BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).

computational biology systems biology
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Jonathan Karr   0000-0002-2605-5080
Pattern for Local Unique Identifiers

Local identifiers in BioSimulators should match this regular expression:

Example Local Unique Identifier
vcell   Resolve
Pattern for CURIES

Compact URIs (CURIEs) constructed from BioSimulators should match this regular expression:

Example CURIE
Metaregistry BioSimulators

The metaregistry provides mappings between the Bioregistry and other registries. There are 3 mappings to external registries for this resource with 3 unique external prefixes.

Registry Name Registry Metaprefix External Prefix Curate
FAIRSharing FAIRSharing logo fairsharing FAIRsharing.pwEima logo miriam biosimulators
re3data Registry of Research Data Repositories logo re3data r3d100013432

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier vcell is used to demonstrate the providers available for BioSimulators. A guide for curating additional providers can be found here.

Name Metaprefix URI
BioSimulators biosimulators
Bioregistry bioregistry miriam