Model annotation and simulation results verification for authors and journals
PLOS Computational Biology
Jason Papin Editor-in-Chief, PLOS Computational Biology Gary Beardmore Managing Editor, PLOS Computational Biology
If your journal is interested in collaborating to provide simulation and results verification services to authors, please contact info@reproduciblebiomodels.org .
Online simulation and visualization for readers, reviewers, and journals
Formalized OMEX metadata specification
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 [...]
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 [...]
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), [...]
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), [...]
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). [...]
Technical consulting
Alzheimer modeling
Jean-Marie Bouteiller Assistant Professor Department of Biomedical Engineering University of Southern California Los Angeles, CA, USA
CompuCell3d multiscale modeling
Drs. Maciek Swat and James Glazier The Biocomplexity Institute Indiana University Bloomington, IN, USA
PRiME: Program for Research on Immune Modeling and Experimentation
Stuart Sealfon Professor Neurology, Neurobiology, and Pharmacology & Systems Therapeutics Icahn School of Medicine at Mount Sinai New York, NY, USA
Systems Biology Center New York
Ravi Iyengar Professor, Department of Pharmacology and Systems Therapeutics Icahn School of Medicine at Mount Sinai New York, NY, USA
Need help?
We would be glad to help you conduct modeling systematically, scalably, and reproducibly. Please use the form below to request our assistance. We will evaluate service requests based on their synergy with the center, potential impact, and feasibility.