Modeling molecular regulatory networks with JigCell and PET.
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.
Shaffer
Clifford A
CA
Department of Computer Science, Virginia Tech, Blacksburg, 24061, USA.
Zwolak
Jason W
JW
Randhawa
Ranjit
R
Tyson
John J
JJ
D000818:Animals; D002453:Cell Cycle; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D053263:Gene Regulatory Networks; D008954:Models, Biological; D012984:Software; D014982:Xenopus laevis / Q000502:physiology