BioModels Database

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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 and PLoS.

The BioModels Database Homepage

1 What is BioModels Database
2 Content of BioModels Database
3 Organization of BioModels Database development
4 Funding for BioModels Database
5 External references

[edit] 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, [XPP], SciLab, [BioPAX] and some graphic formats, such as GIF, SVG and graphic Java applet.

[edit] Content of BioModels Database

The BioModels Database Pipelines

BioModels Database has two branches, one is called curated-pipeline, another is non-curated-pipeline. The models in curated-pipeline are all well curated and annotated. The models, which could be unsimulatable or too huge to be curated, will be put into non-curated-pipeline. Non-curated models can be moved into curated pipeline in some cases. All these models are open to the public and can be easily accessed via web interface or web services. On the homepage, there is also the link for downloading tar ball of all models' SBML files.

BioModels Database announced its 7th Release on Jan. 5, 2007. That release, the largest in terms of number of models or reactions since the initial one, is a milestone in BioModels DB history. Currently, there are 86 curated models, and 29 non-curated models are also made available to the public. These models amount to 5775 species, 6458 reactions and comprise 4420 cross-references to other data resources.

[edit] Organization of BioModels Database development

BioModels Database is developed in collaboration by the [Computational Neurobiology Group] at the EMBL-EBI, UK and the SBML Team in Caltech, USA, plus the [Herbert Sauro's team] at the Keck Graduate Institute, USA, the [Systems Biology Institute], Japan and [JWS Online], Stellenbosch University, ZA.