000015">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006412"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="EmptySet"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Y"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> k1aa </ci>
</apply>
</math>
<listOfParameters>
<parameter metaid="_840221" id="k1aa" value="0.015"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="_000016" id="Reaction7" name="default degradation of cyclin" reversible="false">
<annotation>
<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/">
<rdf:Description rdf:about="#_000016">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0008054"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="Y"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="EmptySet"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> k2 </ci>
<ci> Y </ci>
</apply>
</math>
<listOfParameters>
<parameter metaid="_840223" id="k2" value="0"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="_000017" id="Reaction8" name="cdc2 kinase triggered degration of cyclin" reversible="false">
<annotation>
<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/">
<rdf:Description rdf:about="#_000017">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0008054"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="YP"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="EmptySet"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> k7 </ci>
<ci> YP </ci>
</apply>
</math>
<listOfParameters>
<parameter metaid="_840225" id="k7" value="0.6"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="_000018" id="Reaction9" name="activation of cdc2 kinase" reversible="false">
<annotation>
<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/">
<rdf:Description rdf:about="#_000018">
<bqbiol:hasVersion>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:reactome:REACT_6257"/>
<rdf:li rdf:resource="urn:miriam:reactome:REACT_6175"/>
<rdf:li rdf:resource="urn:miriam:reactome:REACT_6294"/>
</rdf:Bag>
</bqbiol:hasVersion>
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:ec-code:3.1.3.16"/>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006470"/>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0045737"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="pM"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="CT"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cell </ci>
<ci> pM </ci>
<apply>
<plus/>
<ci> k4prime </ci>
<apply>
<times/>
<ci> k4 </ci>
<apply>
<power/>
<apply>
<divide/>
<ci> M </ci>
<ci> CT </ci>
</apply>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
<listOfParameters>
<parameter metaid="_840227" id="k4" value="180"/>
<parameter metaid="_840229" id="k4prime" value="0.018"/>
</listOfParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>