WOLFRAM SYSTEM MODELER
GlycolysisMain model of the example |
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Diagram
Wolfram Language
In[1]:=
SystemModel["BioChem.Examples.YeastGlycolysis.Glycolysis"]
Out[1]:=
Information
The model simulates glycolysis and glycolytic oscillations in intact yeast cells and is based on data measured on a suspension of living cells of Saccharomyces cerevisiae near a Hopf bifurcation, and to a large set of stationary concentrations and other data estimated from comparable batch experiments. The model agrees with almost all experimentally known stationary concentrations and metabolic fluxes, with the frequency of oscillation and with the majority of other experimentally known kinetic and dynamical variables.
Fig. 1 corresponds to Figure 6 in the original publication by F. Hynne et al. (2001) and is the default simulation produced by the model.
Fig. 1 corresponds to Figure 6 in the original publication by F. Hynne et al. (2001) and is the default simulation produced by the model.
References
F. Hynne, S. Danø, and P. G. Sørensen, "Full-Scale Model of Glycolysis in Saccharomyces cerevisiae," Biophysical Chemistry, 94(1-2), 2001 pp. 121-163. doi:10.1016/S0301-4622(01)00229-0Parameters (3)
| mainCompartment |
Value: true Type: Boolean Description: Specifies whether the compartment is a main (top-level) compartment. Used in SBML import/export. |
|---|---|
| cGlcX0 |
Value: 24 / 1000 Type: Concentration (mol/l) Description: Initial concentration of glucose surrounding yeast cell |
| cCnX0 |
Value: 5.6 / 1000 Type: Concentration (mol/l) Description: Initial concentration of cyanide surrounding yeast cell |
Components (22)
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cytosol |
Type: Cytosol Description: Cytosolic compartment |
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GlcX |
Type: GlcX_ Description: Extracellular glucose |
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EtOHX |
Type: EtOHX_ Description: Extracellular ethanol |
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GlycX |
Type: GlycX_ Description: Extracellular glycerol |
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ACAX |
Type: ACAX_ Description: Extracellular acetaldehyde |
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CNX |
Type: CNX_ Description: Extracellular cyanide |
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CNX0 |
Type: CNX0_ Description: Mixed flow cyanide |
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GlcX0 |
Type: GlcX0_ Description: Mixed flow glucose |
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vinGlc |
Type: vinGlc_ Description: Glucose Mixed flow to extracellular medium |
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vGlcTrans |
Type: vGlcTrans_ Description: Glucose uptake |
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vdifEtOH |
Type: vdifEtOH_ Description: Ethanol out |
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voutEtOH |
Type: voutEtOH_ Description: Ethanol flow |
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vdifGlyc |
Type: vdifGlyc_ Description: Glycerol out |
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voutGlyc |
Type: voutGlyc_ Description: Glycerol flow |
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vdifACA |
Type: vdifACA_ Description: Acetaldehyde out |
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voutACA |
Type: voutACA_ Description: Acetaldehyde flow |
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vlacto |
Type: vlacto_ Description: Cyanide-Acetaldehyde flow |
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vinCN |
Type: vinCN_ Description: Cyanide flow |
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P1 |
Type: AmbientSubstance Description: Substance used as a reservoir in reactions |
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P2 |
Type: AmbientSubstance Description: Substance used as a reservoir in reactions |
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P3 |
Type: AmbientSubstance Description: Substance used as a reservoir in reactions |
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P4 |
Type: AmbientSubstance Description: Substance used as a reservoir in reactions |