BioModels

BioModels is a free and open-source repository for storing,

exchanging and retrieving quantitative models of biological
BioModels
interest created in 2006.[1][2][3] All the models in the curated
section of BioModels Database have been described in peer-
reviewed scientific literature.

The models stored in BioModels' curated branch 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.
Content
Modellers can submit the models in SBML and CellML. Models Description A repository for
can subsequently be downloaded in SBML, VCML (http://www.n
storing,
rcam.uchc.edu/), XPP (http://www.math.pitt.edu/~bard/xpp/xpp.ht
exchanging and
ml), SciLab, Octave, BioPAX and RDF/XML. The reaction
retrieving
networks of models are presented in some graphic formats, such as
PNG, SVG and graphic Java applet, in which some networks computational
were presented by following Systems Biology Graphical Notation. models of
And a human readable summary of each model is available in biological
PDF. interest.
Data types computational
Content captured models
Organisms all
BioModels is composed of several branches. The curated branch
Contact
hosts models that are well curated and annotated. The non-curated-
branch provides models that are still not curated, are non-curatable Research center EMBL-EBI, BI,
(spatial models, steady-state models etc.), or too huge to be Caltech
curated. Non-curated models can be later moved into the curated Primary citation PMID 20587024
branch. The repository also hosts models which were
(https://pubme
automatically generated from pathways databases.
d.ncbi.nlm.nih.g
All the models are freely available under the Creative Commons ov/20587024)
CC0 Public Domain Dedication, and can be easily accessed via Release date 2005
the website or Web Services (http://www.ebi.ac.uk/biomodels-mai
Access
n/webservices).[4] One can also download archives of all the
models from the EBI FTP server (http://ftp.ebi.ac.uk/pub/database Standards MIRIAM
s/biomodels/releases/latest/). Data format SBML, BioPAX,
SciLab, Octave,
BioModels announced its 31st release on June 26, 2017.[5] It now
XPP, VCML,
publicly provides 144,710 models. This corresponds to 1,640
RDF/XML
models published in the literature and 143,070 models
automatically generated from pathway resources. Website EBI main
instance (http://
Deposition of models in BioModels is advocated by many www.ebi.ac.uk/b
scientific journals, included Molecular Systems Biology, all the iomodels/),
journals of the Public Library of Science, all the journals of Caltech mirror
BioMed Central and all the journals published by the Royal (http://biomodel
Society of Chemistry. s.caltech.edu/)
Download URL EBI FTP (http://f
Development tp.ebi.ac.uk/pu
b/databases/bio
BioModels is developed by the BioModels.net Team at the
models/)
EMBL-EBI, UK, the Le Novère lab at the Babraham Institute,
UK, and the SBML Team in Caltech, USA.[6] Web service URL SOAP (http://ww
w.ebi.ac.uk/bio
models-main/w
Funding ebservices)

BioModels Development has benefited from the funds of the Tools

European Molecular Biology Laboratory, the Biotechnology and Web Model display,
Biological Sciences Research Council, the Innovative Medicines multiple
Initiative, the Seventh Framework Programme (FP7), the National browsing
Institute of General Medical Sciences, the DARPA, and the strategies,
National Center for Research Resources.
advanced
search, bulk
References download,
model of the
1. Le Novère N., Bornstein B., Broicher A., Courtot M.,
Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., month (http://w
Shapiro B., Snoep J.L., Hucka M. BioModels Database: ww.ebi.ac.uk/bio
A Free, Centralized Database of Curated, Published, models-main/m
Quantitative Kinetic Models of Biochemical and Cellular odelmonth)
Systems. Nucleic Acids Research (2006), 34: D689-
Miscellaneous
D691.
2. Li, Chen; Donizelli, Marco; Rodriguez, Nicolas; Dharuri, License CC0 Public
Harish; Endler, Lukas; Chelliah, Vijayalakshmi; Li, Lu; Domain
He, Enuo; Henry, Arnaud; Stefan, Melanie I; Snoep, Dedication (http
Jacky L; Hucka, Michael; Le Novère, Nicolas; Laibe, s://creativecom
Camille (2010). "BioModels Database: An enhanced, mons.org/public
curated and annotated resource for published domain/zero/1.
quantitative kinetic models" (https://www.ncbi.nlm.nih.go
0/)
v/pmc/articles/PMC2909940). BMC Systems Biology. 4
(1): 92. doi:10.1186/1752-0509-4-92 (https://doi.org/10.1 Version 28 (September
186%2F1752-0509-4-92). PMC 2909940 (https://www.n 2014)
cbi.nlm.nih.gov/pmc/articles/PMC2909940). Curation policy yes (manual)
PMID 20587024 (https://pubmed.ncbi.nlm.nih.gov/2058
7024). Bookmarkable yes
3. Chelliah V., Juty N., Ajmera I., Raza A., Dumousseau entities
M., Glont M., Hucka M., Jalowicki G., Keating S., Knight-
Schrijver V., Lloret-Villas A., Natarajan K., Pettit J.-B.,
Rodriguez N., Schubert M., Wimalaratne S., Zhou Y.,
Hermjakob H., Le Novère N., Laibe C. BioModels: ten
year anniversary. Nucleic Acids Research (2015) 43
(D1): D542-D548
 4. 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
(https://doi.org/10.1093%2Fbib%2Fbbp056)
5. BioModels Database: Hinxton, 26 June 2017 (https://
www.ebi.ac.uk/biomodels-main/static-pages.do?pag
e=release_20170626)
6. Funders and collaborators of BioModels (http://www.
ebi.ac.uk/biomodels-main/acknowledgements)
BioModels Database Pipeline

External links
Official website of BioModels (http://www.ebi.ac.uk/biomodels/)
Caltech Mirror site (http://biomodels.caltech.edu/)

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