Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Methods Mol Biol
2009 Jan 01;500:81-111. doi: 10.1007/978-1-59745-525-1_4.
Show Gene links
Show Anatomy links
Modeling molecular regulatory networks with JigCell and PET.
Shaffer CA, Zwolak JW, Randhawa R, Tyson JJ.
???displayArticle.abstract???
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.
Allen,
Modeling regulatory networks at Virginia Tech.
2003, Pubmed
Allen,
Modeling regulatory networks at Virginia Tech.
2003,
Pubmed Cao,
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems.
2004,
Pubmed Chen,
Integrative analysis of cell cycle control in budding yeast.
2004,
Pubmed Hucka,
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.
2004,
Pubmed Hucka,
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
2003,
Pubmed Kumagai,
Regulation of the cdc25 protein during the cell cycle in Xenopus extracts.
1992,
Pubmed
,
Xenbase Kumagai,
Control of the Cdc2/cyclin B complex in Xenopus egg extracts arrested at a G2/M checkpoint with DNA synthesis inhibitors.
1995,
Pubmed
,
Xenbase Marlovits,
Modeling M-phase control in Xenopus oocyte extracts: the surveillance mechanism for unreplicated DNA.
1998,
Pubmed
,
Xenbase Mendes,
Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3.
1997,
Pubmed Sauro,
Conservation analysis in biochemical networks: computational issues for software writers.
2004,
Pubmed Sauro,
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.
2003,
Pubmed Schaff,
Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell.
2001,
Pubmed Tang,
Two distinct mechanisms for negative regulation of the Wee1 protein kinase.
1993,
Pubmed
,
Xenbase Vass,
The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models.
2006,
Pubmed Vass,
the JigCell model builder and run manager.
2004,
Pubmed Zwolak,
Globally optimised parameters for a model of mitotic control in frog egg extracts.
2005,
Pubmed Zwolak,
Parameter estimation for a mathematical model of the cell cycle in frog eggs.
2005,
Pubmed
