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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/

Countries that developed this resource Austria , Belgium , Croatia , Czech Republic , Denmark , Finland , France , Germany , Greece , Hungary , Iceland , Israel , Italy , Lithuania , Luxembourg , Malta , Montenegro , Netherlands , Norway , Portugal , Republic of Ireland , Slovakia , Spain , Sweden , Switzerland , United Kingdom

Created in 2005

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

COVID-19

In the following recommendations:

How to cite this record FAIRsharing.org: BioModels; BioModels; DOI: https://doi.org/10.25504/FAIRsharing.paz6mh; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Oct 24 2021 11:24 p.m.

Publication for citation BioModels-15 years of sharing computational models in life science. Malik-Sheriff RS,Glont M,Nguyen TVN,Tiwari K,Roberts MG,Xavier A,Vu MT,Men J,Maire M,Kananathan S,Fairbanks EL,Meyer JP,Arankalle C,Varusai TM,Knight-Schrijver V,Li L,Duenas-Roca C,Dass G,Keating SM,Park YM,Buso N,Rodriguez N,Hucka M,Hermjakob H; Nucleic Acids Res ; 2019; 10.1093/nar/gkz1055;

This record is maintained by nsjuty

Record updated: Feb. 24, 2021, 11:09 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.paz6mh' by 'The FAIRsharing Team' at 11:09, 24 Feb 2021 (approved):

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

Edits to 'https://fairsharing.org/FAIRsharing.paz6mh' by 'The FAIRsharing Team' at 16:03, 19 Oct 2020 (approved):

	'user_defined_tags' has been modified:
		Before:
		After:
			COVID-19
		Added:
			COVID-19
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.paz6mh' by 'The FAIRsharing Team' at 17:07, 10 Feb 2020 (approved):

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

	'tools' has been modified:
		Before:
			SPARQL Querying||https://www.ebi.ac.uk/rdf/services/sparql
			SBFC Online||https://www.ebi.ac.uk/biomodels/tools/converters/
		After:
			SPARQL Querying||https://www.ebi.ac.uk/rdf/services/sparql
			SBFC Online||https://www.ebi.ac.uk/biomodels/tools/converters/
			Java library for RESTful Web Services||https://bitbucket.org/biomodels/biomodelswsclient
		Added:
			Java library for RESTful Web Services||https://bitbucket.org/biomodels/biomodelswsclient
		Removed:

	'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
			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
		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
			BioModels-15 years of sharing computational models in life science.|Malik-Sheriff RS,Glont M,Nguyen TVN,Tiwari K,Roberts MG,Xavier A,Vu MT,Men J,Maire M,Kananathan S,Fairbanks EL,Meyer JP,Arankalle C,Varusai TM,Knight-Schrijver V,Li L,Duenas-Roca C,Dass G,Keating SM,Park YM,Buso N,Rodriguez N,Hucka M,Hermjakob H|Nucleic Acids Res|2019
			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-15 years of sharing computational models in life science.|Malik-Sheriff RS,Glont M,Nguyen TVN,Tiwari K,Roberts MG,Xavier A,Vu MT,Men J,Maire M,Kananathan S,Fairbanks EL,Meyer JP,Arankalle C,Varusai TM,Knight-Schrijver V,Li L,Duenas-Roca C,Dass G,Keating SM,Park YM,Buso N,Rodriguez N,Hucka M,Hermjakob H|Nucleic Acids Res|2019
		Removed:

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

	'countries' has been modified:
		Before:
			European Union
		After:
			Austria
			Belgium
			Croatia
			Czech Republic
			Denmark
			Finland
			France
			Germany
			Greece
			Hungary
			Iceland
			Israel
			Italy
			Lithuania
			Luxembourg
			Malta
			Montenegro
			Netherlands
			Norway
			Portugal
			Republic of Ireland
			Slovakia
			Spain
			Sweden
			Switzerland
			United Kingdom
		Added:
			Austria
			Belgium
			Croatia
			Czech Republic
			Denmark
			Finland
			France
			Germany
			Greece
			Hungary
			Iceland
			Israel
			Italy
			Lithuania
			Luxembourg
			Malta
			Montenegro
			Netherlands
			Norway
			Portugal
			Republic of Ireland
			Slovakia
			Spain
			Sweden
			Switzerland
			United Kingdom
		Removed:
			European Union

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

EOSC-Life

ELIXIR Core Data Resources and Deposition Databases

Systems Medicine

Support

General

FAQ	BioModels FAQ
Mailing List	BioModels Mailing List
Mailing List	Support Mailing List
online documentation	News
online documentation	Model space in neurodegeneration - model ...
training	Courses
twitter	@biomodels

Additional Information

Contact

BioModels Team

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/
Java library for RESTful Web Services	https://bitbucket.org/biomodels/biomodelswsclient

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Release

Download

ftp://ftp.ebi.ac.uk/pub/databases/biomodels/

Data Curation

submit

https://www.ebi.ac.uk/biomodels/model/create

Data Access

Search	https://www.ebi.ac.uk/biomodels/search?query=%3A
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