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).

Prefix
biosimulators
Keywords
computational biology systems biology
Links
Homepage Repository
Contact
Jonathan Karr   0000-0002-2605-5080
Pattern for Local Unique Identifiers

Local identifiers in BioSimulators should match this regular expression:
^[a-zA-Z0-9-_]+$

Example Local Unique Identifier
vcell   Resolve
Pattern for CURIES

Compact URIs (CURIEs) constructed from BioSimulators should match this regular expression:
^biosimulators:[a-zA-Z0-9-_]+$

Example CURIE
biosimulators:vcell
Metaregistry BioSimulators

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

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

Providers are various services that resolve CURIEs to URLs. The example CURIE biosimulators:vcell is used to demonstrate the provides available for biosimulators. Generation of OLS and BioPortal URLs requires additional programmatic logic beyond string formatting.

Name Metaprefix URI
BioSimulators biosimulators https://biosimulators.org/simulators/vcell
Bioregistry bioregistry https://bioregistry.io/biosimulators:vcell
Identifiers.org miriam https://identifiers.org/biosimulators:vcell