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 container network analysis systems biology

Links

Homepage

Pattern for Local Unique Identifiers

Local unique 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

Contact

Jonathan Karr   0000-0002-2605-5080

Identifier Space Owner

Icahn School of Medicine at Mount Sinai

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 3 mappings to external registries with 3 unique external prefixes.

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. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.