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BioModels Databse Version 3

Hinxton, Monday 18th August 2008

We are pleased to announce the release of BioModels Databse Version 3.

This new version changed the layout of the interface in order to more efficiently use page space when viewing a model. And tons of new features were added in this version, main of them are:

  • Browse models based on a Gene Ontology tree.
  • A model's elements are displayed in different sections which are presented as tabs.
  • View the related elements of the selected elements in a model.
  • Create the sub-models based on a user's selection of a model's elements.
  • BioModels Online simulation.
  • SBML L2V3 Support
  • Some web services added. Please see detail in
  • And many others.

And some new features only available to curators or annotators are:

  • New AJAX-based annotation interface.
  • Full model history stored.
  • And many others.

For feature request or bug report:


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), Ion Moraru (the Virtual Cell, USA), Jacky Snoep (JWS Online, Stellenbosch (ZA) University, ZA). BioModels Database development is funded by the European Molecular Biology Laboratory (Le Novère team), the Biotechnology and Biological Sciences Research Council (Le Novère team), the National Institute of General Medical Sciences (SBML team and Le Novère team), and the National Center for Research Resources (Virtual Cell team).

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

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

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, Apache 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.