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Library Dependency

This is a placeholder model. It 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 SystemModeler, 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.

The following documentation is taken from the main example of the downloadable model. Once you have downloaded all the model dependencies, the model can be downloaded here.

Glycolysis: Study Oscillations in Yeast Cells

CONTENTS:

ˇ Introduction

ˇ Simulation

Introduction

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 SystemModeler and designed using the BioChem library.

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

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

Simulation

To simulate the model, follow the steps below:

Click the button in the top-right corner.
When the build is finished, click 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.

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 Tools ▶ Initialize ▶ From Experiment. This sets the initial state for the next simulation to be the final state of the previous simulation.