PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing

biological pathway A biological pathway is a series of interactions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on a ...

s. 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. :

History

PathVisio was created primarily at

Maastricht University Maastricht University (abbreviated as UM; nl, Universiteit Maastricht) is a public research university in Maastricht, Netherlands. Founded in 1976, it is the second youngest of the thirteen Dutch universities. In 2021, 22,383 students studied at ...

and

Gladstone Institutes Gladstone Institutes is an independent, non-profit biomedical research organization whose focus is to better understand, prevent, treat and cure cardiovascular, viral and neurological conditions such as heart failure, HIV/AIDS and Alzheimer's dis ...

. The software is developed in

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's List ...

and it's also used as part of the

WikiPathways WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of a ...

framework as an applet. Starting from version 3.0 (released in 2012) plugins are

OSGi OSGi is an open specification and open source project under the Eclipse Foundation. It is a continuation of the work done by the OSGi Alliance (formerly known as the Open Services Gateway initiative), which was an open standards organization for ...

compliant and
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 * Pathway analysis * Integration with

for easy editing/publishing * Integration with

Cytoscape Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available f ...

* Integration with other programming languages via

PathVisioRPC 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 i ...

References

External links

* {{Official website, http://www.pathvisio.org/
PathVisio on Twitter
Free bioinformatics software Systems biology Data visualization software Mathematical and theoretical biology Cross-platform software Java platform software