CaltechAUTHORS
Published January 8, 2020 | Version public
Journal Article Metadata-only

BioModels—15 years of sharing computational models in life science

Creators

Abstract

Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world's largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse.

Additional Information

© 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. 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. Received September 22, 2019; Revised October 22, 2019; Editorial Decision October 23, 2019; Accepted November 06, 2019; Published: 08 November 2019. We would like to acknowledge the COMBINE community for the support and numerous contributions over the years. We are also grateful to the libSBML (http://sbml.org/Software/libSBML) and JSBML (http://sbml.org/Software/JSBML) development teams for empowering us to seamlessly develop SBML support in our tools and services. Funding: Biotechnology and Biological Sciences Research Council [BB/J019305/1, BB/J004456/1, BB/P013384/1, BB/P013406/1, BB/P013414/1, BB/L502224/1]; Innovative Medicines Initiative Joint Undertaking [115156]; European Molecular Biology Laboratory; Innovative Medicines Initiative 2 Joint Undertaking [116030]. Funding for open access charge: Research Councils UK Open Access. Conflict of interest statement. None declared.

Additional details

Identifiers

PMCID
PMC7145643
Eprint ID
99777
DOI
10.1093/nar/gkz1055
Resolver ID
CaltechAUTHORS:20191111-111825904

Related works

Describes
10.1093/nar/gkz1055 (DOI)

Funding

Biotechnology and Biological Sciences Research Council (BBSRC)
BB/J019305/1
Biotechnology and Biological Sciences Research Council (BBSRC)
BB/J004456/1
Biotechnology and Biological Sciences Research Council (BBSRC)
BB/P013384/1
Biotechnology and Biological Sciences Research Council (BBSRC)
BB/P013406/1
Biotechnology and Biological Sciences Research Council (BBSRC)
BB/P013414/1
Biotechnology and Biological Sciences Research Council (BBSRC)
BB/L502224/1
Innovative Medicines Initiative Joint Undertaking
115156
European Molecular Biology Laboratory (EMBL)
Innovative Medicines Initiative Joint Undertaking
116030
Research Councils UK

Dates

Created
2019-11-12
Created from EPrint's datestamp field
Updated
2022-02-15
Created from EPrint's last_modified field