Documentation

From Facile
Jump to: navigation, search

1. Article describing Facile

Research article: Siso-Nadal F, Ollivier JF, Swain PS (2007) Facile: a command-line network compiler for systems biology. BMC Syst Biol 1:36.

Abstract

BACKGROUND: A goal of systems biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unknown. It is therefore important to be able to easily investigate the effects of adding or removing reactions and to easily perform a bifurcation analysis, which shows the qualitative dynamics of a model for a range of parameter values. RESULTS: We present Facile, a Perl command-line tool for analysing the dynamics of a systems biology model. Facile implements the law of mass action to automatically compile a biochemical network (written as, for example, E + S <-> C) into scripts for analytical analysis (Mathematica and Maple), for simulation (XPP and Matlab), and for bifurcation analysis (AUTO). Facile automatically identifies mass conservations and generates the reduced form of a model with the minimum number of independent variables. This form is essential for bifurcation analysis, and Facile produces a C version of the reduced model for AUTO. CONCLUSION: Facile is a simple, yet powerful, tool that greatly accelerates analysis of the dynamics of a biochemical network. By acting at the command-line and because of its intuitive, text-based input, Facile is quick to learn and can be incorporated into larger programs or into automated tasks.


2. Facile User Manual

The Facile_User_Manual has detailed information about Facile.


3. Article describing EasyStoch

Shahrezaei V, Ollivier JF, Swain PS. Colored extrinsic fluctuations and stochastic gene expression. Mol Syst Biol. 2008;4:196. Epub 2008 May 6.


4. EasyStoch User Manual

The EasyStoch_User_Manual has detailed information about EasyStoch.