runBioSimulations tutorial and help
runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA),...
Scientific topics: Simulation experiment, Computational biology, Systems biology
Operations: Modelling and simulation
Keywords: biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL
Resource type: Tutorial, Documentation
runBioSimulations tutorial and help
https://run.biosimulations.org/help
http://tess.elixir-uk.org/materials/runbiosimulations-tutorial-and-help
runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BNGL, SBML). runBioSimulations also provides a REST API for programmatic access to the same simulation capabilities.
The runBioSimulations tutorial and help describes how to use this web application and web service to execute simulations and visualize their results. This includes instructions on how to create COMBINE/OMEX archives of modeling projects.
Jonathan Karr
Ion Moraru
Bilal Shaikh
Gnaneswara Marupilla
Simulation experiment
Computational biology
Systems biology
biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL
modelers
BioSimulators tutorial and help
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,...
Scientific topics: Simulation experiment, Computational biology, Systems biology
Operations: Modelling and simulation
Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL
Resource type: Tutorial, Documentation
BioSimulators tutorial and help
https://biosimulators.org/help
http://tess.elixir-uk.org/materials/biosimulators-help
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.
The BioSimulators help describes how to use this registry:
- How to find a containerized simulation tools that are capable of executing a modeling study.
- How to use containerized simulation tools to execute modeling studies.
- How to containerize a simulation tool and submit it to the BioSimulators registry.
Jonathan Karr
Ion Moraru
Bilal Shaikh
Simulation experiment
Computational biology
Systems biology
Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL
modelers
Computational biologists
software developers, bioinformaticians
CPANG19 - Computational PANGenomics (2019)
Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.
Keywords: Genomics
Resource type: Documentation, Exercise, Handout, Scripts
CPANG19 - Computational PANGenomics (2019)
https://gtpb.github.io/CPANG19/
http://tess.elixir-uk.org/materials/cpang19-computational-pangenomics-2019
Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.
The Gulbenkian Training Programme in Bioinformatics
Erik Garrison
Mikko Rautiainen
Genomics
Academia/ Research Institution
Industry
Non-Profit Organisation
Healthcare
CPANG18 - Computational PANGenomics (2018)
Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.
Keywords: Genomics
Resource type: Documentation, Exercise, Handout, Scripts
CPANG18 - Computational PANGenomics (2018)
https://gtpb.github.io/CPANG18/
http://tess.elixir-uk.org/materials/cpang18-computational-pangenomics-2018
Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.
The Gulbenkian Training Programme in Bioinformatics
Erik Garrison
Mikko Rautiainen
Jordan Eizenga
Genomics
Academia/ Research Institution
Industry
Non-Profit Organisation
