WOLFRAM SYSTEM MODELER

GlycolysisModel

Main model - Extracellular compartment

Diagram

Wolfram Language

In[1]:=
SystemModel["IndustryExamples.LifeSciences.Glycolysis.GlycolysisModel"]
Out[1]:=

Information

Library Dependency

This model requires the BioChem library.

  • The free BioChem library is an extendable, general purpose Modelica library for modeling, simulation and visualization of biological and biochemical systems. The library is designed to be used together with Wolfram System Modeler, which enables several extra features such as Systems Biology Markup Language (SBML) import and export. BioChem can, for instance, be used for selecting drug targets with PK/PD modeling or searching for novel drug targets with mechanistic modeling of the reactions in a cell or organism.

Model

This is the main model in this example, and it simulates glycolytic oscillations in Saccharomyces cerevisiae (yeast cells) as described in 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.

The model has been imported from the BioModels Database using the SBML importer in Wolfram System Modeler and designed using the BioChem library.

To import SBML models in Wolfram System Modeler, the Systems Biology add-on needs to be enabled. To enable this add-on, open the options dialog box by choosing ToolsOptions. The setting is located in the GlobalAdd-On Products view. Note that for the changes to have an effect after changing this setting, System Modeler must be restarted.

More information on the Systems Biology add-on can be found under HelpSystems Biology.

View the model diagram for this model.

Simulation

Simulate the model by clicking the Simulate button:

In its default configuration, the model produces a stable limit cycle. Look at, for instance, the variable cytosol.ATP.c to study the oscillations. Plot the variable by expanding the tree in the Plot view in the Simulation Center. First expand the cytosol branch, then the ATP branch, and finally select the c variable by checking the box next to it.

plotVariable

The plot of the variable will appear in a plot window to the right.

To simulate the model on the other side of the bifurcation point, update the initial conditions of the model by choosing ToolsInitializeFrom Experiment. This sets the initial state for the next simulation to be the final state of the previous simulation.

initialize

Select your current experiment, for instance GlycolysisModel 1, and click OK.

Finally, change the initial value of GlcX0.c from 0.020 to 0.0175 in the Variables tab in Simulation Center.

simSettings

Simulating again, the variable cytosol.ATP.c will now converge back to a steady state.

As you can see, small changes in a bifurcation parameter can qualitatively change the oscillations of protein and molecule concentrations.

Parameters (1)

mainCompartment

Value: true

Type: Boolean

Description: Specifies whether the compartment is a main (top-level) compartment. Used in SBML import/export.

Components (22)

cytosol

Type: Cytosol

Description: Cytosolic compartment

GlcX

Type: GlcX_

Description: Extracellular glucose

EtOHX

Type: EtOHX_

Description: Extracellular ethanol

GlycX

Type: GlycX_

Description: Extracellular glycerol

ACAX

Type: ACAX_

Description: Extracellular acetaldehyde

CNX

Type: CNX_

Description: Extracellular cyanide

CNX0

Type: CNX0_

Description: Mixed flow cyanide

GlcX0

Type: GlcX0_

Description: Mixed flow glucose

vinGlc

Type: vinGlc_

Description: Glucose Mixed flow to extracellular medium

vGlcTrans

Type: vGlcTrans_

Description: Glucose uptake

vdifEtOH

Type: vdifEtOH_

Description: Ethanol out

voutEtOH

Type: voutEtOH_

Description: Ethanol flow

vdifGlyc

Type: vdifGlyc_

Description: Glycerol out

voutGlyc

Type: voutGlyc_

Description: Glycerol flow

vdifACA

Type: vdifACA_

Description: Acetaldehyde out

voutACA

Type: voutACA_

Description: Acetaldehyde flow

vlacto

Type: vlacto_

Description: Cyanide-Acetaldehyde flow

vinCN

Type: vinCN_

Description: Cyanide flow

P1

Type: AmbientSubstance

Description: Substance used as a reservoir in reactions

P2

Type: AmbientSubstance

Description: Substance used as a reservoir in reactions

P3

Type: AmbientSubstance

Description: Substance used as a reservoir in reactions

P4

Type: AmbientSubstance

Description: Substance used as a reservoir in reactions