TY - JOUR
T1 - Simulation and visualization of multiple KEGG pathways using BioNSi
AU - Rubinstein, Amir
AU - Yeheskel, Adva
AU - Reiter, Adam
AU - Pasmanik-Chor, Metsada
N1 - Publisher Copyright:
© 2018 Yeheskel A et al.
PY - 2018
Y1 - 2018
N2 - 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.
AB - 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.
KW - BioNSi
KW - Biological network
KW - Cytoscape
KW - Gene expression
KW - KEGG
KW - Simulation
UR - http://www.scopus.com/inward/record.url?scp=85048865778&partnerID=8YFLogxK
U2 - 10.12688/f1000research.13254.2
DO - 10.12688/f1000research.13254.2
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C2 - 29946422
AN - SCOPUS:85048865778
VL - 6
JO - F1000Research
JF - F1000Research
SN - 2046-1402
M1 - 2120
ER -