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New BioModels Database Release

Hinxton, Monday 05th June 2006

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

It sees the addition of 4 models, that represent 76 species and 144 reactions, including the first model submitted directly by a scientific journal (Molecular Systems Biology). The qualification of annotations now uses BioModels qualifiers. Those qualifications are exported in the SBML version using the forthcoming Level 2 Version 2 specification. An export in BioPAX, the standard for pathway description, has been added. We also started to provide reaction graphs using the SVG format. Other export filters have been improved as well.

BioModels Database annotation process is now based on MIRIAM Database and WebServices, a data resource to be released soon, that implements the support for MIRIAM standard. The search engine has been improved, particularly for taxonomy (search ancestors and descendants) and CheBI (search synonyms).

[Download All Models Under SBML L2 V1 Format]

New Models

BioModels ID Name Publication Id
BIOMD0000000053 Ferreira2003_CML_generation2 12911334
BIOMD0000000054 Ataullahkhanov1996_Adenylate 8733433
BIOMD0000000055 Locke2005_CircClock 10.1038/msb4100018
BIOMD0000000056 Chen2004_CellCycle 15169868

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: Mélanie Courtot, Arnaud Henry, Camille Laibe, Chen Li, Lu Li (Alumni: Marco Donizelli)

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

External contributors: Upinder Bhalla, Christoph Flamm, Ryan Gutenkunst, Adam Halasz, Ken Lau, Rainer Machné, Marc Poolman, Tomas Radivoyevitch, Maria Schilstra, 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, MathSBML, XPP-Aut, SBMLdeSolver (http://www.tbi.univie.ac.at/~raim/odeSolver/) and SBMLeditor

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

Statistics


ReleaseModelsSpeciesReactionsAnnotations
11/April/2005 20 322 631 1084
01/June/2005 30 425 736 1609
28/July/2005 44 596 943 2373
31/January/2006 50 761 1163 3126
25/May/2006 54 837 13073542



Gene Ontology IDTopic# models

GO:0007154 Cell communication 24
GO:0007049 Cell cycle 7
GO:0008152 Metabolism 12
GO:0007623 Circadian rhythm 8
Other 3


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