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BioModels Database


18th BioModels Database Release

Hinxton, Thursday 30th September 2010

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

In this release, 157 new models have been published. The public version of BioModels Database now contains 269 models in the curated and 361 in the non-curated branch. Together, these 630 models comprise 79224 species and 109091 reactions. Some of the existing models have been converted to SBML Level 2 Version 4, while others have been corrected with annotational updates to enhance their reusability. The database now features 20426 cross-references.

Along with the data release, we are introducing several new converters. Models in BioModels Database are now available in these new or updated formats (as well as in the previously supported formats):

  • XPP (updated)
  • BioPAX Level 2 (updated)
  • BioPAX Level 3 (new)
  • Octave (new)

We will soon announce the availability of the source code of these new converters and the associated online service.

Finally, we would like to give a special thank you to Kieran Smallbone, who single-handedly submitted several already annotated models!

[Download All Models Under SBML Format]


BioModels Database is being developed by the Computational Systems Neurobiology group (EMBL-European Bioinformatics Institute, United Kingdom) and the SBML Team (California Institute of Technology, USA). The collaborators are the Database Of Quantitative Cellular Signalling (National Center for Biological Sciences, India), the Virtual Cell (University of Connecticut Health Center, USA), JWS Online (Stellenbosch University, ZA) and the CellML team (Auckland Bioengineering Institute, NZ).

BioModels Database development is funded by the European Molecular Biology Laboratory (Computational Systems Neurobiology group), the UK Biotechnology and Biological Sciences Research Council (Computational Systems Neurobiology group), the National Institute of General Medical Sciences (SBML team and Computational Systems Neurobiology group), and the National Center for Research Resources (Virtual Cell team).

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

Developers: Camille Laibe, Nicolas Rodriguez, Jean-Baptiste Pettit (Alumni: Mélanie Courtot, Marco Donizelli, Arnaud Henry, Chen Li, Lu Li)

Former collaborators and funders: BioModels Database also benefited from the help of Herbert Sauro (University of Washington, 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, JSBML, Apache Tomcat, 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.


30 September 2010630792248276320426
27 April 2010473378524488618950
26 January 2010453337024106917228
02 September 2009429320143929316492
16 June 2009412289013626414611
25 March 2009335287263609313818
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