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Literature DB >> 19399431

Modeling molecular regulatory networks with JigCell and PET.

Clifford A Shaffer¹, Jason W Zwolak, Ranjit Randhawa, John J Tyson.

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.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2009 PMID： 19399431 PMCID： PMC3773233 DOI： 10.1007/978-1-59745-525-1_4

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

17 in total

1. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors: M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal: Bioinformatics Date: 2003-03-01 Impact factor: 6.937

2. Modeling regulatory networks at Virginia Tech.

Authors: Nicholas A Allen; Laurence Calzone; Katherine C Chen; Andrea Ciliberto; Naren Ramakrishnan; Clifford A Shaffer; Jill C Sible; John J Tyson; Marc T Vass; Layne T Watson; Jason W Zwolak
Journal: OMICS Date: 2003

Review 3. Conservation analysis in biochemical networks: computational issues for software writers.

Authors: Herbert M Sauro; Brian Ingalls
Journal: Biophys Chem Date: 2004-04-01 Impact factor: 2.352

4. Parameter estimation for a mathematical model of the cell cycle in frog eggs.

Authors: Jason W Zwolak; John J Tyson; Layne T Watson
Journal: J Comput Biol Date: 2005 Impact factor: 1.479

5. Regulation of the cdc25 protein during the cell cycle in Xenopus extracts.

Authors: A Kumagai; W G Dunphy
Journal: Cell Date: 1992-07-10 Impact factor: 41.582

6. The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models.

Authors: Marc T Vass; Clifford A Shaffer; Naren Ramakrishnan; Layne T Watson; John J Tyson
Journal: IEEE/ACM Trans Comput Biol Bioinform Date: 2006 Apr-Jun Impact factor: 3.710

7. Modeling M-phase control in Xenopus oocyte extracts: the surveillance mechanism for unreplicated DNA.

Authors: G Marlovits; C J Tyson; B Novak; J J Tyson
Journal: Biophys Chem Date: 1998-05-05 Impact factor: 2.352

8. Globally optimised parameters for a model of mitotic control in frog egg extracts.

Authors: J W Zwolak; J J Tyson; L T Watson
Journal: Syst Biol (Stevenage) Date: 2005-06

9. Control of the Cdc2/cyclin B complex in Xenopus egg extracts arrested at a G2/M checkpoint with DNA synthesis inhibitors.

Authors: A Kumagai; W G Dunphy
Journal: Mol Biol Cell Date: 1995-02 Impact factor: 4.138