Name: Computational Modeling
Published: 2016-05-19 11:41:54
License: https://creativecommons.org/licenses/by-sa/4.0/. Please link to https://fairsharing.org and https://fairsharing.org/static/img/home/svg/FAIRsharing-logo.svg for attribution.

Computational Modeling

A collection of the standards and databases covering all aspects of computational modelling. This collection also includes the standards found in the COMBINE Collection.

This record is maintained by: PeteMcQ ORCID

Record added: May 19, 2016, 11:41 a.m..
Record updated: Oct. 5, 2016, 11:06 a.m. by The FAIRsharing Team.

Taxonomic range

All

Knowledge Domains

Subjects

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26 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	Resource metadata Pathway model	All	Gramene Reactome PC PathBank	SBGN GPML	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards
BioModels Ontology	BioModels	Standard	Life Science Ontology and Terminology	Mathematical model Enzymatic reaction Molecular entity Network model Pathway model	All	BioModels	None	None	Computational Modeling
CellML	CellML	Standard	Life Science Physiology	Mathematical model Cell	All	BioModels KiMoSys PMR	SED-ML MIRIAM SBML FieldML MathML Plus 3 more...	EMBO Recommended Databases and Data Standards GGN	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards Genetics & Genomics Next
Chemical Markup Language	CML	Standard	Biochemistry Chemistry Life Science	Mathematical model Reaction data Molecular structure Molecular entity Spectroscopy	All	Rhea CCD eCrystals	XML	None	Computational Modeling Chemistry
Computational Neuroscience Ontology	CNO	Standard	Bioinformatics Computational Neuroscience Life Science Neurobiology Neuroscience Plus 1 more...	None	Homo sapiens	None	None	None	Computational Modeling
General Formal Ontology	GFO	Standard	Biomedical Science Life Science Ontology and Terminology	Mathematical model	All	None	GFO-BIO	None	Computational Modeling
Human Physiome Field Markup Language	FieldML	Standard	Anatomy Bioengineering Biomedical Science Physiology Systems Biology	Modeling and simulation Tissue	Homo sapiens	PMR	CellML XML	None	Computational Modeling The NormSys Registry for Modeling Standards
JWS Online	JWS Online	Database	Systems Biology	Kinetic model Mathematical model	All	BioModels SABIO-RK FAIRDOMHub BiGG Models	SED-ML MIRIAM SBML	EMBO Recommended Databases and Data Standards Rockefeller University Press - Journal Of Cell Biology - Data Deposition Rockefeller University Press - Journal Of Experimental Medicine - Data Deposition	Computational Modeling
Kinetic Simulation Algorithm Ontology	KiSAO	Standard	Computer Science Ontology and Terminology	Kinetic model Algorithm	All	OBO	MIASE SED-ML MIRIAM SBO	None	Computational Modeling FAIRDOM Community Standards
Mathematical Modelling Ontology	MAMO	Standard	Computational Biology Mathematics Ontology and Terminology Systems Biology	None	All	BioModels OBO	SED-ML DRAO	None	Computational Modeling
Minimal Information Required In the Annotation of Models	MIRIAM	Standard	Biochemistry Biomedical Science Life Science	Annotation Mathematical model Chemical entity Enzymatic reaction Pathway model Plus 1 more...	All	Identifiers.org BioModels YEASTNET JWS Online BiGG Models	CellML SED-ML SBML SBOL SBO Plus 4 more...	EMBO Recommended Databases and Data Standards Rockefeller University Press - Journal Of Cell Biology - Data Deposition GGN Rockefeller University Press - Journal Of Experimental Medicine - Data Deposition	Computational Modeling FAIRDOM Community Standards Minimum Information for Biological and Biomedical Investigations Chemistry Genetics & Genomics Next
NeuroML	NeuroML	Standard	Cellular Neuroscience Life Science Neurobiology Neuroscience	Mathematical model Assay Brain Modeling and simulation Network model	All	OSB	XML PyNN	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards INCF Endorsed standards
Numerical Markup Language	NuML	Standard	Computational Biology Computer Science Systems Biology	Kinetic model Mathematical model Reaction data Modeling and simulation	All	None	SBRML SED-ML XML	None	Computational Modeling
Ontology and Knowledge Base of Probability Distributions	ProbOnto	Database	Computational Biology Mathematics Statistics Systems Biology	Mathematical model	None	None	PharmML	None	Computational Modeling
Open Modeling EXchange format	OMEX	Standard	None	Mathematical model	All	None	SED-ML MIRIAM MIASE SBGN CellML Plus 1 more...	None	Computational Modeling
Pharmacometrics Markup Language	PharmML	Standard	Biochemistry Biomedical Science	Reaction data	Vertebrata	ProbOnto	XML	None	Computational Modeling FAIRDOM Community Standards Chemistry The NormSys Registry for Modeling Standards
Physiome Model Repository	PMR	Database	Biomedical Science Life Science Mathematics Physiology Systems Biology	Mathematical model	All	None	CellML SED-ML FieldML SBML	None	Computational Modeling
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	CellML MIRIAM SBML SBO NuML Plus 6 more...	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Synthetic Biology Open Language	SBOL	Standard	Life Science Synthetic Biology	DNA sequence data Nucleic acid design Sequence annotation	All	VPR iGEM SBH	SBOL Visual MIRIAM	None	Computational Modeling (COMBINE) Computational Modeling The NormSys Registry for Modeling Standards
Synthetic Biology Open Language Visual	SBOL Visual	Standard	Data Visualization Life Science Synthetic Biology	DNA sequence data Nucleic acid design Sequence annotation	All	SBH	MIRIAM SBOL	None	Computational Modeling The NormSys Registry for Modeling Standards
Systems Biology Graphical Notation	SBGN	Standard	Life Science	Mathematical model Enzymatic reaction Molecular entity Network model Pathway model	All	MetaCrop 2.0 IPAVS SubtiWiki TopFIND BioModels Plus 2 more...	BioPAX OMEX SBO SBML	None	Computational Modeling (COMBINE) Computational Modeling FAIRDOM Community Standards The NormSys Registry for Modeling Standards
Systems Biology Markup Language	SBML	Standard	Life Science Systems Biology	Mathematical model Enzymatic reaction Molecular entity Network model Pathway model	All	MetaCrop 2.0 IPAVS BRENDA Gramene BioModels Plus 12 more...	CellML SBGN SED-ML MIRIAM OFSMR Plus 3 more...	EMBO Recommended Databases and Data Standards GGN	Computational Modeling (COMBINE) Computational Modeling H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project FAIRDOM Community Standards The NormSys Registry for Modeling Standards Plus 1 more...
Systems Biology Ontology	SBO	Standard	Life Science Systems Biology	Mathematical model Molecular interaction Pathway model	All	BioModels	SBGN SED-ML MIRIAM KiSAO SBML Plus 2 more...	None	Computational Modeling FAIRDOM Community Standards
TErminology for the Description of DYnamics	TEDDY	Standard	Life Science Neurophysiology Ontology and Terminology Synthetic Biology Systems Biology	Modeling and simulation	All	None	SED-ML SBO	None	Computational Modeling FAIRDOM Community Standards
Tumor model repositories Markup Language	TumorML	Standard	Biomedical Science	Mathematical model Tumor Cancer	All	None	XML	None	Computational Modeling
Virtual Parts Repository	VPR	Database	None	None	None	SBH	SBOL SBML	None	Computational Modeling

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