PathVisio

Last updated
PathVisio
Initial release2008
Stable release
3.3.0 / January 28, 2018
Repository
Written in Java
Operating system Any (Java-based)
Type Pathways editing, analysis, visualization
License Apache 2.0
Website www.pathvisio.org

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]

Contents

PathVisio provides a basic set of features for pathway drawing, analysis and visualization. [4] [5] Additional features are available as plugins.

History

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

References

  1. ↑ "What is PathVisio?". Archived from the original on 23 September 2013. Retrieved 19 September 2013.
  2. ↑ 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.
  3. ↑ 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.
  4. ↑ Jaiswal, Pankaj; Usadel, Björn (2016). "Chapter 4: Plant Pathway Databases". Plant Bioinformatics. Springer. pp. 71–87. ISBN   978-1-4939-3166-8.
  5. ↑ 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.
  6. ↑ "About/Core development team". Archived from the original on 23 February 2014. Retrieved 10 February 2014.
  7. ↑ 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.
  8. ↑ "Tutorial 1: Drawing and annotating pathways in PathVisio". Archived from the original on 2015-11-25. Retrieved 2015-11-24.
  9. ↑ "Tutorial 2: Analyzing experimental data in PathVisio (data import, visualization and statistics)". Archived from the original on 2015-11-25. Retrieved 2015-11-24.
  10. ↑ 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.
  11. ↑ 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.
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