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New BioModels Database Release

Hinxton, Thursday 21st August 2008

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

In this new release, 17 new models entered the curated branch. That brings the public version of BioModels Database 259 models representing 27117 reactions. As usual, a significant portion of the annotation of existing models has also been updated. The database now features around 11000 cross-references.

With the new release of BioModels Database software version 3, the interface for viewing the models is enhanced. Now, beside the model lists, the user also can browse a models-tree built based on Gene Ontology. And a model's elements are presented into several sections, which represent different aspects of the model. Furthermore, a submodel of any model can be generated, based on elements selected by the users. Finally, a simple embedded simulation tool is also provided, beside the links to the more powerful JWS interface.

[Download All Models Under SBML 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), Jacky Snoep (JWS Online, Stellenbosch (ZA) University, ZA). BioModels Database development is funded by 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), and the National Center for Research Resources (Virtual Cell team).

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

Developers: Camille Laibe, Chen Li (main developer), Nicolas Rodriguez (Alumni: Melanie 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, Apache 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

21/August/2008 259 21783 27117 10811
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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