Modeling Molecular Regulatory Networks with JigCell and PET

  • Clifford A. Shaffer
  • Jason W. Zwolak
  • Ranjit Randhawa
  • John J. Tyson
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 500)

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 

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Copyright information

© Humana Press 2009

Authors and Affiliations

  • Clifford A. Shaffer
    • 1
  • Jason W. Zwolak
    • 1
  • Ranjit Randhawa
    • 1
  • John J. Tyson
    • 1
  1. 1.Department of Computer ScienceVirginia TechBlacksburg

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