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New BioModels Database Release

Hinxton, Wednesday 25th March 2009

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

In this release, 42 new models entered the curated branch. The public version of BioModels Database now contains 211 models in the curated and 124 in the non-curated branch. Together these 335 models comprise 28726 species and 36093 reactions. Some of the existing models have been slightly changed to correct unit inconsistencies and to enhance reusability. Also the annotations of some existing models have been updated. The database now features around 13818 cross-references.

After last data release, BioModels Database software has added some new features and the first mirror site has been online since 26th February, 2009. Some features concerning public users are:

[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: Chen Li (main developer), Nicolas Rodriguez (Alumni: Melanie Courtot, Marco Donizelli, Arnaud Henry, Lu Li)

Former collaborators and funders: BioModels Database also benefited from the help of Herbert Sauro (Washington University, USA) and Hiroaki Kitano (Systems Biology Institute, Japan), and from the funds of the DARPA (Sauro team).

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, SBMLOdeSolver, SBMLeditor, SBMLmerge, JigCell and XPP-Aut.

Statistics


ReleaseModelsSpeciesReactionsCross-references

25/March/2009 335 28726 36093 13818
03/December/2008 293 27238 34443 13206
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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