standards > model/format > bsg-s001536


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

Abbreviation: BioSimulators standards


General Information
The BioSimulators standards encompass four standards 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.



Awaiting DOI assignment.


This record is maintained by jonrkarr  ORCID

Record added: Oct. 21, 2020, 6:30 p.m.
Record updated: Nov. 19, 2020, 2:59 p.m. by jonrkarr.

Show edit history



Support

General

Additional Information


Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use

Applies to: Database software

Data Release




Publications

No publications available


Related Standards

Reporting Guidelines

No guidelines defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined


Related Databases (2)
BioSimulators
BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.

BioSimulations
BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.

Implementing Policies

This record is not implemented by any policy.


Credit

Record Maintainer

Funds

Maintains

Grant Number(s)

  • P41EB023912 (National Institute of Biomedical Imaging and Bioengineering (NIBIB), USA)