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BioModels Database

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New Release

Hinxton, Wednesday 16th June 2009

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

In this release, 5 new models have gained entry to the curated branch. The public version of BioModels Database now contains 216 models in the curated and 196 in the non-curated branch. Together these 412 models comprise 28901 species and 36264 reactions. Some of the existing models have been slightly changed for correction and to enhance reusability. Also the annotations of some existing models have been updated. The database now features around 14611 cross-references.

Out of the 196 models that are in the non-curated branch, 92 models are imported from the CellML repository (http://www.cellml.org/), which would subsequently be moved to the curated branch in future.

After the last release, the BioModels Database software has been enhanced to alter some new features:

  • Submission of models now accepts models encoded in SBML Level 2 Version 4.
  • On the homepage, besides "Search", there is another button "Go to the model". After giving the model's name or ID, user could directly go the model presentation page.
  • Subversion is adopted for models revision control. When a model is submitted or replaced, a copy of the model will be go into SVN repository.
  • In model's presentation page, there is a new tab called Curation, in which, user can find curation result and model's revisions. Authorized user also could download the past revisions or choose different revisions and compare them.
  • On the top left of model presentation page, there are links for downloading models in different versions of SBML level 2. The link of curated version is highlighted with bold font. Other versions are automatically generated by using libsbml.
  • BioModels Database now stores more complete information of Taxonomy terms to help to improve the search result.
  • Along with the release, there are also some bugs fixed.

[Download All Models Under SBML Format]

Acknowledgements

BioModels Database is being developed by the Computational Neurobiology group (EMBL-European Bioinformatics Institute, United-Kingdom) and the SBML Team (California Institute of Technology, USA). Collaborators include the Database Of Quantitative Cellular Signalling (National Center for Biological Sciences, India), the Virtual Cell (University of Connecticut Health Center, USA), JWS Online (Stellenbosch University, ZA) and the CellML team (Auckland Bioengineering Institute, NZ).

BioModels Database development is funded by the European Molecular Biology Laboratory (Computational Neurobiology group), the Biotechnology and Biological Sciences Research Council (Computational Neurobiology group), the National Institute of General Medical Sciences (SBML team and Computational Neurobiology group), and the National Center for Research Resources (Virtual Cell team).

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

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

Former collaborators and funders: BioModels Database also benefited from the help of Herbert Sauro (University of Washington, USA) and Hiroaki Kitano (Systems Biology Institute, Japan), and from the funds of the DARPA (Sauro team).

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, SBMLOdeSolver, SBMLeditor, SBMLmerge, JigCell and XPP-Aut.

Statistics


ReleaseModelsSpeciesReactionsCross-references

16/June/2009 412 28901 36264 14611
25/March/2009 335 28726 36093 13818
03/December/2008 293 27238 34443 13206
21/August/2008 259 21783 27117 10811
28/March/2008 244 20945 25731 10498
25/September/2007 192 10482 12482 9810
05/June/2007 145 6027 7016 7692
05/January/2007 128 5697 6431 5651
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


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