24 August 2013

The real advantage of a "human readable" model definition format

A colleague of mine wanted to submit a model along with a paper that they had published and had somehow converted from their native format into SBML, unfortunately this had not been entirely successful and I was asked to diagnose the problem after COPASI reported a serious error in the file.

Using PySCeS I converted the file to the PySCeS model format where some translation errors were immediately apparent, could be compared to the original equation and fixed. Reloading the file, testing the steady-state solution and re-exporting it to SBML was a piece of cake.

Not bad going for a Friday afternoon ;-)

1 comment:

  1. This was actually a Mathematica user, but, the nice thing is it also works for MATLAB user who found it easy to translate their scripts into PySCeS MDL. Go the, almost, lost art of LY parsing - the subtleties of which are generally being lost in the current hypertagged world.