Prof Darren Wilkinson Professor of Stochastic Modelling
School of Mathematics & Statistics
Newcastle University

SBML-shorthand mod2sbml.py and sbml2mod.py

This page archives all versions of SBML-shorthand specifications and translation tools.

SBML-shorthand specification

mod2sbml.py model translation tool

Note about libSBML version dependencies! Most of these converters require installation of libSBML and the libsbml python bindings. The libSBML API is currently undergoing a period of rapid change, and so it is vital that you use a version of the scripts that is suitable for the version of libSBML that you have installed. That may mean that you need to use an old version of the conversion scripts. I am trying to keep scripts up to date with current libSBML releases, and I am hoping to get SBML Level 3 support implemented during the SBML Hackathon taking place early May 2010.

Python-only

Python+libsbml < 3.0.0

Python+libsbml >= 3.0.0 (and < 4.0.0)

Python+libsbml >= 4.1.0 (and < 5.0.0)

Note that this translator is written in Python, so you need a working Python environment in order to use it. Most of the scripts also require libSBML and the libSBML Python bindings. The latest version of the code is strongly recommended. The old code is not being maintained.

sbml2mod.py

Python-only

Python+libsbml < 3.0.0

Python+libsbml >= 3.0.0 (and < 4.0.0)

Python+libsbml >= 4.1.0 (and < 5.0.0)

Darren J Wilkinson Book: Stochastic Modelling for
              Systems Biology  
d.j.wilkinson@ncl.ac.uk
http://www.staff.ncl.ac.uk/d.j.wilkinson/