FAME, the Flux Analysis and Modeling Environment

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome / genetics*
  • Internet*
  • Metabolic Networks and Pathways / genetics*
  • Models, Biological*
  • Software*
  • Systems Biology / methods*