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New BioModels Database Release

Hinxton, tuesday 05th June 2007

We are pleased to announce the eigth release of BioModels Database, in memoriam Reinhart Heinrich.

Systems biology studies the cellular networks and their regulation by combining various types of experimental investigation with mathematical description and analysis. Though it appears to be a rather new scientific field, it is based to a large extent on theoretical work done in the last century.
Among the pioneers of a theoretical analysis of biochemical networks was Reinhart Heinrich (1946-2006). Together with Tom Rapoport (and independently of Henrik Kacser and Jim Burns at the same time) he introduced the concept of metabolic control analysis in the early 1970s. This concept was initially largely ignored, but had a breakthrough in the late 1980s. It changed many concepts of biochemists about regulation in metabolic systems, especially the idea of a rate-limiting step. The investigations were part of a broader project to understand erythrocyte metabolism in sufficient detail to simulate their behaviour accurately. Later, Reinhart contributed substantially to the advance of the field by studying optimality in biochemical networks, metabolic oscillations, membrane processes, and quantitative properties of signalling processes as well as a number of different theoretical problems associated to the dynamical behaviour and to the biophysical properties of cellular reaction networks. Beside the intellectual originality, the accurateness and thoroughness of his studies shall remind us that comprehensive and fast accumulation of data is just one side of the coin in scientific research, but that careful analysis based on sound theoretical concepts is necessary to turn the collection of data into knowledge.
[Heinrich R, Rapoport TA (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42: 89-95 - MedLine]

Edda Klipp - Berlin, 30 May 2007

Several models of Reinhart Heinrich are present in BioModels Database, such as BIOMD0000000039 (calcium oscillations), BIOMD0000000084 (ERK cascade), BIOMD0000000090 (respiratory oscillations), BIOMD0000000104 (metabolic pathways and gene regulation).

This new release sees the the addition of 34 models, 27 entering the curated branch. That brings the public version of BioModels Database to 7684 reactions. As usual, a significant portion of the annotation of existing models has also been uptated. The database now features 5330 cross-references.

BioModels Dababase can now be accessed programmatically through WebServices. You can currently get all the models, or query the database by publications or person in order to obtain a relevant subset of models. We welcome any suggestion for new services.

A new search system has been implemented to explore the content of the SBML elements <name> and <notes>, using text indices generated by Lucene. This replacement of the ancient system, an XML database using Xindice, is faster and more robust.

Thanks to our collaboration with the group of Jacky Snoep, most of the models in the curated branch can now be simulated online using JWS Online.

Finally, with this release BioModels Database switch to the new EBI website look and feel. In particular, the generic search form on the top of each page allow-you to search all the resources of the EBIat once (including BioModels DB).

[Download All Models Under SBML L2 V1 Format]

New Models


BioModels ID Name Publication Id
BIOMD0000000088 Maeda2006_MyosinPhosphorylation 16923126
BIOMD0000000089 Locke2006_CircClock_LL 10.1038/msb4100102...
BIOMD0000000090 Wolf2001 respiratory oscillations 11423122
BIOMD0000000091 Proctor2005_Hsp90 15610770
BIOMD0000000092 Fuentes2005_ZymogenActivation 15634334
BIOMD0000000093 Yamada2003_JAK_STAT_pathway 12527385
BIOMD0000000094 Yamada2003_JAK_STAT_SOCS1_knockout 12527385
BIOMD0000000095 Zeilinger2006_PRR7-PRR9-Y 10.1038/msb4100101...
BIOMD0000000096 Zeilinger2006_PRR7-PRR9light-Y 10.1038/msb4100101...
BIOMD0000000097 Zeilinger2006_PRR7-PRR9light-Yprime 10.1038/msb4100101...
BIOMD0000000098 Goldbeter1990_Ca_Oscillations 2304911
BIOMD0000000099 Laub1998_SpontaneousOscillations 9843585
BIOMD0000000100 Rozi2003_GlycogenPhosphorylase_Activation 14556891
BIOMD0000000101 Vilar2006_TGFbeta 16446785
BIOMD0000000102 Legewie2006_apoptosis_WT 10.1371/journal.pcbi...
BIOMD0000000103 Legewie2006_apoptosis_NC 10.1371/journal.pcbi...
BIOMD0000000104 Klipp2002_MetabolicOptimization_linearPathway(n=2) 12423338
BIOMD0000000105 Proctor2007_ubiquitine 10.1186/1752-0509-1-...
BIOMD0000000106 Yang2007_ArachidonicAcid 10.1371/journal.pcbi...
BIOMD0000000107 Novak1993_M_phase_control http://jcs.biologist...
BIOMD0000000108 Kowald2006_SOD 12423338
BIOMD0000000109 Haberichter2007_cellcycle 10.1038/msb4100126...
BIOMD0000000110 Qu2003_CellCycle 14645053
BIOMD0000000111 Novak2001_FissionYeast_CellCycle 12779461
BIOMD0000000112 Clarke2006_Smad_signalling 10.1049/ip-syb:20050...
BIOMD0000000113 Dupont1992_Ca_dpt_protein_phospho 1316185

BioModels ID Name Publication Id
MODEL8262229752 AI2_LB 10.1038/msb4100107...
MODEL4969417017 RanGTPase 12606574
MODEL4968912141 RasGTPase 12667087

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 Molecular Biology Laboratory (Le Novère team), the National Institute of General Medical Sciences (SBML team), and the DARPA (Sauro team)

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

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

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, Lucene, Xalan, Xerces, Axis, 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/June/2007 145 6498 7684 5330
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 (only curated branch)

GO:0007166cell surface receptor linked signal transduction10
GO:0007242intracellular signaling cascade30
GO:0007049Cell cycle 13
GO:0008152Metabolism 29
GO:0007623Circadian rhythm 12
Other19


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