BioModels Database

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BioModels Database
BioModels Database logo
Content
Description A repository for storing, exchanging and retrieving computational models of biological interest.
Data types captured computational models
Organisms all
Contact
Research center EMBL-EBI, BI, Caltech
Primary citation PMID 20587024
Release date 2005
Access
Standards MIRIAM
Data format SBML, BioPAX, SciLab, Octave, XPP, VCML, RDF/XML
Website EBI main instance, Caltech mirror
Download URL EBI FTP
Web service URL SOAP
Tools
Web Model display, multiple browsing strategies, advanced search, bulk download, model of the month
Miscellaneous
License CC0 Public Domain Dedication
Version 27 (April 2014)
Curation policy yes (manual)
Bookmarkable entities yes

BioModels Database is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest.

What is BioModels Database[edit]

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 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, VCML, XPP, SciLab, Octave, BioPAX and RDF/XML. 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.

Content of BioModels Database[edit]

BioModels Database Pipeline

BioModels Database is composed of several 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. The repository also hosts models which were automatically generated from pathways databases.

All the models are freely available under the Creative Commons CC0 Public Domain Dedication, and can be easily accessed via the website or Web Services.[1] One can also download archives of all the models from the EBI FTP server.

BioModels Database announced its 27th release on Apr 11, 2014.[2] It now publicly provides 144,253 models. This corresponds to 1,183 models published in the literature and 143,070 models automatically generated from pathway 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, all the journals of BioMed Central and all the journals published by the Royal Society of Chemistry.

Development[edit]

BioModels Database is developed by the BioModels.net Team at the EMBL-EBI, UK, the Le Novère lab at the Babraham Institute, UK, and the SBML Team in Caltech, USA.[3]

Funding for BioModels Database[edit]

BioModels Development has benefited from the funds of the European Molecular Biology Laboratory, the Biotechnology and Biological Sciences Research Council, the Innovative Medicines Initiative, the Seventh Framework Programme (FP7), the National Institute of General Medical Sciences, the DARPA, and the National Center for Research Resources.

References[edit]

  1. ^ 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
  2. ^ BioModels Database: Hinxton, Friday 11th April 2014
  3. ^ Funders and collaborators of BioModels Database

External references[edit]