- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2006-07-09 07:21:31+12:00
- Desc:
- committing version01 of wolf_passarge_somsen_snoep_heinrich_westerhoff_2000
- Permanent Source URI:
- http://models.cellml.org/workspace/wolf_passarge_somsen_snoep_heinrich_westerhoff_2000/rawfile/29648d07cb4aebb85f31ac21e76c777423b141ec/wolf_passarge_somsen_snoep_heinrich_westerhoff_2000.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : wolf_model_2000.xml
CREATED : 4th April 2001
LAST MODIFIED : 9th April 2003
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/01/2002 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Wolf et al's 2000 model of the intracellular and intercellular dynamics in yeast glycolytic oscillations.
CHANGES:
19/07/2002 - CML - Added more metadata.
09/04/2003 - AAC - Added publication date information.
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:pathway_editor="http://www.physiome.com/pathway_editor/1.0#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="wolf_passarge_somsen_snoep_heinrich_westerhoff_2000_version01" name="wolf_passarge_somsen_snoep_heinrich_westerhoff_2000_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Yeast Glycolytic Oscillations</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This is the original unchecked version of the model imported from the previous
CellML model repository, 24-Jan-2006.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
Under certain well-defined conditions, a population of yeast cells exhibits glycolytic oscillations that synchronise through intercellular acetaldehyde. This implies that the dynamic phenomenon of the oscillation propagates within and between cells. Several theories to explain the mechanisms underlying these oscillations have been suggested, including the idea that the frequency of the oscillations is dependent on several molecular processes, especially glucose transport across the plasma membrane. Due to the highly integrated nature of metabolism it is difficult to study metabolites or even metabolic pathways in isolation. They are part of a much larger metabolic network.
</para>
<para>
In 2000, Jana Wolf, Jutta Passarge, Oscar J.G. Somsen, Jacky L. Snoep, Reinhart Heinrich and Hans V. Westerhoff published a kinetic model describing the transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations (see <xref linkend="fig_reaction_diagram"/> below).
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.biophysj.org/cgi/content/abstract/78/3/1145">Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations</ulink>, Jana Wolf, Jutta Passarge, Oscar J.G. Somsen, Jacky L. Snoep, Reinhart Heinrich and Hans V. Westerhoff, 2000, <ulink url="http://www.biophysj.org/">
<emphasis>Biophysical Journal</emphasis>
</ulink>, 78, 1145-1153. (The <ulink url="http://www.biophysj.org/cgi/reprint/78/3/1145.pdf">PDF</ulink> and <ulink url="http://www.biophysj.org/cgi/content/full/78/3/1145">full text</ulink> versions of the article are available on the Biophysical Journal website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10692304&dopt=Abstract">PubMed ID: 10692304</ulink>
</para>
<para>
The raw CellML description of the model can be downloaded in various formats as described in <xref linkend="sec_download_this_model"/>.
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>schematic diagram</title>
</objectinfo>
<imagedata fileref="wolf_passarge_2000.png"/>
</imageobject>
</mediaobject>
<caption>Schematic representation of the model. The nine variable model includes all shown metabolites as variables where S1 represents glucose, S2 represents fructose-1,6-bisphosphate, S3 represents the triphopshate pool, S4 represents 3-phosphoglycerate, S5 represents pyruvate, S6 represents intracellular acetaldehyde, S6,ex represents extracellular acetaldehyde, A2 is ADP, A3 is ATP, N1 is NAD<superscript>+</superscript> and N2 is NADH.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<!--
We start the model definition with a definition of some named
sets of units for use throughout the model.
-->
<units name="minute">
<unit units="second" multiplier="60.0"/>
</units>
<units name="millimolar">
<unit units="mole" prefix="milli"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="flux">
<unit units="millimolar"/>
<unit units="minute" exponent="-1"/>
</units>
<units name="first_order_rate_constant">
<unit units="minute" exponent="-1"/>
</units>
<units name="second_order_rate_constant">
<unit units="millimolar" exponent="-1"/>
<unit units="minute" exponent="-1"/>
</units>
<component name="environment">
<variable units="minute" public_interface="out" name="time"/>
</component>
<component cmeta:id="S1" name="S1">
<variable units="millimolar" public_interface="out" name="S1"/>
<variable units="flux" public_interface="in" name="Jo"/>
<variable units="flux" public_interface="in" name="delta_S1_rxn1"/>
<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>S1</ci>
</apply>
<apply>
<plus/>
<ci>Jo</ci>
<ci>delta_S1_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="S2" name="S2">
<variable units="millimolar" public_interface="out" name="S2"/>
<variable units="flux" public_interface="in" name="delta_S2_rxn1"/>
<variable units="flux" public_interface="in" name="delta_S2_rxn2"/>
<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>S2</ci>
</apply>
<apply>
<plus/>
<ci>delta_S2_rxn1</ci>
<ci>delta_S2_rxn2</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="S3" name="S3">
<variable units="millimolar" public_interface="out" name="S3"/>
<variable units="flux" public_interface="in" name="delta_S3_rxn2"/>
<variable units="flux" public_interface="in" name="delta_S3_rxn3"/>
<variable units="flux" public_interface="in" name="delta_S3_rxn8"/>
<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>S3</ci>
</apply>
<apply>
<plus/>
<ci>delta_S3_rxn2</ci>
<ci>delta_S3_rxn3</ci>
<ci>delta_S3_rxn8</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="S4" name="S4">
<variable units="millimolar" public_interface="out" name="S4"/>
<variable units="flux" public_interface="in" name="delta_S4_rxn3"/>
<variable units="flux" public_interface="in" name="delta_S4_rxn4"/>
<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>S4</ci>
</apply>
<apply>
<plus/>
<ci>delta_S4_rxn3</ci>
<ci>delta_S4_rxn4</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="S5" name="S5">
<variable units="millimolar" public_interface="out" name="S5"/>
<variable units="flux" public_interface="in" name="delta_S5_rxn4"/>
<variable units="flux" public_interface="in" name="delta_S5_rxn5"/>
<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>S5</ci>
</apply>
<apply>
<plus/>
<ci>delta_S5_rxn4</ci>
<ci>delta_S5_rxn5</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="S6" name="S6">
<variable units="millimolar" public_interface="out" name="S6"/>
<variable units="flux" public_interface="in" name="delta_S6_rxn5"/>
<variable units="flux" public_interface="in" name="delta_S6_rxn6"/>
<variable units="flux" public_interface="in" name="J"/>
<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>S6</ci>
</apply>
<apply>
<plus/>
<ci>delta_S6_rxn5</ci>
<ci>delta_S6_rxn6</ci>
<ci>J</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="S6_ex" name="S6_ex">
<variable units="millimolar" public_interface="out" name="S6_ex"/>
<variable units="dimensionless" name="psi" initial_value="0.1"/>
<variable units="flux" public_interface="in" name="delta_S6_ex_rxn9"/>
<variable units="flux" public_interface="in" name="J"/>
<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>S6_ex</ci>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> psi </ci>
<ci> J </ci>
</apply>
<ci>delta_S6_ex_rxn9</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="A3" name="A3">
<variable units="millimolar" public_interface="out" name="A3"/>
<variable units="flux" public_interface="in" name="delta_A3_rxn1"/>
<variable units="flux" public_interface="in" name="delta_A3_rxn3"/>
<variable units="flux" public_interface="in" name="delta_A3_rxn4"/>
<variable units="flux" public_interface="in" name="delta_A3_rxn7"/>
<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>A3</ci>
</apply>
<apply>
<plus/>
<ci>delta_A3_rxn1</ci>
<ci>delta_A3_rxn3</ci>
<ci>delta_A3_rxn4</ci>
<ci>delta_A3_rxn7</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="A" name="A">
<variable units="millimolar" name="A" initial_value="4.0"/>
<variable units="millimolar" public_interface="out" name="A2"/>
<variable units="millimolar" public_interface="in" name="A3"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>A</ci>
<apply>
<plus/>
<ci> A2 </ci>
<ci> A3 </ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="N2" name="N2">
<variable units="millimolar" public_interface="out" name="N2"/>
<variable units="flux" public_interface="in" name="delta_N2_rxn3"/>
<variable units="flux" public_interface="in" name="delta_N2_rxn6"/>
<variable units="flux" public_interface="in" name="delta_N2_rxn8"/>
<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>N2</ci>
</apply>
<apply>
<plus/>
<ci>delta_N2_rxn3</ci>
<ci>delta_N2_rxn6</ci>
<ci>delta_N2_rxn8</ci>
</apply>
</apply>
</math>
</component>
<component name="N">
<variable units="millimolar" name="N" initial_value="1.0"/>
<variable units="millimolar" public_interface="out" name="N1"/>
<variable units="millimolar" public_interface="in" name="N2"/>
<variable units="minute" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>N</ci>
<apply>
<plus/>
<ci> N1 </ci>
<ci> N2 </ci>
</apply>
</apply>
</math>
</component>
<component name="reaction_1">
<variable units="millimolar" public_interface="in" name="S1"/>
<variable units="millimolar" public_interface="in" name="A3"/>
<variable units="millimolar" public_interface="in" name="S2"/>
<variable units="millimolar" public_interface="in" name="A2"/>
<variable units="millimolar" name="K_i" initial_value="1.0"/>
<variable units="second_order_rate_constant" name="k_1" initial_value="550.0"/>
<variable units="flux" public_interface="out" name="delta_S1_rxn1"/>
<variable units="flux" public_interface="out" name="delta_A3_rxn1"/>
<variable units="flux" public_interface="out" name="delta_S2_rxn1"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="S1">
<role stoichiometry="1" direction="forward" delta_variable="delta_S1_rxn1" role="reactant"/>
</variable_ref>
<variable_ref variable="A3">
<role stoichiometry="2" direction="forward" delta_variable="delta_A3_rxn1" role="reactant"/>
</variable_ref>
<variable_ref variable="S2">
<role stoichiometry="1" direction="forward" delta_variable="delta_S2_rxn1" role="product"/>
</variable_ref>
<variable_ref variable="A2">
<role direction="forward" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_1 </ci>
<ci> S1 </ci>
<ci> A3 </ci>
<apply>
<power/>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> A3 </ci>
<ci> K_i </ci>
</apply>
<cn cellml:units="dimensionless"> 4.0 </cn>
</apply>
</apply>
<cn cellml:units="dimensionless"> -1.0 </cn>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction_2">
<variable units="millimolar" public_interface="in" name="S2"/>
<variable units="millimolar" public_interface="in" name="S3"/>
<variable units="first_order_rate_constant" name="k_2" initial_value="9.8"/>
<variable units="flux" public_interface="out" name="delta_S2_rxn2"/>
<variable units="flux" public_interface="out" name="delta_S3_rxn2"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="S2">
<role stoichiometry="1" direction="forward" delta_variable="delta_S2_rxn2" role="reactant"/>
</variable_ref>
<variable_ref variable="S3">
<role stoichiometry="2" direction="forward" delta_variable="delta_S3_rxn2" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_2 </ci>
<ci> S2 </ci>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction_3">
<variable units="millimolar" public_interface="in" name="S3"/>
<variable units="millimolar" public_interface="in" name="S4"/>
<variable units="millimolar" public_interface="in" name="N1"/>
<variable units="millimolar" public_interface="in" name="N2"/>
<variable units="millimolar" public_interface="in" name="A2"/>
<variable units="millimolar" public_interface="in" name="A3"/>
<variable units="second_order_rate_constant" name="k_GAPDH_plus" initial_value="323.8"/>
<variable units="second_order_rate_constant" name="k_GAPDH_minus" initial_value="57823.1"/>
<variable units="second_order_rate_constant" name="k_PGK_plus" initial_value="76411.1"/>
<variable units="second_order_rate_constant" name="k_PGK_minus" initial_value="23.7"/>
<variable units="flux" public_interface="out" name="delta_S3_rxn3"/>
<variable units="flux" public_interface="out" name="delta_S4_rxn3"/>
<variable units="flux" public_interface="out" name="delta_N2_rxn3"/>
<variable units="flux" public_interface="out" name="delta_A3_rxn3"/>
<variable units="flux" name="r"/>
<reaction reversible="yes">
<variable_ref variable="S3">
<role stoichiometry="1" direction="forward" delta_variable="delta_S3_rxn3" role="reactant"/>
</variable_ref>
<variable_ref variable="N1">
<role direction="forward" role="reactant"/>
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<variable_ref variable="A2">
<role direction="forward" role="reactant"/>
</variable_ref>
<variable_ref variable="S4">
<role stoichiometry="1" direction="forward" delta_variable="delta_S4_rxn3" role="product"/>
</variable_ref>
<variable_ref variable="N2">
<role stoichiometry="1" direction="forward" delta_variable="delta_N2_rxn3" role="product"/>
</variable_ref>
<variable_ref variable="A3">
<role stoichiometry="1" direction="forward" delta_variable="delta_A3_rxn3" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<times/>
<ci> k_GAPDH_plus </ci>
<ci> k_PGK_plus </ci>
<ci> S3 </ci>
<ci> N1 </ci>
<ci> A2 </ci>
</apply>
<apply>
<times/>
<ci> k_GAPDH_minus </ci>
<ci> k_PGK_minus </ci>
<ci> S4 </ci>
<ci> A3 </ci>
<ci> N2 </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k_GAPDH_minus </ci>
<ci> N2 </ci>
</apply>
<apply>
<times/>
<ci> k_PGK_plus </ci>
<ci> A2 </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction_4">
<variable units="millimolar" public_interface="in" name="S4"/>
<variable units="millimolar" public_interface="in" name="A2"/>
<variable units="millimolar" public_interface="in" name="S5"/>
<variable units="millimolar" public_interface="in" name="A3"/>
<variable units="second_order_rate_constant" name="k_4" initial_value="80.0"/>
<variable units="flux" public_interface="out" name="delta_S4_rxn4"/>
<variable units="flux" public_interface="out" name="delta_S5_rxn4"/>
<variable units="flux" public_interface="out" name="delta_A3_rxn4"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="S4">
<role stoichiometry="1" direction="forward" delta_variable="delta_S4_rxn4" role="reactant"/>
</variable_ref>
<variable_ref variable="A2">
<role direction="forward" role="reactant"/>
</variable_ref>
<variable_ref variable="S5">
<role stoichiometry="1" direction="forward" delta_variable="delta_S5_rxn4" role="product"/>
</variable_ref>
<variable_ref variable="A3">
<role stoichiometry="1" direction="forward" delta_variable="delta_A3_rxn4" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_4 </ci>
<ci> S4 </ci>
<ci> A2 </ci>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction_5">
<variable units="millimolar" public_interface="in" name="S5"/>
<variable units="millimolar" public_interface="in" name="S6"/>
<variable units="first_order_rate_constant" name="k_5" initial_value="9.7"/>
<variable units="flux" public_interface="out" name="delta_S5_rxn5"/>
<variable units="flux" public_interface="out" name="delta_S6_rxn5"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="S5">
<role stoichiometry="1" direction="forward" delta_variable="delta_S5_rxn5" role="reactant"/>
</variable_ref>
<variable_ref variable="S6">
<role stoichiometry="1" direction="forward" delta_variable="delta_S6_rxn5" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_5 </ci>
<ci> S5 </ci>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction_6">
<variable units="millimolar" public_interface="in" name="S6"/>
<variable units="millimolar" public_interface="in" name="N1"/>
<variable units="millimolar" public_interface="in" name="N2"/>
<variable units="second_order_rate_constant" name="k_6" initial_value="2000.0"/>
<variable units="flux" public_interface="out" name="delta_S6_rxn6"/>
<variable units="flux" public_interface="out" name="delta_N2_rxn6"/>
<variable units="flux" name="r"/>
<reaction reversible="no">
<variable_ref variable="S6">
<role stoichiometry="1" direction="forward" delta_variable="delta_S6_rxn6" role="reactant"/>
</variable_ref>
<variable_ref variable="N2">
<role stoichiometry="1" direction="forward" delta_variable="delta_N2_rxn6" role="reactant"/>
</variable_ref>
<variable_ref variable="N1">
<role direction="forward" role="product"/>
</variable_ref>
<variable_ref variable="r">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> r </ci>
<apply>
<times/>
<ci> k_6 </ci>
<ci> S6 </ci>
<ci> N2 </ci>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction_7">
<variable units="millimolar" public_interface="in" name="A3"/>
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Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations
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This is the CellML description of Wolf et al's mathematical model of
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The University of Auckland, Bioengineering Institute
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<vCard:Given>Jacky</vCard:Given>
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