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19th BioModels Database Release

Hinxton, Friday 15th April 2011

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

In this release, 69 new models have been published. Moreover, numerous existing models have been updated.

BioModels Database now publicly provides 326 models in the curated and 373 in the non-curated branch. Together, these 699 models comprise 92112 species, 113925 relationships (which include reactions, rate rules, events and assignment rules), and 22969 cross-references.

Along with the data release, we are introducing a new feature: the distribution of additional files. Any model can now be distributed with various related files. You can access and download those files from the curation tab. For example, BIOMD0000000278 is now provided with several variants of the original model as well as the associated COPASI files. Finally, we also modified the underlying filesystem structure in order to improve the general performances.

[Download All Models Under SBML Format]


Acknowledgements


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

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

Scientific Advisory Board: Jacky L. Snoep (Chair, University of Stellenbosch, SA), Upinder S. Bhalla (National Center for Biological Sciences, Bangalore, India), Michael Hucka (California Institute of Technology, USA), Pedro Mendes (University of Manchester, UK), Ion Moraru (University of Connecticut Health Center, USA) and Herbert Sauro (University of Washington, USA).

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!


Statistics


ReleaseModelsSpeciesReactionsCross-references
15 April 2011699921129747022969
30 September 2010630792248276320426
27 April 2010473378524488618950
26 January 2010453337024106917228
02 September 2009429320143929316492
16 June 2009412289013626414611
25 March 2009335287263609313818
03 December 2008293272383444313206
21 August 2008259217832711710811
28 March 2008244209452573110498
25 September 200719210482124829810
05 June 2007145602770167692
05 January 2007128569764315651
03 October 200696412548903074
05 June 20065483713073542
31 January 20065076111633126
28 July 2005445969432373
01 June 2005304257361609
11 April 2005203226311084
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