VFA:一种可视化代谢网络建模工具  

VFA:a visual tool for metabolic network modeling

作　　者：李毅[1] 郑浩然[1] 钮俊清[1] 李恒[1] 周宏[1] 

机构地区：[1]中国科学技术大学计算机科学与技术系,合肥230027

出　　处：《北京生物医学工程》2008年第5期490-493,497,共5页Beijing Biomedical Engineering

基　　金：国家重点基础研究发展计划(2006CB910700)资助

摘　　要：数学建模是代谢工程研究的关键方法之一。目前的代谢网络建模工具在构建代谢通量分析模型时,不能同时建立通量平衡分析(FBA)模型和13C代谢通量分析(13C-MFA)模型,而且大都采用私有格式描述代谢模型,不利于信息共享。为了解决上述问题,作者基于Cytoscape插件开发了一种可视化代谢通量建模工具VFA,它摆脱了繁琐、易出错的文本建模方式,提供友好的图形化用户界面、方便的可视化建模功能,并能够同时对代谢网络进行FBA和13C-MFA建模。VFA的代谢模型描述格式扩展自系统生物学标记语言(SBML),且与后者完全兼容,有利于平台间的模型交换和共享。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 （^13 C-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.

关 键 词：代谢网络 代谢通量 可视化建模 模型描述 

分 类 号：R318.04[医药卫生—生物医学工程]