Meetings & Conferences Software and Tools Standards

TT26: BioModels Database, a database of curated and annotated quantitative models with Web Services and analysis tools (ISMB 2009)

Nicolas Le Novère

Lots of things are called models. He’s NOT going to talk about HMM, Bayesian models, sailboat models, supermodels 🙂 For him, a model is computer-readable, simulatable, and covers biological pathways. Models and their description/metadata need to be accessible. The models in BioModels are from peer-reviewed literature. THey check the model is OK and simulate them before accepting it into the database. Models can be either submitted by curators themselves (e.g. re-implemented from literature), or directly submitted by authors, or a few other ways.

Models also have to be encoded in SBML and follow the MIRIAM guidelines, which are reporting guidelines for the encoding and annotation of models, and is limited at the moment to models that can be quantitatively evaluated. There are seven basic requirements for MIRIAM compliance, which are available online. Within the model, MIRIAM annotations are identified by URIs and are stored as RDF. There’s been a steady increase in the numbers of models in BioModels. There are about 35000 reactions and about 400 models. Standard search functionality available from their website at the EBI (

Can export in CellML, BioPAX and others (though the SBML is the curated, perhaps more “trusted”, version). There are also two simple simulators available directly from the entry’s webpage, and if you want to change parameters you can click through to JWS online. You can also just extract portions of the models: these will end up as valid SBML models in their own right.

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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!