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ISMB/ECCB Stockholm 2009:
ISMB/ECCB
TT26: Nicolas Le Noväre - BioModels Database, a database of curated and annotated quantitative models with Web Services and analysis tools
June 29
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duprat julien, Melanie and Khader Shameer liked this
Lots of things are called models. He's NOT going to talk about HMM, Bayesian models, sailboat models, supermodels :)
- Allyson Lister
Models and their description/metadata need to be accessible
- Allyson Lister
Models have to be encoded in SBML and follow the MIRIAM guidelines
- Allyson Lister
There's been a steady increase in the numbers of models in BioModels. There are about 35000 reactions and about 400 models.
- Allyson Lister
Standard search functionality available from their website at the EBI (http://www.ebi.ac.uk/biomodels)
- Allyson Lister
Can export in CellML, BioPAX and others (though the SBML is the curated, perhaps more "trusted", version).
- Allyson Lister
You can also just extract portions of the models: these will end up as valid SBML models in their own right.
- Allyson Lister
Blog post: http://themindwobbles.wordpress.com/2009...
- Allyson Lister
@Alyson: Sorry to be picky, but the abstract says: "Models are accepted in two common formats, SBML and CellML." :-)
- Dagmar
@Dagmar - good point. I thought so as well, but that's what Nicolas said. Can we say it's his fault for saying the wrong thing about his database? ;) (If indeed it is the wrong thing?)
- Allyson Lister