PathVisio explained

PathVisio
Logo Size:125px
Released:2008
Latest Release Version:3.3.0
Latest Release Date:January 28, 2018
Programming Language:Java
Operating System:Any (Java-based)
Genre:Pathways editing, analysis, visualization
License:Apache 2.0

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

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, 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

External links

Notes and References

  1. Web site: What is PathVisio?. 19 September 2013. 23 September 2013. https://web.archive.org/web/20130923064232/http://www.pathvisio.org/biological-pathways-software/. dead.
  2. van Iersel. Martijn P. Kelder. Thomas. Pico. Alexander R. Hanspers. Kristina. Coort. Susan. Conklin. Bruce R. Evelo. Chris. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 9. 1. 2008. 399. 1471-2105. 10.1186/1471-2105-9-399. 18817533. 2569944 . free .
  3. Kutmon. Martina. van Iersel. Martijn P.. Bohler. Anwesha. Kelder. Thomas. Nunes. Nuno. Pico. Alexander R.. Evelo. Chris T.. Murphy. Robert F.. PathVisio 3: An Extendable Pathway Analysis Toolbox. PLOS Computational Biology. 23 February 2015. 11. 2. e1004085. 10.1371/journal.pcbi.1004085. 25706687. 4338111. 2015PLSCB..11E4085K . free .
  4. Book: Jaiswal. Pankaj. Usadel. Björn. Plant Bioinformatics. 2016. Springer. 978-1-4939-3166-8. 71–87. Chapter 4: Plant Pathway Databases.
  5. Habermann. Bianca. Villaveces. Jose. Koti. Prasanna. Tools for visualization and analysis of molecular networks, pathways, and -omics data. Advances and Applications in Bioinformatics and Chemistry. June 2015. 8. 11–22. 10.2147/AABC.S63534. 26082651. 4461095 . free .
  6. Web site: About/Core development team. 10 February 2014. 23 February 2014. https://web.archive.org/web/20140223024716/http://www.pathvisio.org/about/. dead.
  7. Pico. AR. Kelder T . van Iersel MP . Hanspers K . Conklin BR . WikiPathways: Pathway Editing for the People. 22 July 2008. e184. 10.1371/journal.pbio.0060184. 18651794. 2475545. 6. 7. etal . PLOS Biology . free .
  8. Web site: Tutorial 1: Drawing and annotating pathways in PathVisio. 2015-11-24. 2015-11-25. https://web.archive.org/web/20151125032628/http://www.pathvisio.org/documentation/tutorials/tutorial-1/. dead.
  9. Web site: Tutorial 2: Analyzing experimental data in PathVisio (data import, visualization and statistics). 2015-11-24. 2015-11-25. https://web.archive.org/web/20151125032056/http://www.pathvisio.org/documentation/tutorials/tutorial-2/. dead.
  10. Kutmon. Martina. Lotia. Samad. Evelo. Chris T. Pico. Alexander R. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000Research. 2014. 3. 152. 2046-1402. 10.12688/f1000research.4254.1. 25254103. 4168754 . free .
  11. Bohler. Anwesha. Eijssen. Lars M T. van Iersel. Martijn P. Leemans. Christ. Willighagen. Egon L. Kutmon. Martina. Jaillard. Magali. Evelo. Chris T. Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. BMC Bioinformatics. 2015. 10.1186/s12859-015-0708-8. 16. 1 . 267. 26298294. 4546821 . free .

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "PathVisio".

Except where otherwise indicated, Everything.Explained.Today is © Copyright 2009-2024, A B Cryer, All Rights Reserved. Cookie policy.