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BioModels Database


New Version

Hinxton, Sunday 18th September 2005

We are pleased to announce a new version of the BioModels Database.

This is not a new release, since the public content of the database has not been altered. However, beside the color code, pretty much everything changed!

New Infrastructure

BioModels Database is now based on a dual database system. While the core models are still handled through the XML Native database engine Xindice, all the annotations and associated information are managed through a relational MySQL database.

A complete pipeline of curation and annotation handles each model from its submission to its final publication, taking care of the necessary format conversions, ensuring the model syntax is valid at all time, and in general providing help to the curators and annotators. Models are now accepted in all SBML and CellML formats, and, after a model has been converted to SBML Level 2, syntactic and consistency checks are automatically run.

The search features have been much enhanced, thanks to the move to MySQL. A simplified "one field" search has been introduced, and the advanced search has been completed, with the possibility of textual search in ChEBI and UniProt. A person is now an author of an article, a creator of a model, or a submitter of a model. All the queries are also much faster.

New Export Formats

In addition to SBML, models can now be downloaded in the CellML format, and also as ODE files for the numerical analysis program XPP-Aut. The XSL stylesheets used for the transformation are available here.

New Visualisation Layout

Since the latest release, the graph of the reactions is available, each node being linked to the adequate component of the model.

The mathematical expressions present in a model can now be visualised, as well as the numerical values of all the parameters.

Three levels of unfolding allow a more efficient browsing of a model, particularly in the case of large ones.


BioModels Database is developed in collaboration developed by the teams of Nicolas Le Novère (EMBL-EBI, UK), Michael Hucka (Caltech, USA), Herbert Sauro (Keck Graduate Institute, USA) and Jacky Snoep (Stellenbosch University, ZA), as part of the initiative.

Developers: Marco Donizelli, Melanie Courtot and Lu Li.

Model curators and annotators: Harish Dharuri, Nicolas Le Novère, Bruce Shapiro.

External contributors: Upinder Bhalla, Christoph Flamm, Ryan Gutenkunst, Adam Halasz, Rainer Machné, Marc Poolman, Tomas Radivoyevitch, Oleg Sokolsy (models), Ben Bornstein, Sarah Keating, Joanne Matthews, Maria Schilstra (software), Alexander Broicher, Les Grivell, Noriko Hiroi, Boris Kholodenko, Ursula Kummer, Tjeerd Olde Scheper, Paul Smolen, Yukiko Matsuoka (miscellaneous).