BioModels

{{short description|Database of biological reactions}}

{{infobox biodatabase

|title = BioModels

|logo = Image:BioModels Database, logo 2014.png

|description = A repository for storing, exchanging and retrieving computational models of biological interest.

|scope = computational models

|organism = all

|center = EMBL-EBI, BI, Caltech

|laboratory =

|author =

|pmid = 20587024

|released = 2005

|standard = MIRIAM

|format = SBML, BioPAX, SciLab, Octave, XPP, VCML, RDF/XML

|url = [http://www.ebi.ac.uk/biomodels/ EBI main instance], [http://biomodels.caltech.edu/ Caltech mirror]

|download = [http://ftp.ebi.ac.uk/pub/databases/biomodels/ EBI FTP]

|webservice = [http://www.ebi.ac.uk/biomodels-main/webservices SOAP]

|sql =

|sparql =

|webapp = Model display, multiple browsing strategies, advanced search, bulk download, [http://www.ebi.ac.uk/biomodels-main/modelmonth model of the month]

|standalone =

|license = [https://creativecommons.org/publicdomain/zero/1.0/ CC0 Public Domain Dedication]

|version = 28 (September 2014)

|versioning =

|frequency =

|curation = yes (manual)

|bookmark = yes

}}

BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006.Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems. Nucleic Acids Research (2006), 34: D689-D691.{{cite journal |last1=Li |first1=Chen |last2=Donizelli |first2=Marco |last3=Rodriguez |first3=Nicolas |last4=Dharuri |first4=Harish |last5=Endler |first5=Lukas |last6=Chelliah |first6=Vijayalakshmi |last7=Li |first7=Lu |last8=He |first8=Enuo |last9=Henry |first9=Arnaud |last10=Stefan |first10=Melanie I |last11=Snoep |first11=Jacky L |last12=Hucka |first12=Michael |last13=Le Novère |first13=Nicolas |author-link13=Nicolas Le Novère |last14=Laibe |first14=Camille |date=2010 |title=BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models |journal=BMC Systems Biology |volume=4 |issue=1 |pages=92 |doi=10.1186/1752-0509-4-92 |pmc=2909940 |pmid=20587024 |doi-access=free}}Chelliah V., Juty N., Ajmera I., Raza A., Dumousseau 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 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.

Modellers can submit the models in SBML and CellML. Models can subsequently be downloaded in SBML, [http://www.nrcam.uchc.edu/ VCML] {{Webarchive|url=https://web.archive.org/web/20061209120512/http://www.nrcam.uchc.edu/ |date=2006-12-09 }}, [http://www.math.pitt.edu/~bard/xpp/xpp.html XPP], SciLab, Octave, BioPAX and RDF/XML. The reaction networks of models are presented in some graphic formats, such as PNG, SVG and graphic Java applet, in which some networks were presented by following Systems Biology Graphical Notation. And a human readable summary of each model is available in PDF.