- Author:
- Mona Zhu <devnull@localhost>
- Date:
- 2011-01-17 16:28:43+13:00
- Desc:
- Cleaned up code. Added documentation + metadata to 1.1 model & imports
- Permanent Source URI:
- https://models.fieldml.org/workspace/leloup_goldbeter_2004/rawfile/70b6abc4dc19364efad7751aa5b21a21847c8e1e/law1.cellml
<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.1#" cmeta:id="law1" name="law1">
<!-- documentation -->
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms</title>
<author>
<firstname>Mona</firstname>
<surname>Zhu</surname>
<affiliation>
<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>This is an import for the model "leloup_2004_1.1model.cellml". It is used to define a reoccuring structure within the model and may be used for multiple equations in the model. This file is known to run only in OpenCell in conjunction with the base file.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms, Jean-Christophe Leloup and Albert Goldbeter, 2004,
<emphasis>Journal of Theoretical Biology</emphasis>, 230, 541-562. <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/15363675">PubMed ID: 15363675</ulink>
</para>
</sect1>
</article>
</documentation>
<!-- units -->
<units name="hour">
<unit multiplier="3600.0" units="second"/>
</units>
<units name="nanomolar">
<unit prefix="nano" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="flux">
<unit units="nanomolar"/>
<unit exponent="-1" units="hour"/>
</units>
<units name="first_order_rate_constant">
<unit exponent="-1" units="hour"/>
</units>
<units name="second_order_rate_constant">
<unit exponent="-1" units="nanomolar"/>
<unit exponent="-1" units="hour"/>
</units>
<!-- components -->
<component xmlns:cmeta="http://www.cellml.org/metadata/1.1#" cmeta:id="PC" name="interface">
<variable cmeta:id="PC_PC" initial_value="YC_init" name="YC" public_interface="out" units="nanomolar"/>
<variable name="ks" public_interface="in" units="first_order_rate_constant"/>
<variable name="Kp" public_interface="in" units="nanomolar"/>
<variable name="Kdp" public_interface="in" units="nanomolar"/>
<variable name="ka" public_interface="in" units="first_order_rate_constant"/>
<variable name="kb" public_interface="in" units="second_order_rate_constant"/>
<variable name="kd" public_interface="in" units="first_order_rate_constant"/>
<variable name="V1" public_interface="in" units="flux"/>
<variable name="V2" public_interface="in" units="flux"/>
<variable name="YCP" public_interface="in" units="nanomolar"/>
<variable name="A" public_interface="in" units="nanomolar"/>
<variable name="M" public_interface="in" units="nanomolar"/>
<variable name="time" public_interface="in" units="hour"/>
<variable name="B" public_interface="in" units="nanomolar"/>
<variable name="YC_init" public_interface="in" units="nanomolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>YC</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci>ks</ci>
<ci>M</ci>
</apply>
<apply>
<times/>
<ci>V2</ci>
<apply>
<divide/>
<ci>YCP</ci>
<apply>
<plus/>
<ci>Kdp</ci>
<ci>YCP</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>ka</ci>
<ci>A</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci>V1</ci>
<apply>
<divide/>
<ci>YC</ci>
<apply>
<plus/>
<ci>Kp</ci>
<ci>YC</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>kb</ci>
<ci>YC</ci>
<ci>B</ci>
</apply>
<apply>
<times/>
<ci>kd</ci>
<ci>YC</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<!-- metadata -->
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="">
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Zhu</vCard:Family>
<vCard:Given>Xin Yue</vCard:Given>
<vCard:Other>Mona</vCard:Other>
</vCard:N>
<vCard:EMAIL xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<rdf:value>xzhu055@aucklanduni.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<dcterms:created xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource">
<dcterms:W3CDTF>29-12-2010</dcterms:W3CDTF>
</dcterms:created>
</rdf:Description>
<rdf:Description rdf:about="#leloup_2004_1.1model">
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms</dc:title>
<cmeta:comment rdf:parseType="Resource">
<rdf:value>This is a CellML description of Leloup and Goldbeter's 2004 mathematical model of the mammalian circadian clock.
</rdf:value>
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource">
<vCard:FN xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Mona Zhu</vCard:FN>
</dc:creator>
</cmeta:comment>
<bqs:reference xmlns:bqs="http://www.cellml.org/bqs/1.1#" rdf:parseType="Resource">
<bqs:Pubmed_id>15363675</bqs:Pubmed_id>
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">
<rdf:Seq>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Leloup</vCard:Family>
<vCard:Given>Jean-Christophe</vCard:Given>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
<vCard:Family>Goldbeter</vCard:Family>
<vCard:Given>Albert</vCard:Given>
</vCard:N>
</bqs:Person>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms</dc:title>
<dcterms:issued xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource">
<dcterms:W3CDTF>1999-05</dcterms:W3CDTF>
</dcterms:issued>
<bqs:Journal rdf:parseType="Resource">
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Journal of Theoretical Biology</dc:title>
</bqs:Journal>
<bqs:volume>230</bqs:volume>
<bqs:first_page>541</bqs:first_page>
<bqs:last_page>562</bqs:last_page>
</bqs:JournalArticle>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
</model>
