- Author:
- Catherine Lloyd <c.lloyd@auckland.ac.nz>
- Date:
- 2010-06-02 21:35:38+12:00
- Desc:
- Removed temp doc from the SBML model file and created a new html file instead.
- Permanent Source URI:
- http://models.cellml.org/workspace/novak_tyson_1997/rawfile/a46c4023a12977b901ce4bf08f101a0d23e1afba/novak_tyson_1997.cellml
<?xml version='1.0' encoding='utf-8'?>
<!--
This CellML file was generated on 9/12/2008 at 10:53:37 at a.m. using:
COR (0.9.31.1125)
Copyright 2002-2008 Dr Alan Garny
http://COR.physiol.ox.ac.uk/ - COR@physiol.ox.ac.uk
CellML 1.0 was used to generate this model
http://www.CellML.org/
-->
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<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Modelling the Control of DNA Replication in Fission Yeast</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This CellML model runs in both COR and OpenCell to replicate the results in the original published paper. The units have been checked and they are consistent. Please note that this CellML model is based on the equations from the main body of the paper, not the appendix, and so it does not reproduce the cyclical graphs in the paper. The model does however produce results which match the first cycle of the graphs in the paper. Until events can be described in CellML we are unable to capture the switches in this model.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
ABSTRACT: A central event in the eukaryotic cell cycle is the decision to commence DNA replication (S phase). Strict controls normally operate to prevent repeated rounds of DNA replication without intervening mitoses ("endoreplication") or initiation of mitosis before DNA is fully replicated ("mitotic catastrophe"). Some of the genetic interactions involved in these controls have recently been identified in yeast. From this evidence we propose a molecular mechanism of "Start" control in Schizosaccharomyces pombe. Using established principles of biochemical kinetics, we compare the properties of this model in detail with the observed behavior of various mutant strains of fission yeast: wee1(-) (size control at Start), cdc13Delta and rum1(OP) (endoreplication), and wee1(-) rum1Delta (rapid division cycles of diminishing cell size). We discuss essential features of the mechanism that are responsible for characteristic properties of Start control in fission yeast, to expose our proposal to crucial experimental tests.
</para>
<para>
The original paper reference is cited below:
</para>
<para>
Modeling the control of DNA replication in fission yeast, Bela Novak and John J. Tyson, 1997, <emphasis>Proceedings of the National Academy of Sciences</emphasis>, 94, 9147-9152. <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9256450&dopt=Abstract">PubMed ID: 9256450</ulink>
</para>
<informalfigure float="0" id="fig_reaction_diagram">
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<imageobject>
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<title>cell diagram</title>
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<caption>A schematic diagram of the reaction mechanism which describes the G<subscript>1</subscript>/S and G<subscript>2</subscript>/M controls in fission yeast.</caption>
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<para>
Please note that the following switches in the published model are not included in the CellML description:
<itemizedlist>
<listitem>
<para>
(i) When SPF crosses 0.1 from below, S phase is initiated (Start).
</para>
</listitem>
<listitem>
<para>
(ii) When UbE crosses 0.1 from above, the cell divides functionally (mass->mass/2), although visible cytokinesis may be delayed.
</para>
</listitem>
<listitem>
<para>
(iii) 60 min after Start, kp is divided by 2, and at cell division kp is multiplied by 2.
</para>
</listitem>
</itemizedlist>
(taken from Table 1 of the cited reference).
</para>
</sect1>
</article>
</documentation>
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<ci>Wee1</ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>kw</ci>
<ci>MPF</ci>
<ci>Wee1</ci>
</apply>
<apply>
<plus/>
<ci>Kmw</ci>
<ci>Wee1</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="PG2">
<variable units="dimensionless" public_interface="out" cmeta:id="PG2_PG2" name="PG2" initial_value="0"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2"/>
<variable units="first_order_rate_constant" public_interface="in" name="k7"/>
<variable units="first_order_rate_constant" public_interface="in" name="k4"/>
<variable units="first_order_rate_constant" public_interface="in" name="k25"/>
<variable units="first_order_rate_constant" public_interface="in" name="kwee"/>
<variable units="first_order_rate_constant" public_interface="in" name="k7r"/>
<variable units="dimensionless" public_interface="in" name="PG2R"/>
<variable units="dimensionless" public_interface="in" name="G2K"/>
<variable units="dimensionless" public_interface="in" name="R"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>PG2</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci>kwee</ci>
<ci>G2K</ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<ci>k7r</ci>
<ci>k4</ci>
</apply>
<ci>PG2R</ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<ci>k25</ci>
<ci>k2</ci>
<apply>
<times/>
<ci>k7</ci>
<ci>R</ci>
</apply>
</apply>
<ci>PG2</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="G1R">
<variable units="dimensionless" public_interface="out" cmeta:id="G1R_G1R" name="G1R" initial_value="0"/>
<variable units="first_order_rate_constant" public_interface="in" name="k8"/>
<variable units="first_order_rate_constant" public_interface="in" name="k4"/>
<variable units="first_order_rate_constant" public_interface="in" name="k6_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k8r"/>
<variable units="dimensionless" public_interface="in" name="G1K"/>
<variable units="dimensionless" public_interface="in" name="R"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>G1R</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k8</ci>
<ci>R</ci>
<ci>G1K</ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<ci>k8r</ci>
<ci>k4</ci>
<ci>k6_</ci>
</apply>
<ci>G1R</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="PG2R">
<variable units="dimensionless" public_interface="out" name="PG2R" initial_value="0"/>
<variable units="first_order_rate_constant" public_interface="in" name="k7"/>
<variable units="first_order_rate_constant" public_interface="in" name="k4"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k7r"/>
<variable units="dimensionless" public_interface="in" name="PG2"/>
<variable units="dimensionless" public_interface="in" name="R"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>PG2R</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k7</ci>
<ci>R</ci>
<ci>PG2</ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<ci>k7r</ci>
<ci>k4</ci>
<ci>k2</ci>
<ci>k2_</ci>
</apply>
<ci>PG2R</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="UbE">
<variable units="dimensionless" public_interface="out" cmeta:id="UbE_UbE" name="UbE" initial_value="1"/>
<variable units="first_order_rate_constant" public_interface="in" name="kur"/>
<variable units="first_order_rate_constant" public_interface="in" name="ku"/>
<variable units="dimensionless" public_interface="in" name="Kmur"/>
<variable units="dimensionless" public_interface="in" name="Kmu"/>
<variable units="dimensionless" public_interface="in" name="IE"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>UbE</ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<ci>ku</ci>
<ci>IE</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>UbE</ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>Kmu</ci>
<cn cellml:units="dimensionless">1</cn>
</apply>
<ci>UbE</ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>kur</ci>
<ci>UbE</ci>
</apply>
<apply>
<plus/>
<ci>Kmur</ci>
<ci>UbE</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="mass">
<variable units="dimensionless" public_interface="out" name="mass" initial_value="0.5"/>
<variable units="first_order_rate_constant" public_interface="in" name="mu"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>mass</ci>
</apply>
<apply>
<times/>
<ci>mu</ci>
<ci>mass</ci>
</apply>
</apply>
</math>
</component>
<component name="Cdc25">
<variable units="dimensionless" public_interface="out" cmeta:id="Cdc25_Cdc25" name="Cdc25" initial_value="0"/>
<variable units="first_order_rate_constant" public_interface="in" name="kcr"/>
<variable units="first_order_rate_constant" public_interface="in" name="kc"/>
<variable units="dimensionless" public_interface="in" name="Kmcr"/>
<variable units="dimensionless" public_interface="in" name="Kmc"/>
<variable units="dimensionless" public_interface="in" name="MPF"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Cdc25</ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<ci>kc</ci>
<ci>MPF</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>Cdc25</ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>Kmc</ci>
<cn cellml:units="dimensionless">1</cn>
</apply>
<ci>Cdc25</ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>kcr</ci>
<ci>Cdc25</ci>
</apply>
<apply>
<plus/>
<ci>Kmcr</ci>
<ci>Cdc25</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="Cig2_total">
<variable units="dimensionless" public_interface="out" name="Cig2_total"/>
<variable units="dimensionless" public_interface="in" name="G1K"/>
<variable units="dimensionless" public_interface="in" name="G1R"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Cig2_total</ci>
<apply>
<plus/>
<ci>G1K</ci>
<ci>G1R</ci>
</apply>
</apply>
</math>
</component>
<component name="Rum1_total">
<variable units="dimensionless" public_interface="out" name="Rum1_total"/>
<variable units="dimensionless" public_interface="in" name="R"/>
<variable units="dimensionless" public_interface="in" name="G1R"/>
<variable units="dimensionless" public_interface="in" name="G2R"/>
<variable units="dimensionless" public_interface="in" name="PG2R"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Rum1_total</ci>
<apply>
<plus/>
<ci>R</ci>
<ci>G1R</ci>
<ci>G2R</ci>
<ci>PG2R</ci>
</apply>
</apply>
</math>
</component>
<component name="Cdc13_total">
<variable units="dimensionless" public_interface="out" name="Cdc13_total"/>
<variable units="dimensionless" public_interface="in" name="G2K"/>
<variable units="dimensionless" public_interface="in" name="G2R"/>
<variable units="dimensionless" public_interface="in" name="PG2"/>
<variable units="dimensionless" public_interface="in" name="PG2R"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Cdc13_total</ci>
<apply>
<plus/>
<ci>G2K</ci>
<ci>G2R</ci>
<ci>PG2</ci>
<ci>PG2R</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_2="environment" component_1="G2K"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="R"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="G1K"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="G2R"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="IE"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="UbE2"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Wee1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="PG2"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="G1R"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="PG2R"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="UbE"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="mass"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Cdc25"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Cig2_total"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Rum1_total"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Cdc13_total"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="G2K" component_1="concentration_variables"/>
<map_variables variable_2="G2K" variable_1="G2K"/>
</connection>
<connection>
<map_components component_2="R" component_1="concentration_variables"/>
<map_variables variable_2="SPF" variable_1="SPF"/>
</connection>
<connection>
<map_components component_2="G1K" component_1="concentration_variables"/>
<map_variables variable_2="G1K" variable_1="G1K"/>
</connection>
<connection>
<map_components component_2="IE" component_1="concentration_variables"/>
<map_variables variable_2="MPF" variable_1="MPF"/>
</connection>
<connection>
<map_components component_2="UbE2" component_1="concentration_variables"/>
<map_variables variable_2="MPF" variable_1="MPF"/>
</connection>
<connection>
<map_components component_2="Wee1" component_1="concentration_variables"/>
<map_variables variable_2="MPF" variable_1="MPF"/>
</connection>
<connection>
<map_components component_2="PG2" component_1="concentration_variables"/>
<map_variables variable_2="PG2" variable_1="PG2"/>
</connection>
<connection>
<map_components component_2="Cdc25" component_1="concentration_variables"/>
<map_variables variable_2="MPF" variable_1="MPF"/>
</connection>
<connection>
<map_components component_2="G2K" component_1="rate_constants"/>
<map_variables variable_2="k1" variable_1="k1"/>
<map_variables variable_2="k2" variable_1="k2"/>
<map_variables variable_2="kwee" variable_1="kwee"/>
<map_variables variable_2="k7" variable_1="k7"/>
<map_variables variable_2="k7r" variable_1="k7r"/>
<map_variables variable_2="k4" variable_1="k4"/>
<map_variables variable_2="k25" variable_1="k25"/>
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<connection>
<map_components component_2="R" component_1="rate_constants"/>
<map_variables variable_2="k3" variable_1="k3"/>
<map_variables variable_2="k4" variable_1="k4"/>
<map_variables variable_2="kp" variable_1="kp"/>
<map_variables variable_2="k7" variable_1="k7"/>
<map_variables variable_2="k7r" variable_1="k7r"/>
<map_variables variable_2="k2" variable_1="k2"/>
<map_variables variable_2="k2_" variable_1="k2_"/>
<map_variables variable_2="k8" variable_1="k8"/>
<map_variables variable_2="k8r" variable_1="k8r"/>
<map_variables variable_2="k6_" variable_1="k6_"/>
<map_variables variable_2="Kmp" variable_1="Kmp"/>
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<connection>
<map_components component_2="G1K" component_1="rate_constants"/>
<map_variables variable_2="k5" variable_1="k5"/>
<map_variables variable_2="k6" variable_1="k6"/>
<map_variables variable_2="k8" variable_1="k8"/>
<map_variables variable_2="k8r" variable_1="k8r"/>
<map_variables variable_2="k4" variable_1="k4"/>
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<connection>
<map_components component_2="G2R" component_1="rate_constants"/>
<map_variables variable_2="k7" variable_1="k7"/>
<map_variables variable_2="k7r" variable_1="k7r"/>
<map_variables variable_2="k4" variable_1="k4"/>
<map_variables variable_2="k2" variable_1="k2"/>
<map_variables variable_2="k2_" variable_1="k2_"/>
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<connection>
<map_components component_2="IE" component_1="rate_constants"/>
<map_variables variable_2="ki" variable_1="ki"/>
<map_variables variable_2="kir" variable_1="kir"/>
<map_variables variable_2="Kmi" variable_1="Kmi"/>
<map_variables variable_2="Kmir" variable_1="Kmir"/>
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<connection>
<map_components component_2="UbE2" component_1="rate_constants"/>
<map_variables variable_2="UbE2" variable_1="UbE2"/>
<map_variables variable_2="ku2" variable_1="ku2"/>
<map_variables variable_2="kur2" variable_1="kur2"/>
<map_variables variable_2="Kmu2" variable_1="Kmu2"/>
<map_variables variable_2="Kmur2" variable_1="Kmur2"/>
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<connection>
<map_components component_2="Wee1" component_1="rate_constants"/>
<map_variables variable_2="Wee1" variable_1="Wee1"/>
<map_variables variable_2="kw" variable_1="kw"/>
<map_variables variable_2="kwr" variable_1="kwr"/>
<map_variables variable_2="Kmw" variable_1="Kmw"/>
<map_variables variable_2="Kmwr" variable_1="Kmwr"/>
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<connection>
<map_components component_2="G1R" component_1="rate_constants"/>
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<map_variables variable_2="k8r" variable_1="k8r"/>
<map_variables variable_2="k4" variable_1="k4"/>
<map_variables variable_2="k6_" variable_1="k6_"/>
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<connection>
<map_components component_2="PG2R" component_1="rate_constants"/>
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<map_variables variable_2="k7r" variable_1="k7r"/>
<map_variables variable_2="k4" variable_1="k4"/>
<map_variables variable_2="k2" variable_1="k2"/>
<map_variables variable_2="k2_" variable_1="k2_"/>
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<connection>
<map_components component_2="PG2" component_1="rate_constants"/>
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<map_variables variable_2="k25" variable_1="k25"/>
<map_variables variable_2="k2" variable_1="k2"/>
<map_variables variable_2="k7" variable_1="k7"/>
<map_variables variable_2="k7r" variable_1="k7r"/>
<map_variables variable_2="k4" variable_1="k4"/>
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<connection>
<map_components component_2="UbE" component_1="rate_constants"/>
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<map_variables variable_2="ku" variable_1="ku"/>
<map_variables variable_2="kur" variable_1="kur"/>
<map_variables variable_2="Kmu" variable_1="Kmu"/>
<map_variables variable_2="Kmur" variable_1="Kmur"/>
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<connection>
<map_components component_2="mass" component_1="rate_constants"/>
<map_variables variable_2="mu" variable_1="mu"/>
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<connection>
<map_components component_2="Cdc25" component_1="rate_constants"/>
<map_variables variable_2="Cdc25" variable_1="Cdc25"/>
<map_variables variable_2="kc" variable_1="kc"/>
<map_variables variable_2="kcr" variable_1="kcr"/>
<map_variables variable_2="Kmc" variable_1="Kmc"/>
<map_variables variable_2="Kmcr" variable_1="Kmcr"/>
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<connection>
<map_components component_2="R" component_1="G2K"/>
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<map_variables variable_2="G2K" variable_1="G2K"/>
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<connection>
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<map_variables variable_2="G2K" variable_1="G2K"/>
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<connection>
<map_components component_2="PG2" component_1="G2K"/>
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<map_variables variable_2="G2K" variable_1="G2K"/>
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<connection>
<map_components component_2="mass" component_1="R"/>
<map_variables variable_2="mass" variable_1="mass"/>
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<connection>
<map_components component_2="PG2" component_1="R"/>
<map_variables variable_2="PG2" variable_1="PG2"/>
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<connection>
<map_components component_2="G2R" component_1="R"/>
<map_variables variable_2="G2R" variable_1="G2R"/>
<map_variables variable_2="R" variable_1="R"/>
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<connection>
<map_components component_2="PG2R" component_1="R"/>
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<map_variables variable_2="R" variable_1="R"/>
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<connection>
<map_components component_2="G1K" component_1="R"/>
<map_variables variable_2="G1K" variable_1="G1K"/>
<map_variables variable_2="R" variable_1="R"/>
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<connection>
<map_components component_2="G1R" component_1="R"/>
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<map_variables variable_2="R" variable_1="R"/>
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<connection>
<map_components component_2="G1R" component_1="G1K"/>
<map_variables variable_2="G1R" variable_1="G1R"/>
<map_variables variable_2="G1K" variable_1="G1K"/>
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<connection>
<map_components component_2="PG2R" component_1="PG2"/>
<map_variables variable_2="PG2R" variable_1="PG2R"/>
<map_variables variable_2="PG2" variable_1="PG2"/>
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<connection>
<map_components component_2="IE" component_1="UbE"/>
<map_variables variable_2="IE" variable_1="IE"/>
</connection>
<connection>
<map_components component_2="G1K" component_1="Cig2_total"/>
<map_variables variable_2="G1K" variable_1="G1K"/>
</connection>
<connection>
<map_components component_2="G1R" component_1="Cig2_total"/>
<map_variables variable_2="G1R" variable_1="G1R"/>
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<connection>
<map_components component_2="R" component_1="Rum1_total"/>
<map_variables variable_2="R" variable_1="R"/>
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<connection>
<map_components component_2="G1R" component_1="Rum1_total"/>
<map_variables variable_2="G1R" variable_1="G1R"/>
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<connection>
<map_components component_2="G2R" component_1="Rum1_total"/>
<map_variables variable_2="G2R" variable_1="G2R"/>
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<connection>
<map_components component_2="PG2R" component_1="Rum1_total"/>
<map_variables variable_2="PG2R" variable_1="PG2R"/>
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<connection>
<map_components component_2="G2K" component_1="Cdc13_total"/>
<map_variables variable_2="G2K" variable_1="G2K"/>
</connection>
<connection>
<map_components component_2="G2R" component_1="Cdc13_total"/>
<map_variables variable_2="G2R" variable_1="G2R"/>
</connection>
<connection>
<map_components component_2="PG2" component_1="Cdc13_total"/>
<map_variables variable_2="PG2" variable_1="PG2"/>
</connection>
<connection>
<map_components component_2="PG2R" component_1="Cdc13_total"/>
<map_variables variable_2="PG2R" variable_1="PG2R"/>
</connection>
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<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
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<dcterms:alternative>Rum1</dcterms:alternative>
<dc:title>R</dc:title>
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<vCard:Given>Bela</vCard:Given>
<vCard:Family>Novak</vCard:Family>
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<rdf:value>Initial values for the variables were added to the model. Extra variables were added to create the graphs from the research paper.
This model uses the equations from the main body of the paper, not the appendix, and so does not reproduce the cyclical graphs in the paper. The model does however produce results which match the first cycle of the graphs in the paper.</rdf:value>
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<ns7:boundIntervals rdf:resource="rdf:#$VIla21"/>
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<dc:subject rdf:resource="rdf:#6d379922-9126-4b99-8df1-670701f3833c"/>
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<rdf:Description rdf:about="rdf:#090cd1a5-aa80-4d2c-9e22-65fd94c95f76">
<vCard:Given>John</vCard:Given>
<vCard:Family>Tyson</vCard:Family>
<vCard:Other>J</vCard:Other>
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<rdf:Description rdf:about="rdf:#$WIla21">
<ns7:endingValue>350</ns7:endingValue>
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<rdf:Description rdf:about="rdf:#16a6a1ce-8730-4a4e-9fbc-69427054b8cb">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#4ed62560-2308-44aa-8b45-6b52b7d5be66">
<vCard:N rdf:resource="rdf:#4408b866-4459-4d79-b34d-05a5b62de433"/>
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<rdf:Description rdf:about="rdf:#c656b1bd-b92e-41ed-8f67-ff4e00a5a2f6">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
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<rdf:Description rdf:about="rdf:#0f76c243-3ee2-419c-b6c4-1f687284bcb6">
<dc:title>Proceedings of the National Academy of Sciences USA</dc:title>
</rdf:Description>
<rdf:Description rdf:about="#PG2R">
<dcterms:alternative>Cdc13-P-Cdc2-Rum1 complex</dcterms:alternative>
<dc:title>PG2R</dc:title>
</rdf:Description>
<rdf:Description rdf:about="#novak_1997">
<ns7:simulation rdf:resource="rdf:#$UIla21"/>
<dc:title>Novak and Tyson's 1997 model of the control of DNA replication in
fission yeast.</dc:title>
<cmeta:comment rdf:resource="rdf:#e3b58cf9-c532-4fe9-b74e-65fe6e11e84c"/>
<bqs:reference rdf:resource="rdf:#40109bd1-bb4e-475c-99dd-1d2f5483800a"/>
<bqs:reference rdf:resource="rdf:#6c3f11a1-6286-4bb9-9c08-972091287a4b"/>
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<rdf:Description rdf:about="rdf:#5d5a1e14-ab16-4d0f-96cf-33c59d1974f2">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#2ca8d182-12ed-4d50-a559-b8e8898f1e36">
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
<rdf:value>c.lloyd@auckland.ac.nz</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#6b7d85be-45c6-4180-a961-dc40090b43c4">
<vCard:Given>Jeelean</vCard:Given>
<vCard:Family>Lim</vCard:Family>
<vCard:Other/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#0197290f-5794-40d2-8f9c-f455951f7f9b">
<dcterms:modified rdf:resource="rdf:#9f1b54de-0069-43f6-b1e5-fcd988412453"/>
<rdf:value>added cmeta id's to several variables</rdf:value>
<cmeta:modifier rdf:resource="rdf:#200e983c-e13e-4e22-a335-49b54dfb3af9"/>
</rdf:Description>
<rdf:Description rdf:about="">
<dc:title>Original CellML version of the model</dc:title>
<dc:publisher>The University of Auckland, Auckland Bioengineering Institute</dc:publisher>
<cmeta:comment rdf:resource="rdf:#dd8153d9-2a79-452a-bbbe-1628eac0ecac"/>
<dcterms:created rdf:resource="rdf:#0e221cba-d235-417b-900c-5535c406f15c"/>
<dc:creator rdf:resource="rdf:#402a24d8-bb8c-487e-a53d-ae94d0013758"/>
<cmeta:modification rdf:resource="rdf:#0197290f-5794-40d2-8f9c-f455951f7f9b"/>
<cmeta:modification rdf:resource="rdf:#30b03d72-80a5-4925-995c-dd7701ba22e6"/>
<cmeta:modification rdf:resource="rdf:#4abf44af-7219-4a78-a36b-c62560847896"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#c685f0b7-576c-4ffc-98cf-0071cd53bb86">
<vCard:FN>Jeelean Lim</vCard:FN>
</rdf:Description>
<rdf:Description rdf:about="rdf:#baf281b0-12ba-4d2c-86d9-be9abaa4eb09">
<dc:creator rdf:resource="rdf:#3868e4b5-6521-4775-9f93-fc8da3f27cf8"/>
<dc:title>Modeling the control of DNA replication in fission yeast</dc:title>
<bqs:volume>94</bqs:volume>
<bqs:first_page>9147</bqs:first_page>
<bqs:Journal rdf:resource="rdf:#0f76c243-3ee2-419c-b6c4-1f687284bcb6"/>
<dcterms:issued rdf:resource="rdf:#b73a1613-0e7f-44b9-8a7a-87ecdb40599b"/>
<bqs:last_page>9152</bqs:last_page>
</rdf:Description>
<rdf:Description rdf:about="rdf:#0e221cba-d235-417b-900c-5535c406f15c">
<dcterms:W3CDTF>2003-04-22T00:00:00+00:00</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="#PG2">
<dcterms:alternative>Cdc13-P-Cdc2 complex</dcterms:alternative>
<dc:title>PG2</dc:title>
</rdf:Description>
<rdf:Description rdf:about="#IE">
<dc:title>IE</dc:title>
<dcterms:alternative>intermediary enzyme</dcterms:alternative>
</rdf:Description>
<rdf:Description rdf:about="#G2R">
<dcterms:alternative>Cdc13-Cdc2-Rum1 complex</dcterms:alternative>
<dc:title>G2R</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#40109bd1-bb4e-475c-99dd-1d2f5483800a">
<bqs:Pubmed_id>9256450</bqs:Pubmed_id>
<bqs:JournalArticle rdf:resource="rdf:#baf281b0-12ba-4d2c-86d9-be9abaa4eb09"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#dd8153d9-2a79-452a-bbbe-1628eac0ecac">
<dc:creator rdf:resource="rdf:#c685f0b7-576c-4ffc-98cf-0071cd53bb86"/>
<rdf:value>This CellML version of the model has been checked in COR and PCEnv and the model runs to replicate the results in the original published paper. The units have been checked and are consistent.</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="#G2K">
<dcterms:alternative>Cdc13-Cdc2 complex</dcterms:alternative>
<dc:title>G2K</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#11de7c21-2db5-4128-8b21-0dda411d0e8e">
<vCard:FN>Catherine Lloyd</vCard:FN>
</rdf:Description>
<rdf:Description rdf:about="rdf:#402a24d8-bb8c-487e-a53d-ae94d0013758">
<vCard:ORG rdf:resource="rdf:#a9aba57c-eb2f-4f71-94f0-d1d17e9c4680"/>
<vCard:EMAIL rdf:resource="rdf:#2ca8d182-12ed-4d50-a559-b8e8898f1e36"/>
<vCard:N rdf:resource="rdf:#16a6a1ce-8730-4a4e-9fbc-69427054b8cb"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#4abf44af-7219-4a78-a36b-c62560847896">
<dcterms:modified rdf:resource="rdf:#1ed4098d-4a40-4e85-ae0a-104cc9848ace"/>
<rdf:value>Fixed bullet points in the documentation.</rdf:value>
<cmeta:modifier rdf:resource="rdf:#36dc30c0-1d4b-4162-97c5-8e8e808e26b8"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#6d379922-9126-4b99-8df1-670701f3833c">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value>
<rdf:Bag>
<rdf:li>DNA replication</rdf:li>
<rdf:li>cell cycle</rdf:li>
<rdf:li>yeast</rdf:li>
</rdf:Bag>
</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#b73a1613-0e7f-44b9-8a7a-87ecdb40599b">
<dcterms:W3CDTF>1997-08</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#36dc30c0-1d4b-4162-97c5-8e8e808e26b8">
<vCard:N rdf:resource="rdf:#5d5a1e14-ab16-4d0f-96cf-33c59d1974f2"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#bece523c-f50d-45b6-aa9b-dcb85d6f5323">
<dcterms:W3CDTF>2008-12-09T15:08:56+13:00</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#b6c1410c-2eb1-4e3d-912d-e099ea0f3e39">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#090cd1a5-aa80-4d2c-9e22-65fd94c95f76"/>
</rdf:Description>
<rdf:Description rdf:about="#G1K">
<dcterms:alternative>Cig2-Cdc2 complex</dcterms:alternative>
<dc:title>G1K</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#e3b58cf9-c532-4fe9-b74e-65fe6e11e84c">
<dc:creator rdf:resource="rdf:#11de7c21-2db5-4128-8b21-0dda411d0e8e"/>
<rdf:value>This is the CellML description of Novak and Tyson's 1997 model of the
control of DNA replication in fission yeast.</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#9f1b54de-0069-43f6-b1e5-fcd988412453">
<dcterms:W3CDTF>2009-02-18T13:53:20+13:00</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="#G1R">
<dcterms:alternative>Cig2-Cdc2-Rum1 complex</dcterms:alternative>
<dc:title>G1R</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#4408b866-4459-4d79-b34d-05a5b62de433">
<vCard:Given>Jeelean</vCard:Given>
<vCard:Family>Lim</vCard:Family>
<vCard:Other/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#1ed4098d-4a40-4e85-ae0a-104cc9848ace">
<dcterms:W3CDTF>2007-06-15T10:32:36+12:00</dcterms:W3CDTF>
</rdf:Description>
</rdf:RDF>
</model>
