Facile: a command-line network compiler for systems biology.
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.


CONCLUSIONS
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.
Siso-Nadal
Fernando
F
Centre for Non-linear Dynamics, Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada. fs226@cnd.mcgill.ca
Ollivier
Julien F
JF
Swain
Peter S
PS
D003198:Computer Simulation; D003199:Computer Systems; D003201:Computers; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D017711:Nonlinear Dynamics; D012984:Software; D049490:Systems Biology / Q000295:instrumentation* / Q000379:methods*