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 in Edinburgh.

To download sencillo, right click here. There is no other installation to do, but you will need to have Scientific Python, which is straighforward to install and works on all platforms.

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
  parameter 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 and Python, 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.