title: BioNSi: A Discrete Biological Network Simulator Tool.
abstract: 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 http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found.
authors.affiliation: Blavatnik School of Computer Science, and ‡Department of Neurobiology, George S. Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel.
authors.forename: Amir
authors.initials: A
authors.lastname: Rubinstein
authors.affiliation: Blavatnik School of Computer Science, and ‡Department of Neurobiology, George S. Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel.
authors.forename: Noga
authors.initials: N
authors.lastname: Bracha
authors.affiliation: Blavatnik School of Computer Science, and ‡Department of Neurobiology, George S. Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel.
authors.forename: Liat
authors.initials: L
authors.lastname: Rudner
authors.affiliation: Blavatnik School of Computer Science, and ‡Department of Neurobiology, George S. Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel.
authors.forename: Noga
authors.initials: N
authors.lastname: Zucker
authors.affiliation: Blavatnik School of Computer Science, and ‡Department of Neurobiology, George S. Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel.
authors.forename: Hadas E
authors.initials: HE
authors.lastname: Sloin
authors.affiliation: Blavatnik School of Computer Science, and ‡Department of Neurobiology, George S. Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel.
authors.forename: Benny
authors.initials: B
authors.lastname: Chor
mesh_terms: D003198:Computer Simulation; D020407:Internet; D008954:Models, Biological; D012984:Software
keywords: biological networks; discrete models; modeling; simulation