- Author:
- Mona Zhu <devnull@localhost>
- Date:
- 2011-01-19 17:09:20+13:00
- Desc:
- Changed import locations
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/leloup_gonze_goldbeter_1999/rawfile/bfaac0e80b23726ffe05b02f98b3d1d01a2ee3b7/law4.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="law4" name="law4">
<!-- documentation -->
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora</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_1999_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>
The original paper reference is cited below:
</para>
<para>
Limit Cycle Models for Circadian Rhythms Based on Transcriptional Regulation in <emphasis>Drosophila</emphasis> and <emphasis>Neurospora</emphasis>, Jean-Christophe Leloup, Didier Gonze, and Albert Goldbeter, 1999, <emphasis>Journal of Biological Rhythms</emphasis>, 14, 433-448. <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/10643740">PubMed ID: 10643740</ulink>
</para>
</sect1>
</article>
</documentation>
<!-- units -->
<units name="nanomolar">
<unit prefix="nano" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="hour">
<unit multiplier="3600.0" units="second"/>
</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="P2" name="interface">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#P2">
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">P2</dc:title>
<dcterms:alternative xmlns:dcterms="http://purl.org/dc/terms/">phopshorylated PER</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable cmeta:id="P2_P2" initial_value="Y2_init" name="Y2" public_interface="out" units="nanomolar"/>
<variable name="vd" public_interface="in" units="flux"/>
<variable name="KdP" public_interface="in" units="nanomolar"/>
<variable name="V3" public_interface="in" units="flux"/>
<variable name="V4" public_interface="in" units="flux"/>
<variable name="k3" public_interface="in" units="second_order_rate_constant"/>
<variable name="k4" public_interface="in" units="first_order_rate_constant"/>
<variable name="K3" public_interface="in" units="nanomolar"/>
<variable name="K4" public_interface="in" units="nanomolar"/>
<variable name="kd" public_interface="in" units="first_order_rate_constant"/>
<variable name="Y1" public_interface="in" units="nanomolar"/>
<variable name="Z2" public_interface="in" units="nanomolar"/>
<variable name="C" public_interface="in" units="nanomolar"/>
<variable name="time" public_interface="in" units="hour"/>
<variable name="Y2_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>Y2</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci>V3</ci>
<apply>
<divide/>
<ci>Y1</ci>
<apply>
<plus/>
<ci>K3</ci>
<ci>Y1</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>k4</ci>
<ci>C</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci>V4</ci>
<apply>
<divide/>
<ci>Y2</ci>
<apply>
<plus/>
<ci>K4</ci>
<ci>Y2</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>k3</ci>
<ci>Y2</ci>
<ci>Z2</ci>
</apply>
<apply>
<times/>
<ci>vd</ci>
<apply>
<divide/>
<ci>Y2</ci>
<apply>
<plus/>
<ci>KdP</ci>
<ci>Y2</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>kd</ci>
<ci>Y2</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="law4">
<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>07-01-2011</dcterms:W3CDTF>
</dcterms:created>
</rdf:Description>
<rdf:Description rdf:about="#law4">
<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Limit Cycle Models for Circadian Rhythms Based on Transcriptional Regulation in Drosophila and Neurospora</dc:title>
</rdf:Description>
</rdf:RDF>
</model>
