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

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

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.