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New Release

Hinxton, Friday 05th January 2007

We are pleased to announce the seventh release of BioModels Database, the "DOQCS release". As the nickname of this release indicates, this is the first one incorporating models coming from the Database of Quantitative Cellular Signalling […More]

This new release sees the the addition of 16 models in the curated branch, and 26 in the non-curated branch, bringing BioModels Database to 6458 reactions.

As usual, a significant portion of the annotation of existing models has been uptated. In addition, we kept on adding results of simulation to document the curation process.

[Download All Models Under SBML L2 V1 Format]

New Models

BioModels ID Name Publication Id
BIOMD0000000072 Yi2003_GproteinCycle 12960402
BIOMD0000000073 Leloup2003_CircClock_DD 12775757
BIOMD0000000074 Leloup2003_CircClock_DD_REV-ERBalpha 12775757
BIOMD0000000075 Xu2003_Phosphoinositide_turnover 12771127
BIOMD0000000076 Cronwright2002_Glycerol_Synthesis 12200299
BIOMD0000000077 Blum2000_LHsecretion_1 10662710
BIOMD0000000078 Leloup2003_CircClock_LD 12775757
BIOMD0000000079 Goldbeter2006_weightCycling 16595882
BIOMD0000000080 Thomsen1989_AdenylateCyclase 2574993
BIOMD0000000081 Suh2004_KCNQ_Regulation 15173220
BIOMD0000000082 Thomsen1988_AdenylateCyclase_Inhibition 2904647
BIOMD0000000083 Leloup2003_CircClock_LD_REV-ERBalpha 12775757
BIOMD0000000084 Hornberg2005_ERKcascade 15634347
BIOMD0000000085 Maurya2006_GTPaseCycle_reducedOrder 16986265
BIOMD0000000086 Bornheimer2004_GTPaseCycle 15520372
BIOMD0000000087 Proctor2006_telomere 10.1098/rsif.2006.0148

BioModels ID Name Publication Id
MODEL2463576061 Oda2005_EGFR 10.1038/msb4100014
MODEL2463683119 Oda2006_TollLikeR 10.1038/msb4100057
MODEL3492630792 Fernandez2006_ModelA 10.1371/journal.pcbi.0020176
MODEL3492674214 Fernandez2006_ModelB 10.1371/journal.pcbi.0020176
MODEL4023382414 Vilar2006_TGFbeta 16446785
MODEL4024559990 Clarke2006_TGFbeta 10.1049/ip-syb:20050055
MODEL4025634026 PRR7-PRR9light-Y 10.1038/msb4100101
MODEL4025650992 PRR7-PRR9light-Yprime 10.1038/msb4100101
MODEL4025663985 PRR7-PRR9-Y 10.1038/msb4100101
MODEL4025803561 Locke2006_CircClock 10.1038/msb4100102
MODEL4734733125 Santolini2001_NOS - DOQCS model 11038356
MODEL4779732381 Stone1996_NOsGC - DOQCS model 8573563
MODEL4780181279 Kuroda_GC - DOQCS model 11466441
MODEL4780441670 CondorelliGC - DOQCS model 11325714
MODEL4780784080 NOS_Phosph_regulation - DOQCS model 10400690
MODEL4816599063 SERCA - DOQCS model 10692318
MODEL4821294342 Kierzek_LacZ - DOQCS model 11062240
MODEL8567576821 Legewie2006_apoptosis_WT.xml 10.1371/journal.pcbi.0020120
MODEL8567941122 Legewie2006_apoptosis_NonCompet 10.1371/journal.pcbi.0020120

Acknowledgements

BioModels Database is developed by the teams of Nicolas Le Novère (EMBL-EBI, United-Kingdom) and Michael Hucka (SBML Team, Caltech, USA) in collaboration with Upinder Bhalla (DOQCS, National Center for Biological Sciences, India), Herbert Sauro (Keck Graduate Institute, USA), Hiroaki Kitano (Systems Biology Institute, Japan), Hans Westerhoff and Jacky Snoep (JWS Online, Stellenbosch (ZA) and Manchester (UK) Universities and Stellenbosh University, ZA), as part of the BioModels.net initiative. BioModels Database development has benefitted from funds of the European Mol! ecular Biology Laboratory (Le Novère team) and the National Institute of General Medical Sciences (SBML team).

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

Developers: Mélanie Courtot, Arnaud Henry, Camille Laibe, Chen Li (main developer), Lu Li, Nicolas Rodriguez (Alumni: Marco Donizelli)

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, Jakarta Tomcat, Xindice, Xalan, Xerces, 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, SBMLdeSolver, SBMLeditor, SBMLmerge and XPP-Aut.

Statistics


ReleaseModelsSpeciesReactionsCross-references
05/January/2007 132 5775 6458 4420
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



Gene Ontology IDTopic# models

GO:0007166cell surface receptor linked signal transduction8
GO:0007242intracellular signaling cascade 25
GO:0007049 Cell cycle 8
GO:0008152 Metabolism 21
GO:0007623 Circadian rhythm 8
Other 13


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