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.^[1][2][3]

Initial release	2008
Stable release	3.3.0 / January 28, 2018
Repository	github.com/PathVisio
Written in	Java
Operating system	Any (Java-based)
Type	Pathways editing, analysis, visualization
License	Apache 2.0
Website	www.pathvisio.org

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

• 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]