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New BioModels Database Release

Hinxton, Friday 28th March 2008

We are pleased to announce the tenth release of BioModels Database.

This new release sees the the addition of 52 models, 17 entering the curated branch. That brings the public version of BioModels Database 244 models representing 25731 reactions. As usual, a significant portion of the annotation of existing models has also been uptated. The database now features around 10000 cross-references.

We are now focussing on developing BioModels Database software version 3, that will see pretty much everything rewritten. Therefore the current release is mainly a data-only one. However, we are still adding a few functionalities, such as new methods in the WebServices allowing more efficient retrieval of models.

[Download All Models Under SBML L2 V1 Format]

Acknowledgements

BioModels Database is developed by the teams of Nicolas Le Novère (EMBL-EBI, United-Kingdom) and Michael Hucka (SBML Team, Caltech, USA) in collaboration with Upinder Bhalla (DOQCS, National Center for Biological Sciences, India), Ion Moraru (the Virtual Cell, USA), Herbert Sauro (Washington University, USA), Hiroaki Kitano (Systems Biology Institute, Japan), Hans Westerhoff and Jacky Snoep (JWS Online, Stellenbosch (ZA) and Manchester (UK) Universities and Stellenbosh University, ZA), as part of the BioModels.net initiative. BioModels Database development has benefitted from funds of the European Molecular Biology Laboratory (Le Novère team), the Biotechnology and Biological Sciences Research Council (Le Novère team), the National Institute of General Medical Sciences (SBML team and Le Novère team), the DARPA (Sauro team), and the National Center for Research Resources (Virtual Cell team).

Model curators and annotators: Harish Dharuri, Nicolas Le Novère, Lu Li, Rainer Machne, Bruce Shapiro (Alumni: Maria Schilstra, Enuo He)

Developers: Camille Laibe, Chen Li (main developer), Lu Li, Nicolas Rodriguez (Alumni: Mélanie Courtot, Marco Donizelli, Arnaud Henry, Lu Li)

External contributors: BioModels Database would not exists without the continuous support of many people, whether by their contribution of models, of software, or by their constructive comments and criticisms. It is unfortunately impossible to acknowledge all of them here, without risking to be unfair. Therefore, a big collective thank-you all.

BioModels Database is built thanks to many third-party free software such as libSBML, Jakarta Tomcat, Xindice, Lucene, Xalan, Xerces, Axis, Jena and MySQL, plus all the free software coming with the GNU/Linux systems.

Main software used to curate models: CellDesigner, COPASI, Jarnac, MathSBML, RoadRunner, SBMLdeSolver, SBMLeditor, SBMLmerge and XPP-Aut.

Statistics


ReleaseModelsSpeciesReactionsCross-references

28/March/2008 244 20945 25731 10498
25/September/2007 192 10482 12482 9810
05/June/2007 145 6027 7016 7692
05/January/2007 128 5697 6431 5651
03/October/2006 96 4125 4890 3074
05/June/2006 54 837 1307 3542
31/January/2006 50 761 1163 3126
28/July/2005 44 596 943 2373
01/June/2005 30 425 736 1609
11/April/2005 20 322 631 1084


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