PathVisio
 | |
| Initial release | 2008 |
|---|---|
| Stable release | 3.2 / February 28, 2015 |
| Written in | Java |
| Operating system | Any (Java-based) |
| Type | Pathways editing, analysis, visualization |
| License | Apache 2.0 |
| Website |
www |
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing and analysing 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]
PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins.
History
PathVisio was created primarily at Maastricht University and Gladstone Institutes.[3] The software is developed in Java and it's also used as part of the WikiPathways framework as an applet.[4] Starting from version 3.0 (released in 2012) plugins are OSGi compliant and a plugin directory, 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.
Features
- Pathway drawing and annotation
- Pathway analysis
- Integration with WikiPathways for easy editing/publishing
- Integration with Cytoscape[5]
References
- ↑ "What is PathVisio?". 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.
- ↑ "About/Core development team". 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" 6 (7). p. e184. doi:10.1371/journal.pbio.0060184. PMC 2475545. PMID 18651794. Retrieved 19 September 2013.
- ↑ 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. doi:10.12688/f1000research.4254.1. ISSN 2046-1402.