Facile: a command-line network compiler for systems biology
2007
Facile: A Command-Line Tool for Analyzing Biochemical Networks
publication
Evidence: moderate
Author Information
Author(s): Siso-Nadal Fernando, Ollivier Julien F, Swain Peter S
Primary Institution: Gene Network Sciences, USA; Centre for Non-linear Dynamics, McGill University, Canada
Conclusion
Facile is a simple, yet powerful, tool that greatly accelerates analysis of the dynamics of a biochemical network.
Supporting Evidence
- Facile automatically identifies mass conservations in biochemical networks.
- Facile generates a reduced form of a model in C for bifurcation analysis software.
- Facile can be easily incorporated into larger automated tasks.
Takeaway
Facile is a computer program that helps scientists quickly analyze how chemical reactions in biological systems work by using simple text commands.
Methodology
Facile compiles biochemical networks from text descriptions into formats for analysis, simulation, and bifurcation analysis.
Limitations
Facile is not intended to compete with SBML but is complementary; it requires users to have some programming knowledge.
Digital Object Identifier (DOI)
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