FAME, the Flux Analysis and Modeling Environment

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, rende...

Full description

Saved in:
Bibliographic Details
Published inBMC systems biology Vol. 6; no. 1; p. 8
Main Authors Boele, Joost, Olivier, Brett G, Teusink, Bas
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 30.01.2012
BioMed Central
Subjects
Online AccessGet full text

Cover

Loading…
More Information
Summary: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. 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/. 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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1752-0509
1752-0509
DOI:10.1186/1752-0509-6-8