The BioSimulators format for the specifications of a simulation tool is
a JSON schema for describing the modeling frameworks (e.g., logical,
constraint-based), simulation algorithms (e.g., CVODE, SSA), and
modeling formats (e.g., CellML, COMBINE/OMEX, SBML, SED-ML) that a
simulation tool supports, as well as the parameters of each algorithm
(e.g., random number generator seed), their data types, and their
allowed and default values.
The format can also capture a metadata about each simulation tool
including its
- Name;
- Version;
- Description;
- URL for a standardized Docker image for the tool;
- URL for documentation about about the tool;
- Citations for the tool;
- Citations for each algorithm supported by the tool;
-
Other identifiers for the tool such as for bio.tools, CRAN, or PyPI;
- License for the tool;
- The authors of the tool; and
-
Dates when the tool was submitted to the BioSimulators registry and
last updated.
The schema for the format is available in JSON Schema
and Open API
formats. Documentation for the schema is available at
{{ config.dispatchApiUrl }}.
The schema utilizes several ontologies:
-
Funding agencies: Funder Registry
terms such as the National Science Foundation (10.13039/100000001
), the National Institutes of Health (10.13039/100000002
)
-
Licenses: SPDX
terms such as GNU General Public License v3.0 or later
(GPL-3.0-or-later
)
-
Modeling formats: EDAM
terms such as BNGL (format_3972
), CellML (format_3240
), SBML (format_2585
), SED-ML (format_3685
)
-
Modeling frameworks: SBO
terms such as flux balance analysis framework (SBO:0000624
), non-spatial continuous kinetic framework (SBO:0000293
)
-
Programming languages: Linguist
terms such as C++, Java, JavaScript, Python, R
-
Simulation algorithms: KiSAO
terms such as CVODE (KISAO:0000019
), FBA (KISAO:0000437
), SSA (KISAO:0000029
)
As an example, below is the specifications for tellurium
.