BioModels Database
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| Content | |
| Description | A database for storing, exchanging and retrieving published quantitative models of biological interest. |
| Data types captured | computational models |
| Organism(s) | all |
| Contact | |
| Research center | European Bioinformatics Institute, Caltech |
| Laboratory | http://www.ebi.ac.uk/compneur/ |
| Primary Citation | PMID 20587024 |
| Release date | 2005 |
| Access | |
| Standards | MIRIAM |
| Data format | SBML |
| Website | http://www.ebi.ac.uk/biomodels/ |
| Web Service URL | http://www.ebi.ac.uk/biomodels-main/webservices |
| Tools | |
| Miscellaneous | |
| License | http://www.ebi.ac.uk/biomodels-main/termsofuse |
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.
Contents |
[edit] What is BioModels Database
BioModels Database is an online resource for storing and serving quantitative models of biomedical interest. All the models in the curated section of 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 run in simulations, they provide the same results as 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, VCML, XPP, SciLab, Octave, BioPAX. The reaction networks of models are presented in some graphic formats, such as PNG, SVG and graphic Java applet, in which some networks were presented by following Systems Biology Graphical Notation. And a human readable summary of each model is available in PDF.
[edit] Content of BioModels Database
BioModels Database is composed of two branches. The curated branch hosts models that are well curated and annotated. The non-curated-branch provides models that are still not curated, are non-curatable (spatial models, steady-state models etc), or too huge to be curated. Non-curated models can be later moved into the curated branch. All these models are freely and publicly available and can be easily accessed via the website or Web Services[1]. One can also download archives of all the models.
BioModels Database announced its 21th release on February 8, 2012[2]. It now provides 409 curated models and 420 non-curated models to the public. These 829 models amount to 130800 species, 151274 relationships (which include reactions, rate rules, events and assignment rules), and 106210 cross-references to other data resources.
Deposition of models in BioModels Database is 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.
[edit] Organization of BioModels Database development
BioModels Database is developed by the Computational Systems Neurobiology Group at the EMBL-EBI, UK and the SBML Team in Caltech, USA. Past and present collaborating groups include DOQCS at the National Center for Biological Sciences, India, JWS Online at Stellenbosch University, ZA, the CellML team at the Auckland Bioengineering Institute, NZ, the Virtual Cell, USA, Herbert Sauro's team at the University of Washington, Seattle, and the Systems Biology Institute, Japan.
[edit] 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.
[edit] References
- ^ Li C., Courtot M., Le Novère N. and Laibe C (2009) BioModels.net Web Services, a free and integrated toolkit for computational modelling software, Briefings in Bioinformatics, doi:10.1093/bib/bbp056
- ^ BioModels Database: Hinxton, Wednesday 8th February 2012
[edit] External references
- Official website of BioModels Database (There is also a mirror site in the USA: Caltech Mirror site)
- Li C., Donizelli M., Rodriguez N., Dharuri H., Endler L., Chelliah V., Li L., He E., Henry A., Stefan M.I., Snoep J.L., Hucka M., Le Novère N. and Laibe C. (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 2010, 4:92
- 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.
- 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.
- Website of the BioModels.net initiative
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