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Parasim is a tool for robustness analysis. Given a SBML model, a property and perturbation set, it computes the robustness of model over the perturbation set with respect to the property. Perturbation set consists of intervals over model parameters and initial variable values. Properties are entered in the form of signal temporal logic formulae.

For more information about principles behind this tool see Bibliography.

Downloads

Version	Changelog	Downloads
1.0.0.Final	[changelog] (https://github.com/sybila/parasim/issues?milestone=3&page=1&state=closed)	[Parasim CLI] (http://repository-sybila.forge.cloudbees.com/release/org/sybila/parasim/application/parasim-cli/1.0.0.Final/parasim-cli-1.0.0.Final-dist.jar), [Parasim GUI] (http://repository-sybila.forge.cloudbees.com/release/org/sybila/parasim/application/parasim-gui/1.0.0.Final/parasim-gui-1.0.0.Final-dist.jar)
1.0.0.M4	[changelog] (https://github.com/sybila/parasim/issues?milestone=6&page=1&state=closed)	[Parasim CLI] (http://repository-sybila.forge.cloudbees.com/release/org/sybila/parasim/application/parasim-cli/1.0.0.M4/parasim-cli-1.0.0.M4-dist.jar), [Parasim GUI] (http://repository-sybila.forge.cloudbees.com/release/org/sybila/parasim/application/parasim-gui/1.0.0.M4/parasim-gui-1.0.0.M4-dist.jar)
1.0.0.M3	[changelog] (https://github.com/sybila/parasim/issues?milestone=2&page=1&state=closed)	[Parasim CLI] (http://repository-sybila.forge.cloudbees.com/release/org/sybila/parasim/application/parasim-cli/1.0.0.M3/parasim-cli-1.0.0.M3-dist.jar)

For Users

• Use parasim GUI
• Learn to use parasim GUI
• Browse analysis results using projection plotter

Advanced Topics

• Execute parasim from command line
• Experiment file format
• Project naming and placement conventions
• Build parasim from source

For Developers

• Sybila repository
• Build your own extension
• XML Import and Export

Extensions

Core Extensions

The most of these extensions are loaded before the manager starts (the org.sybila.parasim.core.event.ManagerStarted event is fired).

• Descriptor Loader provides automatized loading of configuration
• Enrichment provides an easy way to decorate your classes
• Extension Loader provides automatized loading of user defined extensions.
• Interceptors
• Lifecycle
• Logging

Extensions for Computation

• Computation Model provides an easy way to execute your algorithm concurrently.
• Density
• Execution
• Lifecycle
• Simulation
• Verification

Extensions for Visualisation

• Swing Plotter

GUI extensions

• Project Manager
• Progress Logger provides window displaying messages.

Other Extensions

• Performence