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VFA:a visual tool for metabolic network modeling

Hong Zhou

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Abstract

Mathematical modeling is a vital method for metabolic engineering study.When used to deal with metabolic fluxes,currently various tools for metabolic network modeling may however just construct Flux Balance Analysis(FBA) or 13C Metabolite Flux Analysis(13C-MFA) models respectively.Most of them use local format to describe metabolic models,which may lead to the inconvenience of information sharing.To resolve such a problem,we developed a tool of VFA(Visual Flux Analyzer) based on Cytoscape plug-in.Compared with VFA,the modeling method based on text may be niggling and error-prone.Moreover,VFA has a friendly GUI,expedient visual presentation and modeling functions,which can build both FBA and 13C-MFA models on given metabolic networks.Since the format of description for metabolic models in VFA is extended from and completely compatible with Systems Biology Markup Language(SBML),it may be beneficial to models sharing and exchange among different platforms.

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What this paper is about

Mathematical modeling is a vital method for metabolic engineering study.When used to deal with metabolic fluxes,currently various tools for metabolic network modeling may however just construct Flux Balance Analysis(FBA) or 13C Metabolite Flux Analysis(13C-MFA) models respectively.Most of them use local format to describe metabolic models,which may lead to the inconvenience of information sharing.To resolve such a problem,we developed a tool of VFA(Visual Flux Analyzer) based on Cytoscape plug-in.Compared with VFA,the modeling method based on text may be niggling and error-prone.Moreover,VFA has a friendly GUI,expedient visual presentation and modeling functions,which can build both FBA and 13C-MFA models on given metabolic networks.Since the format of description for metabolic models in VFA is extended from and completely compatible with Systems Biology Markup Language(SBML),it may be beneficial to models sharing and exchange among different platforms.

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Available abstract

Mathematical modeling is a vital method for metabolic engineering study.When used to deal with metabolic fluxes,currently various tools for metabolic network modeling may however just construct Flux Balance Analysis(FBA) or 13C Metabolite Flux Analysis(13C-MFA) models respectively.Most of them use local format to describe metabolic models,which may lead to the inconvenience of information sharing.To resolve such a problem,we developed a tool of VFA(Visual Flux Analyzer) based on Cytoscape plug-in.Compared with VFA,the modeling method based on text may be niggling and error-prone.Moreover,VFA has a friendly GUI,expedient visual presentation and modeling functions,which can build both FBA and 13C-MFA models on given metabolic networks.Since the format of description for metabolic models in VFA is extended from and completely compatible with Systems Biology Markup Language(SBML),it may be beneficial to models sharing and exchange among different platforms.

Key concepts: SBML, Metabolic network, Flux balance analysis, Markup language, Computer science, Metabolic flux analysis, Metabolic engineering, Flux (metallurgy)

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