BioSimulators formats for the inputs, outputs, and capabilities of biosimulation software tools

Other names: BioSimulators formats

The BioSimulators conventions encompass several conventions for biosimulation tools (see below). In combination with modeling languages such as Cell-ML and SBML, SED-ML, KISAO, and COMBINE/OMEX, the BioSimulators standards enable investigators to use compliant biosimulation tools to execute simulations with the same syntax and generate consistent results. (a) A format for describing the specifications of a biosimulation tool including its name and version; a description of the tool; the modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BNGL, SBML) that the tool supports; the parameters of each algorithm, their data types, and their default values; links to the tool and documentation about the tool; and additional metadata such as citations for the tool. (b) Specifications for the syntax and semantics of the inputs (command-line arguments) and outputs (reports and charts of simulation results) of command-line interfaces for biosimulation tools. (c) Specifications for (i) the entry points of Docker images of biosimulation tools and (ii) using Docker labels to annotate basic metadata about images such as the name and version of the simulation tool inside the image. (d) A format for describing reports of simulation results, including the numerical predictions, as well as metadata about the semantic meaning of each axis and each individual row and column.

Webpage:
https://biosimulators.org/conventions

Tags:

kinetic model mathematical model network simulation software

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