BioModels Database

BioModels Database is a free and open-source database for storing, exchanging and retrieving published quantitative models of biological interest. Deposition of models upon publication is currently supported by Nature Publishing Group, PLoS and BioMed Central.

What is BioModels Database

BioModels Database is an online resource for storing and serving quantitative models of biomedical interest. All the models in BioModels Database have been described in the peer-reviewed scientific literature.

The models stored in the curated branch of BioModels Database are compliant with MIRIAM, the standard of model curation and annotation. The models have been simulated by curators to check that when intentiated in simulations, they provide the same results that described in the publication. Model components are annotated, so the users can conveniently identify each model element and retrieve further information from other resources.

Modellers can submit the models in SBML and CellML. Models can subsequently be downloaded in SBML, CellML, [http://www.math.pitt.edu/~bard/xpp/xpp.html XPP] , SciLab, [http://www.biopax.org/ BioPAX] and some graphic formats, such as GIF, SVG and graphic Java applet.

Content of BioModels Database

BioModels Database has two branches, one is called curated-branch, another is non-curated-branch. The models in curated-branch are all well curated and annotated. The models that are still uncurated, non-curatable (spatial models, steady-state models etc), or too huge to be curated, are put into non-curated-branch. Non-curated models can be later moved into the curated branch. All these models are open to the public and can be easily accessed via web interface or [http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=webservices BioModels Web Services] . On the homepage, there is also the link for downloading tar ball of all models' files in SBML format.

BioModels Database announced its [http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_21August2008 11th Release] on August 21, 2008. Currently, there are 185 curated models and 74 non-curated models available to the public. These models amount to 21783 species, 27117 reactions and comprise 10811 cross-references to other data resources.

Deposition of models in BioModels Database is now advocated by many scientific journals, included Molecular Systems Biology, all the journals of the Public Library of Science and all the journals of BioMed Central.

Organization of BioModels Database development

BioModels Database is developed in collaboration by the [http://www.ebi.ac.uk/compneur Computational Neurobiology Group] at the EMBL-EBI, UK and the SBML Team in Caltech, USA, plus [http://doqcs.ncbs.res.in/ DOQCS] at the National Center for Biological Sciences, India, the [http://www.ccam.uchc.edu/ Virtual Cell] , USA, [http://sbw.kgi.edu/ Herbert Sauro's team] at the Keck Graduate Institute, USA, the [http://sbi.jp/ Systems Biology Institute] , Japan and [http://jjj.biochem.sun.ac.za/ JWS Online] at Stellenbosch University, ZA.

Funding for BioModels Database

BioModels Development has benefited from the funds of the European Molecular Biology Laboratory, the Biotechnology and Biological Sciences Research Council, the National Institute of General Medical Sciences, the DARPA, and the National Center for Research Resources.

External references

* [http://www.ebi.ac.uk/biomodels/ Official website of BioModels Database]
* [http://dx.doi.org/10.1093/nar/gkj092 Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res., 34: D689-D691.]
* [http://dx.doi.org/10.1038/nbt1156 Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM) Nature Biotechnology, 23: 1509-1515.]
* [http://www.biomodels.net/ Website of the BioModels.net initiative]