Simulation and visualization of multiple KEGG pathways using BioNSi [version 2; referees: 2 approved, 1 approved with reservations]
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 an...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2018-05-01
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| Series: | F1000Research |
| Subjects: | |
| Online Access: | https://f1000research.com/articles/6-2120/v2 |
| _version_ | 1818172703175081984 |
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| author | Adva Yeheskel Adam Reiter Metsada Pasmanik-Chor Amir Rubinstein |
| author_facet | Adva Yeheskel Adam Reiter Metsada Pasmanik-Chor Amir Rubinstein |
| author_sort | Adva Yeheskel |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T19:16:49Z |
| format | Article |
| id | doaj.art-9f7c36cbddb84426bc750a68e273ad60 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-11T19:16:49Z |
| publishDate | 2018-05-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-9f7c36cbddb84426bc750a68e273ad602022-12-22T00:53:37ZengF1000 Research LtdF1000Research2046-14022018-05-01610.12688/f1000research.13254.216110Simulation and visualization of multiple KEGG pathways using BioNSi [version 2; referees: 2 approved, 1 approved with reservations]Adva Yeheskel0Adam Reiter1Metsada Pasmanik-Chor2Amir Rubinstein3Bioinformatics unit, Faculty of Life Science, Tel Aviv University, Tel Aviv, IsraelSchool of Computer Science, Tel Aviv University, Tel Aviv, IsraelBioinformatics unit, Faculty of Life Science, Tel Aviv University, Tel Aviv, IsraelSchool of Computer Science, Tel Aviv University, Tel Aviv, IsraelMotivation: 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.https://f1000research.com/articles/6-2120/v2BioinformaticsGenomics |
| spellingShingle | Adva Yeheskel Adam Reiter Metsada Pasmanik-Chor Amir Rubinstein Simulation and visualization of multiple KEGG pathways using BioNSi [version 2; referees: 2 approved, 1 approved with reservations] F1000Research Bioinformatics Genomics |
| title | Simulation and visualization of multiple KEGG pathways using BioNSi [version 2; referees: 2 approved, 1 approved with reservations] |
| title_full | Simulation and visualization of multiple KEGG pathways using BioNSi [version 2; referees: 2 approved, 1 approved with reservations] |
| title_fullStr | Simulation and visualization of multiple KEGG pathways using BioNSi [version 2; referees: 2 approved, 1 approved with reservations] |
| title_full_unstemmed | Simulation and visualization of multiple KEGG pathways using BioNSi [version 2; referees: 2 approved, 1 approved with reservations] |
| title_short | Simulation and visualization of multiple KEGG pathways using BioNSi [version 2; referees: 2 approved, 1 approved with reservations] |
| title_sort | simulation and visualization of multiple kegg pathways using bionsi version 2 referees 2 approved 1 approved with reservations |
| topic | Bioinformatics Genomics |
| url | https://f1000research.com/articles/6-2120/v2 |
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