BioModels—15 years of sharing computational models in life science
Top Cited Papers
Open Access
- 8 November 2019
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 48 (D1), D407-D415
- https://doi.org/10.1093/nar/gkz1055
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.Keywords
Funding Information
- 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 (115156, 116030)
- European Molecular Biology Laboratory
This publication has 40 references indexed in Scilit:
- Path2Models: large-scale generation of computational models from biochemical pathway mapsBMC Systems Biology, 2013
- An online model composition tool for system biology modelsBMC Systems Biology, 2013
- The impact of mathematical modeling on the understanding of diabetes and related complicationsCPT: Pharmacometrics & Systems Pharmacology, 2013
- Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup LanguageBMC Systems Biology, 2011
- Virtual Cell: computational tools for modeling in cell biologyWires Systems Biology and Medicine, 2011
- Retrieval, alignment, and clustering of computational models based on semantic annotationsMolecular Systems Biology, 2011
- COPASI—a COmplex PAthway SImulatorBioinformatics, 2006
- Minimum information requested in the annotation of biochemical models (MIRIAM)Nature Biotechnology, 2005
- CellML: its future, present and pastProgress in Biophysics and Molecular Biology, 2004
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsBioinformatics, 2003