BioSimulations supports all modeling frameworks. However, currently
BioSimulations can only simulate the logical, Flux Balance Analysis
(FBA), continuous kinetic (ordinary differential equations (ODE) and
differential-algebraic equations (DAE)), and discrete kinetic (e.g.,
Stochastic Simulation Algorithms (SSA)) frameworks. This includes
rule-based models. BioSimulations uses the BioSimulators collection of
simulation tools to simulate models. Please see BioSimulators
for more information about supported modeling frameworks.
Models can be shared in any format. However, currently BioSimulations
can only simulate models encoded in the BioNetGen Language (BNGL)
and the Systems Biology Markup Language (SBML)
. BioSimulations uses the BioSimulators collection of simulation tools
to simulate models. Please see BioSimulators
for more information about supported model formats.
Currently, BioSimulations can only simulate models that use core and
Flux Balance Constraints (fbc)
or Qualitative Models (qual)
packages.
BioSimulations supports numerous algorithms for simulating logical, Flux
Balance Analysis (FBA), continuous kinetic (ordinary differential
equations (ODE) and differential-algebraic equations (DAE)), and
discrete kinetic (e.g., Stochastic Simulation Algorithms (SSA)) models.
BioSimulations uses the BioSimulators collection of simulation tools to
simulate models. Please see BioSimulators
for more information about supported simulation algorithms.
BioSimulations provides a form for describing simulations. Internally,
BioSimulations represents simulations using its own format which is
similar to Simulation Experiment Description Markup Language (SED-ML)
. BioSimulations can export simulations to SED-ML.
Please submit an issue
to request support for another modeling framework.
Please submit an issue
to request support for another algorithm.
Please submit an issue
to request support for another model format.
BioSimulations stores results permanently.
To ensure the provenance of simulation results, simulation results can
only be generated by BioSimulations.
To credit authors for their contributions, this web application requires
an account to execute simulations. Please use our standalone web
application at
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or standalone web service at
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to execute COMBINE archives without an account. This web application and
this web service provide the same simulation capabilities (programs and
algorithms) as this web application through simpler interfaces. These
simpler interface don't require accounts, and they only have the
capability to execute simulations and visualize their results.
BioSimulations uses the BioSimulators collection of containerized
simulation software tools. Please see
https://biosimulators.org
for information about the available simulation tools, including the
modeling frameworks, simulation algorithms, and model formats supported
by each tool.
BioSimulations uses the BioSimulators collection of containerized
simulation software tools. These containers make it easy to execute
simulations by all providing the same command-line interface. The
containers are easy to install and run on your own machine. The
containers can be used on top of any operating system. Please see
https://biosimulators.org
for more information about how to install and run these containers.
Currently, simulations can only be uploaded in Vega format
.
Currently, BioSimulations supports the Creative Commons licenses
.
Please submit an issue
to request support for another license.
Please contact us via email
to request edits to published a model, simulation, or visualization.
To ensure the community has permanent access to published resources,
published models, simulations, and visualizations cannot be deleted.