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Name of Collaboratory :


BioModels Database


URL :  

Collaboratory Status :

Operational   Start Date : 2005 End Date : Info Last Updated : Fri, Dec 3 2010 4:01am PST

Primary Collaboratory Function :

  Community Data Systems  

Secondary Collaboratory Functions :


Domain(s) :

  BIOLOGICAL/AGRICULTURAL SCIENCES >Biological Sciences >Biochemistry  

Brief Description of the Collaboratory :


BioModels Database, is a database of curated quantitative models in Biology that have been described in peer-reviewed publications. Models are annotated and cross-referenced with relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. The curation process ensures that the model is syntactically correct XML, and is valid with respect to its encoding schema. In addition, there is verification of logical model composition, the accuracy of the biological information contained in the model, as well as confirmation that the model published will, within reasonable bounds, reproduce the behaviour attributed it. Users can browse or search the database, and download models in SBML format, as well as various other formats, regardless of whether they encode models (CellML, XPP, SciLab), pathways (BioPAX) or graphs (gif or SVG).


Access to Instruments :


Access to Information Resources :

  All of the models in the database are freely accessible via the Internet.  

Access to People as Resources :

  They have a yearly meeting/conference/hackathon. The annual BioModels meeting is a gathering of BioModels resources developers and curators, users, developers of third-party tools, and people who would know more about it. The meeting will feature presentations from the various attendees, demo of the new features of BioModels Database, tutorials, and discussion sessions.  

Funding Agency or Sponsor :

Biotechnology and Biological Sciences Research Council (BBSRC)
European Molecular Biology Laboratory (EMBL)
United States Department of Health and Human Services
National Institutes of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
National Center for Research Resources (NCRR)

Notes on Funding Agencies/Sponsors:
This project was also previously funded partially by DARPA.

Organizations with Funded Participants:
Organization name:
Approx # of participants:
Description of organization's role(s):
Stellenbosch University
   Department of Biochemistry (Stellenbosch University)
California Institute of Technology (Caltech)
   Department of Computing and Mathematical Sciences (Caltech)
European Molecular Biology Laboratory (EMBL)
   European Bioinformatics Institute (EBI)
National Centre for Biological Sciences (NCBS)
Systems Biology Institute (SBI)
Former collaborator
University of Connecticut (UConn)
   University of Connecticut Health Center
University of Washington
Former collaborator

Notes on Participants/Organizations:
They have a scientific advisory board consisting of 7 members. Members of the scientific community contribute models to the database.


Communications Technology Used :


Technical Capabilities :

  Key Articles :    

Project-reported performance data :

  BioModels Database latest release was its 18th release on September 30, 2010, which provides 269 curated models and 361 non-curated models to the public. These models amount to 79224 species, 109091 reactions and comprise 20426 cross-references to other data resources.  
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