Protocol

Systems Biology

Volume 500 of the series Methods in Molecular Biology pp 81-111

Date:

Modeling Molecular Regulatory Networks with JigCell and PET

  • Clifford A. ShafferAffiliated withDepartment of Computer Science, Virginia Tech Email author 
  • , Jason W. ZwolakAffiliated withDepartment of Computer Science, Virginia Tech
  • , Ranjit RandhawaAffiliated withDepartment of Computer Science, Virginia Tech
  • , John J. TysonAffiliated withDepartment of Computer Science, Virginia Tech

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Summary

We demonstrate how to model macromolecular regulatory networks with JigCell and the Parameter Estimation Toolkit (PET). These software tools are designed specifically to support the process typically used by systems biologists to model complex regulatory circuits. A detailed example illustrates how a model of the cell cycle in frog eggs is created and then refined through comparison of simulation output with experimental data. We show how parameter estimation tools automatically generate rate constants that fit a model to experimental data.

Keywords

Systems biology Parameter estimation Model validation