Online simulation and visualization

Enhanced SED-ML libraries and specification

The Simulation Experiment Description Markup Language (SED-ML) is a standardized, community-based format that explicitly describes simulation processes for biochemical models, ensuring that researchers who are interested in a published model can efficiently reproduce and build upon that model. Its use is independent of specific operating systems or versions of software. The CRBM and COMBINE [...]

BioSimulations

BioSimulations is a free platform for sharing and re-using biomodels, simulations, simulation results, and visualizations of simulation results. BioSimulations supports a wide range of frameworks (e.g., logical, Flux-Balance Analysis (FBA), continuous kinetic, discrete kinetic), simulation algorithms (e.g., FBA, SSA), model formats (e.g., SBML), and tools (e.g., COBRApy, COPASI, tellurium). BioSimulations, developed by Jonathan Karr, [...]

2022-07-27T19:57:04-07:00February 2nd, 2022|Online simulation and visualization|

runBioSimulations

runBioSimulations is a free tool for running a wide range of biological simulations. Through the BioSimulators registry of biosimulation tools, runBioSimulations supports a broad range of modeling frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), modeling formats (e.g., SBML, SED-ML), and simulation tools (e.g., COBRApy, COPASI). run.biosimulations.org

2022-07-26T19:09:16-07:00December 20th, 2021|Online simulation and visualization|

BioSimulators

BioSimulators is a free registry of biosimulation tools. The registry includes tools for a broad range of frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), and model formats (e.g., BNGL, CellML, NeuroML/LEMS, SBML, Smoldyn). Many of the simulation tools provide Python packages, command-line programs, and Docker images with consistent interfaces. Together, BioSimulators makes it [...]

2022-07-26T18:31:01-07:00December 2nd, 2021|Online simulation and visualization|
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