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New BioModels Database Release

Hinxton, Tuesday 31st January 2006

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

It sees the addition of 6 models that represent 220 reactions, the biggest increase since the creation of the resource. Most importantly, this release introduces the qualification of annotations, following the recommendation of the MIRIAM standard. Those qualifications are exported in the SBML version using the Finney/Le Novère framework. Most of the existing unqualified annotation has been converted. The remaining models will be converted in the near future.

[Download All Models Under SBML L2 V1 Format]

New Models


BioModels ID Name Publication Id
BIOMD0000000046 Olsen2003_peroxidase 12823550
BIOMD0000000047 Oxhamre2005_Ca_oscillation 15596518
BIOMD0000000048 Kholodenko1999_EGFRsignaling 10514507
BIOMD0000000049 Sasagawa2005_MAPK 15793571
BIOMD0000000050 Martins2003_AmadoriDegradation 12873422
BIOMD0000000052 Brands2002_MonosaccharideCasein 12405768

Acknowledgements

BioModels Database is developed in collaboration by the teams of Nicolas Le Novère (EMBL-EBI, United-Kingdom), Michael Hucka (SBML Team, Caltech, USA), Herbert Sauro (Keck Graduate Institute, USA) and Jacky Snoep (JWS Online, Stellenbosch University, ZA), as part of the BioModels.net initiative. BioModels Database development is funded by the European Molecular Biology Laboratory and the National Institute of General Medical Sciences.

Developers: Chen Li, Lu Li, Mélanie Courtot, Marco Donizelli.

Model curators and annotators: Nicolas Le Novère, Harish Dharuri, Lu Li.

External contributors: Upinder Bhalla, Christoph Flamm, Ryan Gutenkunst, Adam Halasz, Ken Lau, Rainer Machné, Marc Poolman, Tomas Radivoyevitch, Birgit Schoeberl, Bruce Shapiro, Oleg Sokolsy, Molecular Systems Biology (models), Ben Bornstein, Sarah Keating, Joanne Matthews, Nicolas Rodriguez, Maria Schilstra (software), Samuel Bandara, Alexander Broicher, Les Grivell, Noriko Hiroi, Boris Kholodenko, Ursula Kummer, Adrian Lopez Garcia de Lomana, Yukiko Matsuoka , Robert Phair, Tjeerd olde Scheper, Henning Schmidt, Paul Smolen (Miscellaneous)

Software used to curate the models: CellDesigner, COPASI, Jarnac and SBMLodeSolver

Software used to build the resource: Jakarta Tomcat, Xindice, Xalan, Xerces and MySQL.

Statistics


Release 1 (11/April/2005)Release 2 (01/June/2005)Release 3 (28/July/2005)Release 4 (31/January/2006)

Models 20 30 44 50
Species 322 425 596 761
Reactions 631 736 943 1163
Annotations 1084 1609 2373 3126


Gene Ontology IDTopic# models

GO:0007154Cell communication 24
GO:0007049Cell cycle 6
GO:0008152Metabolism 10
GO:0007623Circadian rhythm 7
Other 3


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