JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations

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• 作者：Alida Palmisano ; Stefan Hoops ; Layne T. Watson ; Thomas C. Jones Jr…
• 关键词：Systems biology ; Biological networks ; Mathematical modeling ; Chemical reaction systems ; COPASI ; SBML ; Software ; Model editor ; Parameter hierarchy ; Mutants
• 刊名：BMC Systems Biology
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：9
• 期：1
• 全文大小：3,719 KB
• 刊物主题：Bioinformatics; Systems Biology; Simulation and Modeling; Computational Biology/Bioinformatics; Physiological, Cellular and Medical Topics; Algorithms;
• 出版者：BioMed Central
• ISSN：1752-0509

文摘

Background Most biomolecular reaction modeling tools allow users to build models with a single list of parameter values. However, a common scenario involves different parameterizations of the model to account for the results of related experiments, for example, to define the phenotypes for a variety of mutations (gene knockout, over expression, etc.) of a specific biochemical network. This scenario is not well supported by existing model editors, forcing the user to manually generate, store, and maintain many variations of the same model.