BioModels

Recommended

General Information

BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-linked to publicly available reference information.

Homepage https://www.ebi.ac.uk/biomodels/

Developed in European Union

Created in 2005

Taxonomic range

All

Knowledge Domains BETA

Subjects BETA

In the following recommendations:

How to cite this record FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: Jan. 15, 2019, 12:51 p.m.; Last accessed: Feb 16 2019 10:15 p.m.

Publication for citation BioModels: expanding horizons to include more modelling approaches and formats. Glont M,Nguyen TVN,Graesslin M,Halke R,Ali R,Schramm J,Wimalaratne SM,Kothamachu VB,Rodriguez N,Swat MJ,Eils J,Eils R,Laibe C,Malik-Sheriff RS,Chelliah V,Le Novere N,Hermjakob H; Nucleic Acids Res ; 2017; 10.1093/nar/gkx1023;

This record is maintained by nsjuty

Record updated: Jan. 15, 2019, 12:50 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.paz6mh' by 'The FAIRsharing Team' at 12:50, 15 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Maintains
		After:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			BBSRC Babraham Institute, Cambridge, UK|http://www.babraham.ac.uk|Maintains
			SBML Community|http://sbml.org/About|Maintains
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Innovative Medicines Initiative (IMI), Europe|http://www.imi.europa.eu|Funds
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			BBSRC Babraham Institute, Cambridge, UK|http://www.babraham.ac.uk|Maintains
			SBML Community|http://sbml.org/About|Maintains
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Innovative Medicines Initiative (IMI), Europe|http://www.imi.europa.eu|Funds
		Removed:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Maintains

	'grants' has been modified:
		Before:
		After:
			Multimod, BB/N019482/1
			TransQST, 116030
		Added:
			Multimod, BB/N019482/1
			TransQST, 116030
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.paz6mh' by 'The FAIRsharing Team' at 13:09, 21 Dec 2018 (approved):

	'name' has been modified:
		Before: A repository of mathematical models of biological and biomedical systems
		After: BioModels

Edits to 'https://fairsharing.org/FAIRsharing.paz6mh' by 'The FAIRsharing Team' at 13:08, 21 Dec 2018 (approved):

	'organizations' has been modified:
		Before:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
		After:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.ebi.ac.uk/biomodels-main/faq
			TeSS training|https://tess.elixir-europe.org/materials/biomodels-database-quick-tour
			mailing list|https://lists.sourceforge.net/lists/listinfo/biomodels-net-discuss
			mailing list|biomodels-net-support@lists.sf.net
			training|http://www.ebi.ac.uk/biomodels-main/courses
			twitter|@biomodels
		After:
			FAQ|https://www.ebi.ac.uk/biomodels/faq
			TeSS training|https://tess.elixir-europe.org/materials/biomodels-database-quick-tour
			mailing list|https://lists.sourceforge.net/lists/listinfo/biomodels-net-discuss
			mailing list|biomodels-net-support@lists.sf.net
			online documentation|https://www.ebi.ac.uk/biomodels/content/news
			online documentation|https://www.ebi.ac.uk/biomodels/agedbrain
			training|https://www.ebi.ac.uk/biomodels/courses
			twitter|@biomodels
		Added:
			FAQ|https://www.ebi.ac.uk/biomodels/faq
			online documentation|https://www.ebi.ac.uk/biomodels/content/news
			online documentation|https://www.ebi.ac.uk/biomodels/agedbrain
			training|https://www.ebi.ac.uk/biomodels/courses
		Removed:
			FAQ|http://www.ebi.ac.uk/biomodels-main/faq
			training|http://www.ebi.ac.uk/biomodels-main/courses

	'tools' has been modified:
		Before:
		After:
			SPARQL Querying||https://www.ebi.ac.uk/rdf/services/sparql
			SBFC Online||https://www.ebi.ac.uk/biomodels/tools/converters/
		Added:
			SPARQL Querying||https://www.ebi.ac.uk/rdf/services/sparql
			SBFC Online||https://www.ebi.ac.uk/biomodels/tools/converters/
		Removed:

	'dataProcesses' has been modified:
		Before:
			search
			Download
			submit
		After:
			search
			Download
			submit
			Browse by GO Category
			Parameter Search
		Added:
			Browse by GO Category
			Parameter Search
		Removed:

	'miriam_id' has been modified:
		Before: None
		After: MIR:00000007

	'publications' has been modified:
		Before:
			BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.|Le Novre N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep JL., Hucka M., |Nucleic Acids Res.|2006
			BioModels: Content, Features, Functionality, and Use.|Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novre N, Laibe C, Chelliah V.|CPT Pharmacometrics Syst Pharmacol.|2015
		After:
			BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.|Le Novre N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep JL., Hucka M., |Nucleic Acids Res.|2006
			BioModels: Content, Features, Functionality, and Use.|Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novre N, Laibe C, Chelliah V.|CPT Pharmacometrics Syst Pharmacol.|2015
			BioModels: expanding horizons to include more modelling approaches and formats.|Glont M,Nguyen TVN,Graesslin M,Halke R,Ali R,Schramm J,Wimalaratne SM,Kothamachu VB,Rodriguez N,Swat MJ,Eils J,Eils R,Laibe C,Malik-Sheriff RS,Chelliah V,Le Novere N,Hermjakob H|Nucleic Acids Res|2017
		Added:
			BioModels: expanding horizons to include more modelling approaches and formats.|Glont M,Nguyen TVN,Graesslin M,Halke R,Ali R,Schramm J,Wimalaratne SM,Kothamachu VB,Rodriguez N,Swat MJ,Eils J,Eils R,Laibe C,Malik-Sheriff RS,Chelliah V,Le Novere N,Hermjakob H|Nucleic Acids Res|2017
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://www.ebi.ac.uk/biomodels/docs/|BioModels API
		Added:
			REST|https://www.ebi.ac.uk/biomodels/docs/|BioModels API
		Removed:

	'homepage' has been modified:
		Before: http://www.ebi.ac.uk/biomodels-main/
		After: https://www.ebi.ac.uk/biomodels/

In Collections

ELIXIR Core Data and Data Deposition Resources

Support

General

FAQ	BioModels FAQ
Mailing List	BioModels Mailing List
Mailing List	None
online documentation	News
online documentation	Model space in neurodegeneration - model ...
training	Courses
twitter	@biomodels

Additional Information

Contact	BioModels Team
Identifiers.org	MIR:00000007

TeSS training resources

Biomodels database quick tour

Tools

SPARQL Querying	https://www.ebi.ac.uk/rdf/services/sparql
SBFC Online	https://www.ebi.ac.uk/biomodels/tools/converters/

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Curation

submit

https://www.ebi.ac.uk/biomodels/model/create?execution=e1s1

Data Access

search	https://www.ebi.ac.uk/biomodels/search?query=%3A
Download	ftp://ftp.ebi.ac.uk/pub/databases/biomodels/
Browse by GO Category	https://www.ebi.ac.uk/biomodels/goChart/index
Parameter Search	https://www.ebi.ac.uk/biomodels/parameterSearch/index

REST Web Services

BioModels API

https://www.ebi.ac.uk/biomodels/docs/

Publications

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep JL., Hucka M.,
Nucleic Acids Res. 2006

View Paper (PubMed) View Publication

BioModels: Content, Features, Functionality, and Use.

Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.
CPT Pharmacometrics Syst Pharmacol. 2015

View Paper (PubMed) View Publication

BioModels: expanding horizons to include more modelling approaches and formats.

Glont M,Nguyen TVN,Graesslin M,Halke R,Ali R,Schramm J,Wimalaratne SM,Kothamachu VB,Rodriguez N,Swat MJ,Eils J,Eils R,Laibe C,Malik-Sheriff RS,Chelliah V,Le Novere N,Hermjakob H
Nucleic Acids Res 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Credit

Record Maintainer

This record is maintained by nsjuty

Funds

European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (Research institute)
Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
Innovative Medicines Initiative (IMI), Europe (Consortium)

Maintains

European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute) Lead
BBSRC Babraham Institute, Cambridge, UK (Government body)
SBML Community (Consortium)

Grant Number(s)

Multimod, BB/N019482/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
TransQST, 116030 (Innovative Medicines Initiative (IMI), Europe)

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