A command-line compiler for systems biology

We have Facile, a Perl version of the compiler, written by Julien Ollivier and Fernando Siso-Nadal in Montreal, and sencillo, a Python version, written by Peter Swain and Alan Munoz Gonzalez in Edinburgh.

To download sencillo, right click here.

If you use sencillo, please cite F Siso-Nadal, JF Ollivier, and PS Swain, BMC Syst Biol 1:36 (2007).

A model in sencillo is specified as a text file. An example for a two-stage model of gene expression is

  parameter a= 20
  parameter b= 2.5
  parameter d1= 5.0e-4
  variable d0= d1/10.0

  D -> M + D; v0= a*d1
  M -> null ; d0
  M -> M + A ; v1= b*d0
  A -> null ; d1

  D= 1

for DNA D, mRNA M, and protein A.

Sencillo can convert this model into ordinary differential equations for numerical solution in either Matlab, Python and Julia, into a format for algebraic (but not yet numerical) manipulation by Mathematica, into SBML version 2 (if the SBML toolbox is available), and into XML for stochastic simulation by Stochkit.

Once downloaded, typing

  python sencillo.py -h

provides further help and examples.