As a common language to represent annotations for models, we have developed, in close collaboration with the COMBINE community, the OMEX metadata specification. This standard provides not only the specification of sharable, RDF formatted annotations, but also detailed examples and a set of recommended biological ontologies to use in those annotations. This standard is [...]
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 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, [...]
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
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 [...]
Jean-Marie Bouteiller Assistant Professor Department of Biomedical Engineering University of Southern California Los Angeles, CA, USA
Jason Papin Editor-in-Chief, PLOS Computational Biology Gary Beardmore Managing Editor, PLOS Computational Biology
Drs. Maciek Swat and James Glazier The Biocomplexity Institute Indiana University Bloomington, IN, USA
Stuart Sealfon Professor Neurology, Neurobiology, and Pharmacology & Systems Therapeutics Icahn School of Medicine at Mount Sinai New York, NY, USA
Dr. Joy Ku Stanford University Stanford, CA, USA
