BioNSi: A discrete biological network simulator tool

Amir Rubinstein, Noga Bracha, Liat Rudner, Noga Zucker, Hadas E. Sloin, Benny Chor

Research output: Contribution to journalArticlepeer-review


Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) 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. BioNSi is freely available at, where a complete user guide and a step-by-step manual can also be found.

Original languageEnglish
Pages (from-to)2871-2880
Number of pages10
JournalJournal of Proteome Research
Issue number8
StatePublished - 5 Aug 2016


  • biological networks
  • discrete models
  • modeling
  • simulation


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