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BMC Syst Biol. 2012 Jan 30;6:8. doi: 10.1186/1752-0509-6-8.

FAME, the Flux Analysis and Modeling Environment.

Author information

1
Systems Bioinformatics/AIMMS, VU University Amsterdam, De Boelelaan 1085, 1081HV, Amsterdam, The Netherlands.

Abstract

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.

PMID:
22289213
PMCID:
PMC3317868
DOI:
10.1186/1752-0509-6-8
[Indexed for MEDLINE]
Free PMC Article
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