Uses and Examples of SystemModeler

Glycolysis: Study Oscillations in Yeast Cells

Glycolytic oscillations in yeast cells of the species Saccharomyces cerevisiae is a well-studied phenomenon. This example simulates the oscillations near a so-called Hopf bifurcation. Changing a parameter slightly around the bifurcation point qualitatively changes the behavior of the system.

To run this example, you'll need

SystemModeler 3.

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Import SBML Models

Easily import the model in the Systems Biology Markup Language (SBML) format.

Simulate Different Scenarios

Compare how small changes in the bifurcation parameter affect the oscillations of protein and molecule concentrations.
         
 
BioChem example model
for yeast glycolysis
Cytosol component
ATP oscillations on different
sides of the bifurcation point
  
   
   
         
Visualize Biological Reaction Networks

Use the built-in BioChem library to visualize and simulate the model.
 
Hynne et al., 2001. Full-scale model of glycolysis in Saccharomyces cerevisiae.
Biophys Chem. 94(1–2):121–63.
  
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