How To Use BioNSi?

Installation is easy, and then our toy example will guide you step-by-step on how to use BioNSi. After that you will be able to start exploring your own network.


For more advanced features, please look at our user guide, and real biological examples..

           Why BioNSi?

Modeling and simulation of biological networks is an eff ective and widely used research methodology. BioNSi (Biological Network Simulator) is a tool for modeling biological networks and simulating their discrete-time
dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions.


To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise.

Two published papers describing this tool can be found here and here.


We gladly share the source code of this tool. So if you are interested in taking it on from here and extend it - you can find the source files here.

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