SBML Hackathon 2009: Afternoon Session

Falko Krause presented ubuntu 4 systems biology, a live cd with some applications pre-installed, so you can try it out without having to actually install it. He says if you have any software you'd like to include, to let them know and they'll include it. They'll package your software, and your video. They have libsbml, curated biomodels, semantic sbml, copasi, and others are already installed.

Then there was a presentation of the updates on the SBML Test Suite by Sarah Keating. She went over the various options available for each semantic test case. What has changed from the first incarnation? There is L2V4 support, the settings file has changed, and some of the models have changed based on user feedback. For instance, some models used initial values that were very very low, which caused problems for some people.

I also learnt that there are three of us working on automated model annotation of varying types that are here at the SBML Hackathon. This is great news, as until recently I couldn't find anyone working on it. Here are the links to the three projects:

1. Saint: SBML Model Annotation Integration Interface. Saint allows quick and straightforward model annotation (of MIRIAM annotations, species names, sboTerms, and new reactions plus more coming soon) using a web interface. Developed by CISBAN and recently presented at a talk at BioSysBio 2009 (video and slides available soon).
2. A MIRIAM Annoation helper, developed by MCISB
3. Semantic SBML. Created initially as SBMLmerge, for merging models together, this is both a web interface and a standalone application that adds MIRIAM annotation.

There was also an interesting discussion about starting up an SBML/CellML competition with various categories.

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else's. I'm happy to correct any errors you may spot – just let me know!

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