New SBML editors for 2014 :-)

Awesome news to end 2013 is that after a community vote I, together with Dagmar Waltemath, have been elected to serve as an SBML editors. This is a great opportunity to contribute to the development of standards in the Life Science community and I'm really looking forward to it.

Software and standards poster presented at NISB 2012

This is a poster I presented at the NISB meeting in 2012: NISB 2012 Poster

Generic annotation in constraint based models

During COMBINE 2013 Frank and myself tried to come up with a compromise proposal that would combine the best elements of the two current "generic annotation" proposals that are under discussion.

When we presented this at COMBINE 2013 it was well received by the members of the community that attended the FBC session. For background on this discussion please see this document.

We call this proposal AdditionalProperties and an initial specification can be found here.

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