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 dat… Show more
“…This suggests an interesting signal path of the HRG drug response, which may offer new targets for treatment. We note that the PI3K/AKT/mTOR and STAT pathway genes are predominantly changed following HRG artificial treatment prediction, pathways that may affect cell proliferation and apoptosis, as recently suggested
5,
26 .…”
Section: Use Casessupporting
confidence: 66%
“…It enables "plugging in" in the form of dedicated software called applications (Apps), which are developed by users. BioNSi
5 is one such application that provides a user friendly tool for simulating the dynamics of biological regulatory networks. It is implemented under Cytoscape version 3.…”
Section: Methodsmentioning
confidence: 99%
“…In addition, we focused on biologist-friendly tools that require very little computational background and in particular no script writing skills. The last tool in
Table 1 is BioNSi - Biological Network Simulator
5 , whose extensions are the focus of this paper, as will be described later.…”
Section: Introductionmentioning
confidence: 99%
“…BioNSi - A high level descriptionBioNSi is a biological network simulation tool
5 . It allows constructing a regulatory network and simulating its behavior.…”
Many biologists are discouraged from using network simulation Motivation: tools because these require manual, often tedious network construction. This situation calls for building new tools or extending existing ones with the ability to import biological pathways previously deposited in databases and analyze them, in order to produce novel biological insights at the pathway level.We have extended a network simulation tool (BioNSi), which now Results: allows merging of multiple pathways from the KEGG pathway database into a single, coherent network, and visualizing its properties. Furthermore, the enhanced tool enables loading experimental expression data into the network and simulating its dynamics under various biological conditions or perturbations. As a proof of concept, we tested two sets of published experimental data, one related to inflammatory bowel disease condition and the other to breast cancer treatment. We predict some of the major observations obtained following these laboratory experiments, and provide new insights that may shed additional light on these results. Cytoscape 3.x, JAVA 8 Tool requirements:The tool is freely available at , where a Availability:http://bionsi.wix.com/bionsi complete user guide and a step-by-step manual can also be found.Amir Rubinstein ( )
“…This suggests an interesting signal path of the HRG drug response, which may offer new targets for treatment. We note that the PI3K/AKT/mTOR and STAT pathway genes are predominantly changed following HRG artificial treatment prediction, pathways that may affect cell proliferation and apoptosis, as recently suggested
5,
26 .…”
Section: Use Casessupporting
confidence: 66%
“…It enables "plugging in" in the form of dedicated software called applications (Apps), which are developed by users. BioNSi
5 is one such application that provides a user friendly tool for simulating the dynamics of biological regulatory networks. It is implemented under Cytoscape version 3.…”
Section: Methodsmentioning
confidence: 99%
“…In addition, we focused on biologist-friendly tools that require very little computational background and in particular no script writing skills. The last tool in
Table 1 is BioNSi - Biological Network Simulator
5 , whose extensions are the focus of this paper, as will be described later.…”
Section: Introductionmentioning
confidence: 99%
“…BioNSi - A high level descriptionBioNSi is a biological network simulation tool
5 . It allows constructing a regulatory network and simulating its behavior.…”
Many biologists are discouraged from using network simulation Motivation: tools because these require manual, often tedious network construction. This situation calls for building new tools or extending existing ones with the ability to import biological pathways previously deposited in databases and analyze them, in order to produce novel biological insights at the pathway level.We have extended a network simulation tool (BioNSi), which now Results: allows merging of multiple pathways from the KEGG pathway database into a single, coherent network, and visualizing its properties. Furthermore, the enhanced tool enables loading experimental expression data into the network and simulating its dynamics under various biological conditions or perturbations. As a proof of concept, we tested two sets of published experimental data, one related to inflammatory bowel disease condition and the other to breast cancer treatment. We predict some of the major observations obtained following these laboratory experiments, and provide new insights that may shed additional light on these results. Cytoscape 3.x, JAVA 8 Tool requirements:The tool is freely available at , where a Availability:http://bionsi.wix.com/bionsi complete user guide and a step-by-step manual can also be found.Amir Rubinstein ( )
“… Box 1. BioNSi - A high level description BioNSi is a biological network simulation tool 5 . It allows constructing a regulatory network and simulating its behavior.…”
Motivation: Many biologists are discouraged from using network simulation tools because these require manual, often tedious network construction. This situation calls for building new tools or extending existing ones with the ability to import biological pathways previously deposited in databases and analyze them, in order to produce novel biological insights at the pathway level.
Results: We have extended a network simulation tool (BioNSi), which now allows merging of multiple pathways from the KEGG pathway database into a single, coherent network, and visualizing its properties. Furthermore, the enhanced tool enables loading experimental expression data into the network and simulating its dynamics under various biological conditions or perturbations. As a proof of concept, we tested two sets of published experimental data, one related to inflammatory bowel disease condition and the other to breast cancer treatment. We predict some of the major observations obtained following these laboratory experiments, and provide new insights that may shed additional light on these results.
Tool requirements: Cytoscape 3.x, JAVA 8
Availability: The tool is freely available at
http://bionsi.wix.com/bionsi, where a complete user guide and a step-by-step manual can also be found.
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