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.īiology is becoming a quantitative science. Conclusionįacile is a simple, yet powerful, tool that greatly accelerates analysis of the dynamics of a biochemical network. This form is essential for bifurcation analysis, and Facile produces a C version of the reduced model for AUTO. Facile automatically identifies mass conservations and generates the reduced form of a model with the minimum number of independent variables. 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). We present Facile, a Perl command-line tool for analysing the dynamics of a systems biology model. 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. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unknown. See the reference guide for a complete list of supported programming languages.Ĭode is usually stored in a source file, therefore a command that automatically pulls code from a file becomes very handy.A goal of systems biology is the quantitative modelling of biochemical networks.

The additional parameter inside brackets enables code highlighting for this particular programming language (Python), special words are in boldface font and comments are italicized. The code above produces the following output:

VT = np.zeros((n*m,1), int) #dummy variable

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