PathVisio
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible. PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins.
| PathVisio | |
|---|---|
 | |
| Initial release | 2008 |
| Stable release | 3.3.0
/ January 28, 2018 |
| Written in | Java |
| Operating system | Any (Java-based) |
| Type | Pathways editing, analysis, visualization |
| License | Apache 2.0 |
| Website | www.pathvisio.org |
| Repository | |
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible.[1][2][3]
PathVisio provides a basic set of features for pathway drawing, analysis and visualization.[4][5] Additional features are available as plugins.
History
[edit]PathVisio was created primarily at Maastricht University and Gladstone Institutes.[6] The software is developed in Java and it's also used as part of the WikiPathways framework as an applet.[7] Starting from version 3.0 (released in 2012) plugins are OSGi compliant and a plugin directory Archived 2015-03-11 at the Wayback Machine, describing them, was developed. In 2015 version 3.2 was released. This was the first signed version with a certificate issued by a certification authority. Many of the running issues introduced by java 1.7 and 1.8 with the new security rules were solved. Since 2013 a javascript version (PVJS) is being developed to replace the applet. From 2015 it also allows small edits and in the future it will be a full editor.
Features
[edit]- Pathway drawing and annotation[8]
- Pathway analysis[9]
- Integration with WikiPathways for easy editing/publishing
- Integration with Cytoscape[10]
- Integration with other programming languages via PathVisioRPC[11]
References
[edit]- ^ "What is PathVisio?". Archived from the original on 23 September 2013. Retrieved 19 September 2013.
- ^ van Iersel, Martijn P; Kelder, Thomas; Pico, Alexander R; Hanspers, Kristina; Coort, Susan; Conklin, Bruce R; Evelo, Chris (2008). "Presenting and exploring biological pathways with PathVisio". BMC Bioinformatics. 9 (1): 399. doi:10.1186/1471-2105-9-399. ISSN 1471-2105. PMC 2569944. PMID 18817533.
- ^ Kutmon, Martina; van Iersel, Martijn P.; Bohler, Anwesha; Kelder, Thomas; Nunes, Nuno; Pico, Alexander R.; Evelo, Chris T.; Murphy, Robert F. (23 February 2015). "PathVisio 3: An Extendable Pathway Analysis Toolbox". PLOS Computational Biology. 11 (2) e1004085. Bibcode:2015PLSCB..11E4085K. doi:10.1371/journal.pcbi.1004085. PMC 4338111. PMID 25706687.
- ^ Jaiswal, Pankaj; Usadel, Björn (2016). "Chapter 4: Plant Pathway Databases". Plant Bioinformatics. Springer. pp. 71–87. ISBN 978-1-4939-3166-8.
- ^ Habermann, Bianca; Villaveces, Jose; Koti, Prasanna (June 2015). "Tools for visualization and analysis of molecular networks, pathways, and -omics data". Advances and Applications in Bioinformatics and Chemistry. 8: 11–22. doi:10.2147/AABC.S63534. PMC 4461095. PMID 26082651.
- ^ "About/Core development team". Archived from the original on 23 February 2014. Retrieved 10 February 2014.
- ^ Pico, AR; Kelder T; van Iersel MP; Hanspers K; Conklin BR; et al. (22 July 2008). "WikiPathways: Pathway Editing for the People". PLOS Biology. 6 (7) e184. doi:10.1371/journal.pbio.0060184. PMC 2475545. PMID 18651794.
- ^ "Tutorial 1: Drawing and annotating pathways in PathVisio". Archived from the original on 2015-11-25. Retrieved 2015-11-24.
- ^ "Tutorial 2: Analyzing experimental data in PathVisio (data import, visualization and statistics)". Archived from the original on 2015-11-25. Retrieved 2015-11-24.
- ^ Kutmon, Martina; Lotia, Samad; Evelo, Chris T; Pico, Alexander R (2014). "WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization". F1000Research. 3: 152. doi:10.12688/f1000research.4254.1. ISSN 2046-1402. PMC 4168754. PMID 25254103.
- ^ Bohler, Anwesha; Eijssen, Lars M T; van Iersel, Martijn P; Leemans, Christ; Willighagen, Egon L; Kutmon, Martina; Jaillard, Magali; Evelo, Chris T (2015). "Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment". BMC Bioinformatics. 16 (1): 267. doi:10.1186/s12859-015-0708-8. PMC 4546821. PMID 26298294.