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Computational Modeling (COMBINE)

Computational Modeling Standards recommended by the COMBINE group. COMBINE is a network formed by the communities developing standards and formats to share computational models. It is expected that these federated projects will develop a set of interoperable standards covering all the aspects of computational modeling. Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE helps foster or support fledging efforts aimed at filling gaps or new needs. The standard description formats will ultimately cover the various types of models used in biology, the different views of a model and the different steps of the modeling and simulation activity.

This record is maintained by: MHucka ORCID , FAIRsharingTeam , matthiaskoenig ORCID

Record added: Feb. 16, 2016, 8:05 p.m..
Record updated: April 27, 2020, 4:30 p.m. by The FAIRsharing Team.

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Edits to 'https://fairsharing.org/bsg-c000012' by 'The FAIRsharing Team' at 16:29, 27 Apr 2020 (approved):

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Computational Neuroscience
			Synthetic Biology
			Systems Biology
		Added:
			Computational Neuroscience
			Synthetic Biology
			Systems Biology
		Removed:
			Life Science

	'onto_domains' has been modified:
		Before:
			Mathematical model
		After:
			Mathematical model
			Network simulation
			modeling and simulation objective
			network model
			pathway
		Added:
			Network simulation
			modeling and simulation objective
			network model
			pathway
		Removed:

	'standards' has been modified:
		Before:
			Biological Pathway eXchange
			CellML
			Systems Biology Graphical Notation
			NeuroML
			Simulation Experiment Description Markup Language
			Systems Biology Markup Language
			Synthetic Biology Open Language
		After:
			Biological Pathway eXchange
			CellML
			Systems Biology Graphical Notation
			NeuroML
			Simulation Experiment Description Markup Language
			Systems Biology Markup Language
			Synthetic Biology Open Language
			Synthetic Biology Open Language Visual
		Added:
			Synthetic Biology Open Language Visual
		Removed:

8 records in view

Name	Abbreviation	Type	Subject	Domain	Taxonomy	Related Database	Related Standard	Related Policy	In Collection/Recommendation
Biological Pathway eXchange	BioPAX	Standard	Bioinformatics Life Science Systems Biology	Mathematical model Resource metadata Modeling and simulation Pathway model	All	Rhea Gramene Reactome PC PathBank	GPML RDF/XML OWL MIRIAM SBGN	None	Computational Modeling (COMBINE) FAIRDOM Community Standards ISO/CD 20691 Collection - DRAFT Systems Medicine
CellML	CellML	Standard	Life Science Physiology	Mathematical model Cell Modeling and simulation	All	BioModels KiMoSys PMR	RDF MathML XML BioSimulators formats MIRIAM Plus 4 more...	EMBO Recommended Databases and Data Standards Advanced Genetics	Computational Modeling (COMBINE) FAIRDOM Community Standards The NormSys Registry for Modeling Standards ISO/CD 20691 Collection - DRAFT Advanced Genetics Plus 1 more...
NeuroML	NeuroML	Standard	Cellular Neuroscience Computational Neuroscience Life Science Neurobiology Neuroscience	Mathematical model Assay Brain Modeling and simulation Network model	All	OSB EBRAINS	XML PyNN SED-ML	None	Computational Modeling (COMBINE) FAIRDOM Community Standards The NormSys Registry for Modeling Standards ISO/CD 20691 Collection - DRAFT Systems Medicine Plus 1 more...
Simulation Experiment Description Markup Language	SED-ML	Standard	Life Science Systems Biology	Mathematical model Enzymatic reaction Modeling and simulation	All	BioModels WholeCellSimDB PMR JWS Online BioSimulators Plus 1 more...	CellML NeuroML MIRIAM SBML NuML Plus 8 more...	None	Computational Modeling (COMBINE) FAIRDOM Community Standards The NormSys Registry for Modeling Standards ISO/CD 20691 Collection - DRAFT Systems Medicine
Synthetic Biology Open Language	SBOL	Standard	Life Science Synthetic Biology	DNA sequence data Nucleic acid design Sequence annotation Modeling and simulation	All	VPR iGEM SBH	MIRIAM FASTA GenBank Sequence Format RDF/XML JSON-LD Plus 2 more...	None	Computational Modeling (COMBINE) The NormSys Registry for Modeling Standards ISO/CD 20691 Collection - DRAFT Systems Medicine
Synthetic Biology Open Language Visual	SBOL Visual	Standard	Data Visualization Life Science Synthetic Biology	DNA sequence data Nucleic acid design Sequence annotation Modeling and simulation	All	SBH	SBOL MIRIAM	None	Computational Modeling (COMBINE) The NormSys Registry for Modeling Standards ISO/CD 20691 Collection - DRAFT Systems Medicine
Systems Biology Graphical Notation	SBGN	Standard	Systems Biology	Mathematical model Enzymatic reaction Molecular entity Network model Pathway model	All	MetaCrop 2.0 IPAVS SubtiWiki TopFIND BioModels Plus 5 more...	SBO OMEX BioPAX SBML	None	Computational Modeling (COMBINE) FAIRDOM Community Standards The NormSys Registry for Modeling Standards Systems Medicine
Systems Biology Markup Language	SBML	Standard	Systems Biology	Mathematical model Enzymatic reaction Modeling and simulation Molecular entity Network model Plus 1 more...	All	MetaCrop 2.0 IPAVS BRENDA Gramene BioModels Plus 12 more...	CellML SED-ML SBGN MIRIAM OFSMR Plus 5 more...	EMBO Recommended Databases and Data Standards Advanced Genetics	Computational Modeling (COMBINE) H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards The NormSys Registry for Modeling Standards ISO/CD 20691 Collection - DRAFT Plus 2 more...

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