COMBINE 2013 presentations

It was really fantastic to leave a great meeting like COMBINE in Paris and fly straight to South Africa for a vacation. I'll post some vacation pictures elsewhere but for now here are links to my presentation and the slides I made while chairing the FBC session.

A short presentation: Modelling at genome scale: introducing the SBML3 FBC package

And some technical stuff on a new proposal for generic annotation and a formal UML description of the gene association extension discussed during HARMONY 2013.

COMBINE 2013: standards ride again!

Just finished having a very productive meeting at COMBINE 2013, nice to see how standards are developing, especially, that rhere are a number of things that are finally stable enough to implement. Heading up the list: SBML Groups and COMBINE Archive.

Feeling all geeked out so perhaps this is a great time for a vacation ;-)

ICSB 2013 SBML3FBC and PySCeS CBMPy

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 ;-)

Funky Amsterdam promotional video

This is a new advertisement for Amsterdam as a cool tourist destination ... and why its nice to live there ;-)

Finally registered on GitHub

After using Subversion since it replaced CVS I've decided to get going with Git (username: bgoli) and have committed the PySCeS 0.9.0 release to GitHub to play around with.