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This CellML file was generated on 19/02/2009 at 9:48:35 at a.m. using:
COR (0.9.31.1175)
Copyright 2002-2009 Dr Alan Garny
http://COR.physiol.ox.ac.uk/ - COR@physiol.ox.ac.uk
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http://www.CellML.org/
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<title>A Model for Restriction Point Control of the Mammalian Cell Cycle</title>
<author>
<firstname>Jeelean</firstname>
<surname>Lim</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This CellML version of the model runs in PCEnv but in order to reproduce the published results, requires initial concentrations that are not listed in the paper. The switch "mass = mass/2 when Cdh1 crosses 0.2 from below" has not been implemented in this CellML description.
</para>
<para>ValidateCellML verifies this model as valid CellML.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
ABSTRACT: Inhibition of protein synthesis by cycloheximide blocks subsequent division of a mammalian cell, but only if the cell is exposed to
the drug before the restriction point (i.e. within the first several hours after birth). If exposed to cycloheximide after the restriction
point, a cell proceeds with DNA synthesis, mitosis and cell division and halts in the next cell cycle. If cycloheximide is later removed
from the culture medium, treated cells will return to the division cycle, showing a complex pattern of division times post-treatment,
as first measured by Zetterberg and colleagues.
</para>
<para>
We simulate these physiological responses of mammalian cells to transient inhibition
of growth, using a set of nonlinear differential equations based on a realistic model of the molecular events underlying progression
through the cell cycle. The model relieson our earlier work on the regulation of cyclin-dependent protein kinases during the cell
division cycle of yeast. The yeast model is supplemented with equations describing the effects of retinoblastoma protein on cell
growth and the synthesis of cyclins A and E, and with a primitive representation of the signaling pathway that controls synthesis of
cyclin D.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
A model for restriction point control of the mammalian cell cycle, Bela Novak, and John J Tyson, 2004,
<emphasis>Journal of Theoretical Biology</emphasis>
, 230, 563-579. (A PDF version of the article is available to subscribers on the <emphasis>Journal of Theoretical Biology</emphasis> website.) <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/15363676?dopt=Abstract">PubMed ID: 15363676</ulink>
</para>
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<title>figure 1</title>
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<caption>Molecular network regulating the progression of mammalian cells through the cell cycle.</caption>
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</apply>
<apply>
<plus/>
<ci>J_4</ci>
<ci>Cdc20</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>k_12</ci>
<ci>Cdc20</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="Cdc20_T">
<variable units="dimensionless" public_interface="out" name="Cdc20_T"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_11_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_11"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_12"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<variable units="dimensionless" public_interface="in" name="epsilon"/>
<variable units="hour" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Cdc20_T</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>epsilon</ci>
<apply>
<plus/>
<ci>k_11_</ci>
<apply>
<times/>
<ci>k_11</ci>
<ci>CycB</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>k_12</ci>
<ci>Cdc20_T</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="IEP">
<variable units="dimensionless" public_interface="out" name="IEP"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_31"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_32"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<variable units="dimensionless" public_interface="in" name="PPX"/>
<variable units="dimensionless" public_interface="in" name="J_31"/>
<variable units="dimensionless" public_interface="in" name="J_32"/>
<variable units="hour" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>IEP</ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<ci>k_31</ci>
<ci>CycB</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>IEP</ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>J_31</ci>
<cn cellml:units="dimensionless">1</cn>
</apply>
<ci>IEP</ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>k_32</ci>
<ci>PPX</ci>
<ci>IEP</ci>
</apply>
<apply>
<plus/>
<ci>J_32</ci>
<ci>IEP</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="PPX">
<variable units="dimensionless" public_interface="out" name="PPX"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_33"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_34"/>
<variable units="dimensionless" public_interface="in" name="epsilon"/>
<variable units="hour" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>PPX</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>epsilon</ci>
<ci>k_33</ci>
</apply>
<apply>
<times/>
<ci>k_34</ci>
<ci>PPX</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="E2F">
<variable units="dimensionless" public_interface="out" name="E2F"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_22"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_23_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_23"/>
<variable units="dimensionless" public_interface="in" name="E2FT"/>
<variable units="dimensionless" public_interface="in" name="CycA"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<variable units="hour" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>E2F</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_22</ci>
<apply>
<minus/>
<ci>E2FT</ci>
<ci>E2F</ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<ci>k_23_</ci>
<apply>
<times/>
<ci>k_23</ci>
<apply>
<plus/>
<ci>CycA</ci>
<ci>CycB</ci>
</apply>
</apply>
</apply>
<ci>E2F</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="Cdh1">
<variable units="dimensionless" public_interface="out" name="Cdh1"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_3_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_3"/>
<variable units="first_order_rate_constant" public_interface="in" name="V_4"/>
<variable units="dimensionless" public_interface="in" name="Cdc20"/>
<variable units="dimensionless" public_interface="in" name="J_3"/>
<variable units="dimensionless" public_interface="in" name="J_4"/>
<variable units="hour" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Cdh1</ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<apply>
<plus/>
<ci>k_3_</ci>
<apply>
<times/>
<ci>k_3</ci>
<ci>Cdc20</ci>
</apply>
</apply>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>Cdh1</ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>J_3</ci>
<cn cellml:units="dimensionless">1</cn>
</apply>
<ci>Cdh1</ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>Cdh1</ci>
<ci>V_4</ci>
</apply>
<apply>
<plus/>
<ci>J_4</ci>
<ci>Cdh1</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="GM">
<variable units="dimensionless" public_interface="out" name="GM"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_27"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_28"/>
<variable units="dimensionless" public_interface="in" name="Rb_hypo"/>
<variable units="dimensionless" public_interface="in" name="Rb_T"/>
<variable units="dimensionless" public_interface="in" name="mass"/>
<variable units="dimensionless" name="H"/>
<variable units="hour" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>H</ci>
<piecewise>
<piece>
<cn cellml:units="dimensionless">0</cn>
<apply>
<gt/>
<apply>
<divide/>
<ci>Rb_hypo</ci>
<ci>Rb_T</ci>
</apply>
<cn cellml:units="dimensionless">0.8</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="dimensionless">1</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>GM</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_27</ci>
<ci>mass</ci>
<ci>H</ci>
</apply>
<apply>
<times/>
<ci>k_28</ci>
<ci>GM</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="mass">
<variable units="dimensionless" public_interface="out" name="mass" initial_value="1"/>
<variable units="first_order_rate_constant" public_interface="in" name="mu"/>
<variable units="dimensionless" public_interface="in" name="epsilon"/>
<variable units="dimensionless" public_interface="in" name="GM"/>
<variable units="hour" 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>epsilon</ci>
<ci>mu</ci>
<ci>GM</ci>
</apply>
</apply>
</math>
</component>
<component name="PP1_A">
<variable units="dimensionless" public_interface="out" name="PP1_A"/>
<variable units="dimensionless" public_interface="out" name="PP1_T" initial_value="1"/>
<variable units="dimensionless" public_interface="in" name="K_21"/>
<variable units="dimensionless" public_interface="in" name="phi_E"/>
<variable units="dimensionless" public_interface="in" name="phi_B"/>
<variable units="dimensionless" public_interface="in" name="CycE"/>
<variable units="dimensionless" public_interface="in" name="CycA"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>PP1_A</ci>
<apply>
<divide/>
<ci>PP1_T</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<times/>
<ci>K_21</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>phi_E</ci>
<apply>
<plus/>
<ci>CycE</ci>
<ci>CycA</ci>
</apply>
</apply>
<apply>
<times/>
<ci>phi_B</ci>
<ci>CycB</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="Rb_hypo">
<variable units="dimensionless" public_interface="out" name="Rb_hypo"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_20"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_19_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_19"/>
<variable units="dimensionless" public_interface="out" name="Rb_T" initial_value="10"/>
<variable units="dimensionless" public_interface="in" name="PP1_T"/>
<variable units="dimensionless" public_interface="in" name="PP1_A"/>
<variable units="dimensionless" public_interface="in" name="lambda_D"/>
<variable units="dimensionless" public_interface="in" name="lambda_E"/>
<variable units="dimensionless" public_interface="in" name="lambda_A"/>
<variable units="dimensionless" public_interface="in" name="lambda_B"/>
<variable units="dimensionless" public_interface="in" name="CycE"/>
<variable units="dimensionless" public_interface="in" name="CycA"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<variable units="dimensionless" public_interface="in" name="CycD_T"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Rb_hypo</ci>
<apply>
<divide/>
<ci>Rb_T</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<divide/>
<apply>
<times/>
<ci>k_20</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>lambda_D</ci>
<ci>CycD_T</ci>
</apply>
<apply>
<times/>
<ci>lambda_E</ci>
<ci>CycE</ci>
</apply>
<apply>
<times/>
<ci>lambda_A</ci>
<ci>CycA</ci>
</apply>
<apply>
<times/>
<ci>lambda_B</ci>
<ci>CycB</ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci>k_19_</ci>
<apply>
<minus/>
<ci>PP1_T</ci>
<ci>PP1_A</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_19</ci>
<ci>PP1_A</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="E2FA">
<variable units="dimensionless" public_interface="out" name="E2FA"/>
<variable units="dimensionless" public_interface="in" name="E2F"/>
<variable units="dimensionless" public_interface="out" name="E2FT" initial_value="5"/>
<variable units="dimensionless" public_interface="in" name="E2F_Rb"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>E2FA</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>E2F</ci>
<apply>
<minus/>
<ci>E2FT</ci>
<ci>E2F_Rb</ci>
</apply>
</apply>
<ci>E2FT</ci>
</apply>
</apply>
</math>
</component>
<component name="E2F_Rb">
<variable units="dimensionless" public_interface="out" name="E2F_Rb"/>
<variable units="dimensionless" public_interface="in" name="E2FT"/>
<variable units="dimensionless" public_interface="in" name="L"/>
<variable units="dimensionless" public_interface="in" name="Rb_hypo"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>E2F_Rb</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="dimensionless">2</cn>
<ci>E2FT</ci>
<ci>Rb_hypo</ci>
</apply>
<apply>
<plus/>
<ci>E2FT</ci>
<ci>Rb_hypo</ci>
<ci>L</ci>
<apply>
<root/>
<apply>
<minus/>
<apply>
<power/>
<apply>
<plus/>
<ci>E2FT</ci>
<ci>Rb_hypo</ci>
<ci>L</ci>
</apply>
<cn cellml:units="dimensionless">2</cn>
</apply>
<apply>
<times/>
<cn cellml:units="dimensionless">4</cn>
<ci>E2FT</ci>
<ci>Rb_hypo</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_2">
<variable units="first_order_rate_constant" public_interface="out" name="V_2"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_2_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_2"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_2__"/>
<variable units="dimensionless" public_interface="in" name="Cdh1"/>
<variable units="dimensionless" public_interface="in" name="Cdc20"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>V_2</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>k_2_</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>Cdh1</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_2</ci>
<ci>Cdh1</ci>
</apply>
<apply>
<times/>
<ci>k_2__</ci>
<ci>Cdc20</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_4">
<variable units="first_order_rate_constant" public_interface="out" name="V_4"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_4"/>
<variable units="dimensionless" public_interface="in" name="gamma_A"/>
<variable units="dimensionless" public_interface="in" name="gamma_B"/>
<variable units="dimensionless" public_interface="in" name="CycA"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>V_4</ci>
<apply>
<times/>
<ci>k_4</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>gamma_A</ci>
<ci>CycA</ci>
</apply>
<apply>
<times/>
<ci>gamma_B</ci>
<ci>CycB</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_6">
<variable units="first_order_rate_constant" public_interface="out" name="V_6"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_6_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_6"/>
<variable units="dimensionless" public_interface="in" name="eta_E"/>
<variable units="dimensionless" public_interface="in" name="eta_A"/>
<variable units="dimensionless" public_interface="in" name="eta_B"/>
<variable units="dimensionless" public_interface="in" name="CycA"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<variable units="dimensionless" public_interface="in" name="CycE"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>V_6</ci>
<apply>
<plus/>
<ci>k_6_</ci>
<apply>
<times/>
<ci>k_6</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>eta_E</ci>
<ci>CycE</ci>
</apply>
<apply>
<times/>
<ci>eta_A</ci>
<ci>CycA</ci>
</apply>
<apply>
<times/>
<ci>eta_B</ci>
<ci>CycB</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_8">
<variable units="first_order_rate_constant" public_interface="out" name="V_8"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_8_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_8"/>
<variable units="dimensionless" public_interface="in" name="psi_E"/>
<variable units="dimensionless" public_interface="in" name="psi_B"/>
<variable units="dimensionless" public_interface="in" name="J_8"/>
<variable units="dimensionless" public_interface="in" name="CycE"/>
<variable units="dimensionless" public_interface="in" name="CycA"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<variable units="dimensionless" public_interface="in" name="CycE_T"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>V_8</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>k_8_</ci>
<ci>k_8</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>psi_E</ci>
<apply>
<plus/>
<ci>CycE</ci>
<ci>CycA</ci>
</apply>
</apply>
<apply>
<times/>
<ci>psi_B</ci>
<ci>CycB</ci>
</apply>
</apply>
<cn cellml:units="hour">1</cn>
</apply>
<apply>
<plus/>
<ci>J_8</ci>
<ci>CycE_T</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="L">
<variable units="dimensionless" public_interface="out" name="L"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_26r"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_26"/>
<variable units="first_order_rate_constant" public_interface="in" name="k_20"/>
<variable units="dimensionless" public_interface="in" name="lambda_D"/>
<variable units="dimensionless" public_interface="in" name="lambda_E"/>
<variable units="dimensionless" public_interface="in" name="lambda_A"/>
<variable units="dimensionless" public_interface="in" name="lambda_B"/>
<variable units="dimensionless" public_interface="in" name="CycD"/>
<variable units="dimensionless" public_interface="in" name="CycE"/>
<variable units="dimensionless" public_interface="in" name="CycA"/>
<variable units="dimensionless" public_interface="in" name="CycB"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>L</ci>
<apply>
<plus/>
<apply>
<divide/>
<ci>k_26r</ci>
<ci>k_26</ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<ci>k_20</ci>
<ci>k_26</ci>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci>lambda_D</ci>
<ci>CycD</ci>
</apply>
<apply>
<times/>
<ci>lambda_E</ci>
<ci>CycE</ci>
</apply>
<apply>
<times/>
<ci>lambda_A</ci>
<ci>CycA</ci>
</apply>
<apply>
<times/>
<ci>lambda_B</ci>
<ci>CycB</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="rate_constants">
<variable units="first_order_rate_constant" public_interface="out" name="k_1_" initial_value="0.1"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_1" initial_value="0.6"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_2_" initial_value="0.05"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_2" initial_value="20"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_2__" initial_value="1"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_3_" initial_value="7.5"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_3" initial_value="140"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_4" initial_value="40"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_5" initial_value="20"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_6_" initial_value="10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_6" initial_value="100"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_7_" initial_value="0"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_7" initial_value="0.6"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_8_" initial_value="0.1"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_8" initial_value="2"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_9" initial_value="2.5"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_10" initial_value="5"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_11_" initial_value="0"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_11" initial_value="1.5"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_12" initial_value="1.5"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_13" initial_value="5"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_14" initial_value="2.5"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_15" initial_value="0.25"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_16" initial_value="0.25"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_17_" initial_value="0.35"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_17" initial_value="10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_18" initial_value="10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_19_" initial_value="0"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_19" initial_value="20"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_20" initial_value="10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_22" initial_value="1"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_23_" initial_value="0.005"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_23" initial_value="1"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_24" initial_value="1000"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_24r" initial_value="10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_25" initial_value="1000"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_25r" initial_value="10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_26" initial_value="10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_26r" initial_value="200"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_27" initial_value="0.2"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_28" initial_value="0.2"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_29" initial_value="0.05"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_30" initial_value="20"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_31" initial_value="0.7"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_32" initial_value="1.8"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_33" initial_value="0.05"/>
<variable units="first_order_rate_constant" public_interface="out" name="k_34" initial_value="0.05"/>
<variable units="first_order_rate_constant" public_interface="out" name="mu" initial_value="0.061"/>
</component>
<component name="dimensionless_constants">
<variable units="dimensionless" public_interface="out" name="J_1" initial_value="0.1"/>
<variable units="dimensionless" public_interface="out" name="J_3" initial_value="0.01"/>
<variable units="dimensionless" public_interface="out" name="J_4" initial_value="0.01"/>
<variable units="dimensionless" public_interface="out" name="J_8" initial_value="0.1"/>
<variable units="dimensionless" public_interface="out" name="J_13" initial_value="0.005"/>
<variable units="dimensionless" public_interface="out" name="J_14" initial_value="0.005"/>
<variable units="dimensionless" public_interface="out" name="J_15" initial_value="0.1"/>
<variable units="dimensionless" public_interface="out" name="J_17" initial_value="0.3"/>
<variable units="dimensionless" public_interface="out" name="J_31" initial_value="0.01"/>
<variable units="dimensionless" public_interface="out" name="J_32" initial_value="0.01"/>
<variable units="dimensionless" public_interface="out" name="K_21" initial_value="1"/>
<variable units="dimensionless" public_interface="out" name="phi_E" initial_value="25"/>
<variable units="dimensionless" public_interface="out" name="phi_B" initial_value="2"/>
<variable units="dimensionless" public_interface="out" name="gamma_A" initial_value="0.3"/>
<variable units="dimensionless" public_interface="out" name="gamma_B" initial_value="1"/>
<variable units="dimensionless" public_interface="out" name="eta_E" initial_value="0.5"/>
<variable units="dimensionless" public_interface="out" name="eta_A" initial_value="0.5"/>
<variable units="dimensionless" public_interface="out" name="eta_B" initial_value="1"/>
<variable units="dimensionless" public_interface="out" name="lambda_D" initial_value="3.3"/>
<variable units="dimensionless" public_interface="out" name="lambda_E" initial_value="5"/>
<variable units="dimensionless" public_interface="out" name="lambda_A" initial_value="3"/>
<variable units="dimensionless" public_interface="out" name="lambda_B" initial_value="5"/>
<variable units="dimensionless" public_interface="out" name="psi_E" initial_value="1"/>
<variable units="dimensionless" public_interface="out" name="psi_B" initial_value="0.05"/>
<variable units="dimensionless" public_interface="out" name="epsilon" initial_value="1"/>
</component>
<connection>
<map_components component_2="environment" component_1="ERG"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="DRG"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Kip1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CycA_Kip1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CycD_Kip1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CycE_Kip1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CycA"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CycB"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CycE"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="CycD"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Cdc20"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Cdc20_T"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="IEP"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="PPX"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="E2F"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="Cdh1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="GM"/>
<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="rate_constants" component_1="ERG"/>
<map_variables variable_2="k_15" variable_1="k_15"/>
<map_variables variable_2="k_16" variable_1="k_16"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="ERG"/>
<map_variables variable_2="J_15" variable_1="J_15"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
</connection>
<connection>
<map_components component_2="DRG" component_1="ERG"/>
<map_variables variable_2="DRG" variable_1="DRG"/>
<map_variables variable_2="ERG" variable_1="ERG"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="DRG"/>
<map_variables variable_2="k_17_" variable_1="k_17_"/>
<map_variables variable_2="k_17" variable_1="k_17"/>
<map_variables variable_2="k_18" variable_1="k_18"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="DRG"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
<map_variables variable_2="J_17" variable_1="J_17"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="Kip1"/>
<map_variables variable_2="k_5" variable_1="k_5"/>
<map_variables variable_2="k_24" variable_1="k_24"/>
<map_variables variable_2="k_24r" variable_1="k_24r"/>
<map_variables variable_2="k_10" variable_1="k_10"/>
<map_variables variable_2="k_25" variable_1="k_25"/>
<map_variables variable_2="k_25r" variable_1="k_25r"/>
<map_variables variable_2="k_30" variable_1="k_30"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="Kip1"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
</connection>
<connection>
<map_components component_2="V_6" component_1="Kip1"/>
<map_variables variable_2="V_6" variable_1="V_6"/>
</connection>
<connection>
<map_components component_2="V_8" component_1="Kip1"/>
<map_variables variable_2="V_8" variable_1="V_8"/>
</connection>
<connection>
<map_components component_2="CycD" component_1="Kip1"/>
<map_variables variable_2="CycD" variable_1="CycD"/>
<map_variables variable_2="Kip1" variable_1="Kip1"/>
</connection>
<connection>
<map_components component_2="CycA" component_1="Kip1"/>
<map_variables variable_2="CycA" variable_1="CycA"/>
<map_variables variable_2="Kip1" variable_1="Kip1"/>
</connection>
<connection>
<map_components component_2="CycE" component_1="Kip1"/>
<map_variables variable_2="CycE" variable_1="CycE"/>
<map_variables variable_2="Kip1" variable_1="Kip1"/>
</connection>
<connection>
<map_components component_2="CycD_Kip1" component_1="Kip1"/>
<map_variables variable_2="CycD_Kip1" variable_1="CycD_Kip1"/>
<map_variables variable_2="Kip1" variable_1="Kip1"/>
</connection>
<connection>
<map_components component_2="CycA_Kip1" component_1="Kip1"/>
<map_variables variable_2="CycA_Kip1" variable_1="CycA_Kip1"/>
<map_variables variable_2="Kip1" variable_1="Kip1"/>
</connection>
<connection>
<map_components component_2="CycE_Kip1" component_1="Kip1"/>
<map_variables variable_2="CycE_Kip1" variable_1="CycE_Kip1"/>
<map_variables variable_2="Kip1" variable_1="Kip1"/>
</connection>
<connection>
<map_components component_2="Cdc20" component_1="Kip1"/>
<map_variables variable_2="Cdc20" variable_1="Cdc20"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="CycA_Kip1"/>
<map_variables variable_2="k_25" variable_1="k_25"/>
<map_variables variable_2="k_25r" variable_1="k_25r"/>
<map_variables variable_2="k_30" variable_1="k_30"/>
</connection>
<connection>
<map_components component_2="V_6" component_1="CycA_Kip1"/>
<map_variables variable_2="V_6" variable_1="V_6"/>
</connection>
<connection>
<map_components component_2="CycA" component_1="CycA_Kip1"/>
<map_variables variable_2="CycA" variable_1="CycA"/>
<map_variables variable_2="CycA_Kip1" variable_1="CycA_Kip1"/>
</connection>
<connection>
<map_components component_2="Cdc20" component_1="CycA_Kip1"/>
<map_variables variable_2="Cdc20" variable_1="Cdc20"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="CycD_Kip1"/>
<map_variables variable_2="k_24" variable_1="k_24"/>
<map_variables variable_2="k_24r" variable_1="k_24r"/>
<map_variables variable_2="k_10" variable_1="k_10"/>
</connection>
<connection>
<map_components component_2="V_6" component_1="CycD_Kip1"/>
<map_variables variable_2="V_6" variable_1="V_6"/>
</connection>
<connection>
<map_components component_2="CycD" component_1="CycD_Kip1"/>
<map_variables variable_2="CycD" variable_1="CycD"/>
<map_variables variable_2="CycD_Kip1" variable_1="CycD_Kip1"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="CycE_Kip1"/>
<map_variables variable_2="k_25" variable_1="k_25"/>
<map_variables variable_2="k_25r" variable_1="k_25r"/>
</connection>
<connection>
<map_components component_2="V_6" component_1="CycE_Kip1"/>
<map_variables variable_2="V_6" variable_1="V_6"/>
</connection>
<connection>
<map_components component_2="V_8" component_1="CycE_Kip1"/>
<map_variables variable_2="V_8" variable_1="V_8"/>
</connection>
<connection>
<map_components component_2="CycE" component_1="CycE_Kip1"/>
<map_variables variable_2="CycE" variable_1="CycE"/>
<map_variables variable_2="CycE_Kip1" variable_1="CycE_Kip1"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="CycA"/>
<map_variables variable_2="k_29" variable_1="k_29"/>
<map_variables variable_2="k_30" variable_1="k_30"/>
<map_variables variable_2="k_25" variable_1="k_25"/>
<map_variables variable_2="k_25r" variable_1="k_25r"/>
</connection>
<connection>
<map_components component_2="V_6" component_1="CycA"/>
<map_variables variable_2="V_6" variable_1="V_6"/>
<map_variables variable_2="CycA" variable_1="CycA"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="CycA"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
</connection>
<connection>
<map_components component_2="E2FA" component_1="CycA"/>
<map_variables variable_2="E2FA" variable_1="E2FA"/>
</connection>
<connection>
<map_components component_2="Cdc20" component_1="CycA"/>
<map_variables variable_2="Cdc20" variable_1="Cdc20"/>
</connection>
<connection>
<map_components component_2="mass" component_1="CycA"/>
<map_variables variable_2="mass" variable_1="mass"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="CycB"/>
<map_variables variable_2="k_1_" variable_1="k_1_"/>
<map_variables variable_2="k_1" variable_1="k_1"/>
</connection>
<connection>
<map_components component_2="V_2" component_1="CycB"/>
<map_variables variable_2="V_2" variable_1="V_2"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="CycB"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
<map_variables variable_2="J_1" variable_1="J_1"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="CycE"/>
<map_variables variable_2="k_7_" variable_1="k_7_"/>
<map_variables variable_2="k_7" variable_1="k_7"/>
<map_variables variable_2="k_25" variable_1="k_25"/>
<map_variables variable_2="k_25r" variable_1="k_25r"/>
</connection>
<connection>
<map_components component_2="V_8" component_1="CycE"/>
<map_variables variable_2="V_8" variable_1="V_8"/>
<map_variables variable_2="CycE" variable_1="CycE"/>
<map_variables variable_2="CycE_T" variable_1="CycE_T"/>
</connection>
<connection>
<map_components component_2="V_6" component_1="CycE"/>
<map_variables variable_2="V_6" variable_1="V_6"/>
<map_variables variable_2="CycE" variable_1="CycE"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="CycE"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
</connection>
<connection>
<map_components component_2="E2FA" component_1="CycE"/>
<map_variables variable_2="E2FA" variable_1="E2FA"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="CycD"/>
<map_variables variable_2="k_9" variable_1="k_9"/>
<map_variables variable_2="k_24r" variable_1="k_24r"/>
<map_variables variable_2="k_24" variable_1="k_24"/>
<map_variables variable_2="k_10" variable_1="k_10"/>
</connection>
<connection>
<map_components component_2="V_6" component_1="CycD"/>
<map_variables variable_2="V_6" variable_1="V_6"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="CycD"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
</connection>
<connection>
<map_components component_2="DRG" component_1="CycD"/>
<map_variables variable_2="DRG" variable_1="DRG"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="Cdc20"/>
<map_variables variable_2="k_13" variable_1="k_13"/>
<map_variables variable_2="k_14" variable_1="k_14"/>
<map_variables variable_2="k_12" variable_1="k_12"/>
</connection>
<connection>
<map_components component_2="IEP" component_1="Cdc20"/>
<map_variables variable_2="IEP" variable_1="IEP"/>
</connection>
<connection>
<map_components component_2="Cdc20_T" component_1="Cdc20"/>
<map_variables variable_2="Cdc20_T" variable_1="Cdc20_T"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="Cdc20"/>
<map_variables variable_2="J_13" variable_1="J_13"/>
<map_variables variable_2="J_4" variable_1="J_4"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="Cdc20_T"/>
<map_variables variable_2="k_11_" variable_1="k_11_"/>
<map_variables variable_2="k_11" variable_1="k_11"/>
<map_variables variable_2="k_12" variable_1="k_12"/>
</connection>
<connection>
<map_components component_2="CycB" component_1="Cdc20_T"/>
<map_variables variable_2="CycB" variable_1="CycB"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="Cdc20_T"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="IEP"/>
<map_variables variable_2="k_31" variable_1="k_31"/>
<map_variables variable_2="k_32" variable_1="k_32"/>
</connection>
<connection>
<map_components component_2="CycB" component_1="IEP"/>
<map_variables variable_2="CycB" variable_1="CycB"/>
</connection>
<connection>
<map_components component_2="PPX" component_1="IEP"/>
<map_variables variable_2="PPX" variable_1="PPX"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="IEP"/>
<map_variables variable_2="J_31" variable_1="J_31"/>
<map_variables variable_2="J_32" variable_1="J_32"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="PPX"/>
<map_variables variable_2="k_33" variable_1="k_33"/>
<map_variables variable_2="k_34" variable_1="k_34"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="PPX"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="E2F"/>
<map_variables variable_2="k_22" variable_1="k_22"/>
<map_variables variable_2="k_23_" variable_1="k_23_"/>
<map_variables variable_2="k_23" variable_1="k_23"/>
</connection>
<connection>
<map_components component_2="E2FA" component_1="E2F"/>
<map_variables variable_2="E2FT" variable_1="E2FT"/>
<map_variables variable_2="E2F" variable_1="E2F"/>
</connection>
<connection>
<map_components component_2="CycA" component_1="E2F"/>
<map_variables variable_2="CycA" variable_1="CycA"/>
</connection>
<connection>
<map_components component_2="CycB" component_1="E2F"/>
<map_variables variable_2="CycB" variable_1="CycB"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="Cdh1"/>
<map_variables variable_2="k_3_" variable_1="k_3_"/>
<map_variables variable_2="k_3" variable_1="k_3"/>
</connection>
<connection>
<map_components component_2="V_4" component_1="Cdh1"/>
<map_variables variable_2="V_4" variable_1="V_4"/>
</connection>
<connection>
<map_components component_2="Cdc20" component_1="Cdh1"/>
<map_variables variable_2="Cdc20" variable_1="Cdc20"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="Cdh1"/>
<map_variables variable_2="J_3" variable_1="J_3"/>
<map_variables variable_2="J_4" variable_1="J_4"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="GM"/>
<map_variables variable_2="k_27" variable_1="k_27"/>
<map_variables variable_2="k_28" variable_1="k_28"/>
</connection>
<connection>
<map_components component_2="Rb_hypo" component_1="GM"/>
<map_variables variable_2="Rb_hypo" variable_1="Rb_hypo"/>
<map_variables variable_2="Rb_T" variable_1="Rb_T"/>
</connection>
<connection>
<map_components component_2="mass" component_1="GM"/>
<map_variables variable_2="mass" variable_1="mass"/>
<map_variables variable_2="GM" variable_1="GM"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="mass"/>
<map_variables variable_2="mu" variable_1="mu"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="mass"/>
<map_variables variable_2="epsilon" variable_1="epsilon"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="PP1_A"/>
<map_variables variable_2="K_21" variable_1="K_21"/>
<map_variables variable_2="phi_E" variable_1="phi_E"/>
<map_variables variable_2="phi_B" variable_1="phi_B"/>
</connection>
<connection>
<map_components component_2="CycE" component_1="PP1_A"/>
<map_variables variable_2="CycE" variable_1="CycE"/>
</connection>
<connection>
<map_components component_2="CycA" component_1="PP1_A"/>
<map_variables variable_2="CycA" variable_1="CycA"/>
</connection>
<connection>
<map_components component_2="CycB" component_1="PP1_A"/>
<map_variables variable_2="CycB" variable_1="CycB"/>
</connection>
<connection>
<map_components component_2="rate_constants" component_1="Rb_hypo"/>
<map_variables variable_2="k_20" variable_1="k_20"/>
<map_variables variable_2="k_19_" variable_1="k_19_"/>
<map_variables variable_2="k_19" variable_1="k_19"/>
</connection>
<connection>
<map_components component_2="PP1_A" component_1="Rb_hypo"/>
<map_variables variable_2="PP1_T" variable_1="PP1_T"/>
<map_variables variable_2="PP1_A" variable_1="PP1_A"/>
</connection>
<connection>
<map_components component_2="dimensionless_constants" component_1="Rb_hypo"/>
<map_variables variable_2="lambda_D" variable_1="lambda_D"/>
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