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BioModels Database


New BioModels Database Release

Hinxton, Friday 28th July 2005

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

It sees the addition of 15 models representing 171 reactions, and as usual the annotation of many preexisting models has been upgraded. The topology of each model can now be visualised on an hyperlinked graph. You can download the XSL we use to convert SBML L2 V1 into a DOT file, usable with GraphViz. This XSL is covered by the General Public Licence.

[Download All Models Under SBML L2 V1 Format]

New Models

BioModels ID Name Publication Id
BIOMD0000000032 Kofahl2004_pheromone 15300679
BIOMD0000000033 Brown2004_NGF_EGF_signaling 14525003
BIOMD0000000034 Smolen2004_CircClock 15111397
BIOMD0000000035 Vilar2002_Oscillator 11972055
BIOMD0000000036 Tyson1999_CircClock 10545344
BIOMD0000000037 Marwan_Genetics_2003 12750324
BIOMD0000000038 Rohwer2000_Phosphotransferase_System 10889194
BIOMD0000000039 Marhl_CaOscillations 11004387
BIOMD0000000040 Field1974_Oregonator 10.1063/1.1681288...
BIOMD0000000041 Kongas2001_creatine http://www.icsb2001....
BIOMD0000000042 Nielsen1998_Glycolysis 10.1016/S0301-4622(9...
BIOMD0000000043 Borghans1997_CaOscillation_model1 10.1016/S0301-4622(9...
BIOMD0000000044 Borghans1997_CaOscillation_model2 10.1016/S0301-4622(9...
BIOMD0000000045 Borghans1997_CaOscillation_model3 10.1016/S0301-4622(9...


The BioModels Database is part of the initiative, a collaboration developed by the teams of Michael Hucka (Caltech, USA), Nicolas Le Novère (EMBL-EBI, UK), Herbert Sauro (Keck Graduate Institute, USA), Jacky Snoep (Stellenbosch University, ZA) and Hiroaki Kitano (Systems Biology Institute, JP).

Developers: Marco Donizelli, Melanie Courtot and Lu Li.

Model curators and annotators: Harish Dharuri, Nicolas Le Novère, Bruce Shapiro with the help of Rainer Machné.

External contributors: Upinder Bhalla, Christoph Flamm, Ryan Gutenkunst, Adam Halasz, Rainer Machné, Marc Poolman, Tomas Radivoyevitch, Oleg Sokolsy (models), Ben Bornstein, Sarah Keating, Joanne Matthews, Maria Schilstra (software), Alexander Broicher, Les Grivell, Boris Kholodenko, Tjeerd Olde Scheper, Paul Smolen, Yukiko Matsuoka (miscellaneous).


Release 1 (11/April/2005)Release 2 (01/June/2005)Release 3 (28/July/2005)

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

Gene Ontology IDTopic# models

GO:0007154Cell communication21
GO:0007049Cell cycle 6
GO:0008152Metabolism 7
GO:0007623Circadian rhythm 7