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Published January 28, 2015 | Published
Journal Article Open

BioModels: ten-year anniversary


BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140 000 models automatically generated from pathway resources. This represents an approximate 60-fold growth for literature-based model numbers alone, since BioModels' first release a decade ago. This article describes updates to the resource over this period, which include changes to the user interface, the annotation profiles of models in the curation pipeline, major infrastructure changes, ability to perform online simulations and the availability of model content in Linked Data form. We also outline planned improvements to cope with a diverse array of new challenges.

Additional Information

© 2014 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. Received October 06, 2014; Revised October 29, 2014; Accepted October 31, 2014. First published online: November 20, 2014. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. BioModels acknowledges its collaborators, who include the SBML Team (California Institute of Technology, USA), the Database Of Quantitative Cellular Signalling (National Center for Biological Sciences, India), the Virtual Cell (University of Connecticut Health Center, USA), JWS Online (Stellenbosch University, ZA), in particular Jacky Snoep, and the CellML team (Auckland Bioengineering Institute, NZ). BioModels gratefully acknowledges all contributors to its 'model of the month' feature: Benedetta Baldi, VC, Denis Brun, Ranjita Dutta Roy, Lukas Endler, Martina Fröhlich, Enuo He, Noriko Hiroi, NJ, Vladimir Kiselev, VK-S, Christian Knüpfer, Massimo Lai, AL-V, NLN, Lu Li, Michele Mattioni, Antonia Mayer, Stuart Moodie, Anika Oellrich, Renaud Schiappa, Christine Seeliger, Michael Schubert, Maciej Swat, Dominic P. Tolle, Florent Yvon, Judith Zaugg, Youwei Zheng and Junmei Zhu. The authors also thank the current members of the BioModels Database Scientific Advisory Board (SAB): Carole Goble, Thomas Lemberger, Pedro Mendes, Wolfganf Mueller and Philippe Sanseau. The BioModels team would also like to express their gratitude to the Computational Systems Biology community, in particular members of the SBML forum, not only for models contributed, but also for the tools and facilities upon which we rely, including JSBML, libSBML, SOSlib and Identifiers.org. Biotechnology and Biological Sciences Research Council (BBSRC) [BB/J019305/1, BB/K016946/1]; the Innovative Medicines Initiative Joint Undertaking [115156]; the European Commission [312455, 305299]; the National Institute of General Medical Sciences [R01 GM070923]; the BBSRC CASE Studentship; the Babraham Institute; the European Molecular Biology Laboratory. Conflict of interest statement. None declared.

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Published - Nucl._Acids_Res.-2015-Chelliah-D542-8.pdf


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August 20, 2023
August 20, 2023