期刊
BMC SYSTEMS BIOLOGY
卷 6, 期 -, 页码 -出版社
BMC
DOI: 10.1186/1752-0509-6-8
关键词
-
资金
- National Institutes of Health [GM068837, GM057089, GM062791]
Background: The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoint code, which adds additional actions to the analysis routine and, in our experience, renders these applications suboptimal for routine use by (systems) biologists. Results: The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/. Conclusions: With FAME, we present the community with an open source, user-friendly, web-based one stop shop for stoichiometric modeling. We expect the application will be of substantial use to investigators and educators alike.
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