BioSimulators

General Information

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.

Homepage https://biosimulators.org

Countries that developed this resource United States

Created in 2020

Taxonomic range

Not applicable

Knowledge Domains

Subjects

User-defined Tags

Docker

Genome Scale Metabolic Model

Multi-scale model

container

How to cite this record FAIRsharing.org: BioSimulators; BioSimulators; DOI: https://doi.org/10.25504/FAIRsharing.pwEima; Last edited: Jan. 25, 2021, 4:28 p.m.; Last accessed: Apr 13 2021 3:29 p.m.

This record is maintained by jonrkarr ORCID

Record added: Oct. 21, 2020, 6:02 p.m.
Record updated: Dec. 14, 2020, 9:21 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.pwEima' by 'The FAIRsharing Team' at 09:21, 14 Dec 2020 (approved):

	'user_defined_tags' has been modified:
		Before:
			COMBINE
			Docker
			Genome Scale Metabolic Model
			Multi-scale model
			container
		After:
			Docker
			Genome Scale Metabolic Model
			Multi-scale model
			container
		Added:
		Removed:
			COMBINE

Edits to 'https://fairsharing.org/FAIRsharing.pwEima' by 'The FAIRsharing Team' at 09:47, 17 Nov 2020 (approved):

	'standardsImplemented' has been modified:
		Before:
			Kinetic Simulation Algorithm Ontology
			Systems Biology Ontology
			EDAM Bioimaging Ontology
			BioSimulators container format
			Simulation Experiment Description Markup Language
		After:
			Kinetic Simulation Algorithm Ontology
			Systems Biology Ontology
			EDAM Bioimaging Ontology
			BioSimulators container format
			Simulation Experiment Description Markup Language
			Open Modeling EXchange format
		Added:
			Open Modeling EXchange format
		Removed:

	'miriam_id' has been modified:
		Before: None
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Edits to 'https://fairsharing.org/FAIRsharing.pwEima' by 'The FAIRsharing Team' at 10:27, 25 Oct 2020 (approved):

	'doi' has been modified:
		Before: None
		After: 

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

Edits to 'https://fairsharing.org/FAIRsharing.pwEima' by 'jonrkarr' at 18:32, 21 Oct 2020 (approved):

	'standardsImplemented' has been modified:
		Before:
			Kinetic Simulation Algorithm Ontology
			Systems Biology Ontology
			EDAM Bioimaging Ontology
			BioSimulators container format
		After:
			Simulation Experiment Description Markup Language
			Kinetic Simulation Algorithm Ontology
			Systems Biology Ontology
			EDAM Bioimaging Ontology
			BioSimulators container format
		Added:
			Simulation Experiment Description Markup Language
		Removed:

Support

General

FAQ	FAQ
contact form	Issue tracker
support email	Email
help	Tutorial and help
online documentation	API documentation

Additional Information

Contact

Jonathan Karr ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Database software

MIT Licence

REST Web Services

REST API

https://api.biosimulators.org

Publications

No publications available

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

BioSimulations

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by jonrkarr ORCID

Funds

National Institute of Biomedical Imaging and Bioengineering (NIBIB), USA (Government body)

Maintains

Center for Reproducible Biomedical Modeling (Research institute) Lead

Grant Number(s)

P41EB023912 (National Institute of Biomedical Imaging and Bioengineering (NIBIB), USA)

BioSimulators

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