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
Biological Networks
Scooter Morris (http://www.cgl.ucsf.edu/home/scooter/) talks about the opportunities and challenges in mapping biological networks and gives an brief overview of Cytoscape (http://www.cytoscape.org/), an open source bioinformatics software platform for visualizing molecular interaction...
Scientific topics: Pathway or network
Keywords: Cells and Organisms, Pathway
Resource type: Video
Biological Networks
https://bivi.co/presentation/biological-networks
http://tess.elixir-uk.org/materials/biological-networks
Scooter Morris (http://www.cgl.ucsf.edu/home/scooter/) talks about the opportunities and challenges in mapping biological networks and gives an brief overview of Cytoscape (http://www.cytoscape.org/), an open source bioinformatics software platform for visualizing molecular interaction networks.(PLEASE NOTE: There is a small formatting problem with the presentation slides for the first 2 min of the talk only). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Dr. Scooter Morris
Pathway or network
Cells and Organisms, Pathway
2017-01-31
