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

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.

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