{{Short description|Software for pathway editing and visualisation}} {{Infobox software | name = PathVisio | title = | logo = PathVisio_logo.svg | logo size = 125px | logo caption = | screenshot = | caption = | collapsible = | author = | developer = | released = 2008 | discontinued = | latest release version = 3.3.0 | latest release date = January 28, 2018 | latest preview version = | latest preview date = <!-- {{Start date and age|YYYY|MM|DD|df=yes/no}} --> | frequently updated = <!-- DO NOT include this parameter unless you know what it does --> | status = | programming language = [[Java platform|Java]] | operating system = Any ([[Java platform|Java]]-based) | platform = | size = | language = | language count = <!-- DO NOT include this parameter unless you know what it does --> | language footnote = | genre = Pathways editing, analysis, visualization | license = [[Apache 2.0]] | alexa = | website = {{URL|http://www.pathvisio.org/}} | standard = | AsOf = }}
'''PathVisio''' is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing [[biological pathway]]s. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible.<ref>{{cite web|title=What is PathVisio?|url=http://www.pathvisio.org/biological-pathways-software/|access-date=19 September 2013|archive-date=23 September 2013|archive-url=https://web.archive.org/web/20130923064232/http://www.pathvisio.org/biological-pathways-software/}}</ref><ref name="van IerselKelder2008">{{cite journal|last1=van Iersel|first1=Martijn P|last2=Kelder|first2=Thomas|last3=Pico|first3=Alexander R|last4=Hanspers|first4=Kristina|last5=Coort|first5=Susan|last6=Conklin|first6=Bruce R|last7=Evelo|first7=Chris|title=Presenting and exploring biological pathways with PathVisio|journal=BMC Bioinformatics|volume=9|issue=1|year=2008|page=399|issn=1471-2105|doi=10.1186/1471-2105-9-399|pmid=18817533|pmc=2569944 |doi-access=free }}</ref><ref>{{cite journal|last1=Kutmon|first1=Martina|last2=van Iersel|first2=Martijn P.|last3=Bohler|first3=Anwesha|last4=Kelder|first4=Thomas|last5=Nunes|first5=Nuno|last6=Pico|first6=Alexander R.|last7=Evelo|first7=Chris T.|last8=Murphy|first8=Robert F.|title=PathVisio 3: An Extendable Pathway Analysis Toolbox|journal=PLOS Computational Biology|date=23 February 2015|volume=11|issue=2|article-number=e1004085|doi=10.1371/journal.pcbi.1004085|pmid=25706687|pmc=4338111|bibcode=2015PLSCB..11E4085K |doi-access=free }}</ref>
PathVisio provides a basic set of features for pathway drawing, analysis and visualization.<ref>{{cite book|last1=Jaiswal|first1=Pankaj|last2=Usadel|first2=Björn|title=Plant Bioinformatics|date=2016|publisher=Springer|isbn=978-1-4939-3166-8|pages=71–87|chapter=Chapter 4: Plant Pathway Databases}}</ref><ref>{{cite journal|last1=Habermann|first1=Bianca|last2=Villaveces|first2=Jose|last3=Koti|first3=Prasanna|title=Tools for visualization and analysis of molecular networks, pathways, and -omics data|journal=Advances and Applications in Bioinformatics and Chemistry|date=June 2015|volume=8|pages=11–22|doi=10.2147/AABC.S63534|pmid=26082651|pmc=4461095 |doi-access=free }}</ref> Additional features are available as plugins. :
==History== PathVisio was created primarily at [[Maastricht University]] and [[Gladstone Institutes]].<ref>{{cite web|url=http://www.pathvisio.org/about/|access-date=10 February 2014|title=About/Core development team|archive-date=23 February 2014|archive-url=https://web.archive.org/web/20140223024716/http://www.pathvisio.org/about/}}</ref> The software is developed in [[Java (programming language)|Java]] and it's also used as part of the [[WikiPathways]] framework as an applet.<ref>{{cite journal|last=Pico|first=AR|author2=Kelder T |author3=van Iersel MP |author4=Hanspers K |author5=Conklin BR |title=WikiPathways: Pathway Editing for the People|date=22 July 2008|article-number=e184|doi=10.1371/journal.pbio.0060184|pmid=18651794|pmc=2475545|volume=6|issue=7|display-authors=etal |journal=PLOS Biology |doi-access=free }}</ref> Starting from version 3.0 (released in 2012) plugins are [[OSGi]] compliant and a [http://www.pathvisio.org/plugins/plugins-repo/ plugin directory] {{Webarchive|url=https://web.archive.org/web/20150311143404/http://www.pathvisio.org/plugins/plugins-repo/ |date=2015-03-11 }}, 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<ref>{{cite web|title=Tutorial 1: Drawing and annotating pathways in PathVisio|url=http://www.pathvisio.org/documentation/tutorials/tutorial-1/|access-date=2015-11-24|archive-date=2015-11-25|archive-url=https://web.archive.org/web/20151125032628/http://www.pathvisio.org/documentation/tutorials/tutorial-1/}}</ref> * Pathway analysis<ref>{{cite web|title=Tutorial 2: Analyzing experimental data in PathVisio (data import, visualization and statistics)|url=http://www.pathvisio.org/documentation/tutorials/tutorial-2/|access-date=2015-11-24|archive-date=2015-11-25|archive-url=https://web.archive.org/web/20151125032056/http://www.pathvisio.org/documentation/tutorials/tutorial-2/}}</ref> * Integration with [[WikiPathways]] for easy editing/publishing * Integration with [[Cytoscape]]<ref name="KutmonLotia2014">{{cite journal|last1=Kutmon|first1=Martina|last2=Lotia|first2=Samad|last3=Evelo|first3=Chris T|last4=Pico|first4=Alexander R|title=WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization|journal=F1000Research|year=2014|volume=3|page=152|issn=2046-1402|doi=10.12688/f1000research.4254.1|pmid=25254103|pmc=4168754 |doi-access=free }}</ref> * Integration with other programming languages via [[PathVisioRPC]]<ref name="Bohler2015">{{cite journal|last1=Bohler|first1=Anwesha|last2=Eijssen|first2=Lars M T|last3=van Iersel|first3=Martijn P|last4=Leemans|first4=Christ|last5=Willighagen|first5=Egon L|last6=Kutmon|first6=Martina|last7=Jaillard|first7=Magali|last8=Evelo|first8=Chris T|title=Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment|journal=BMC Bioinformatics|year=2015|doi=10.1186/s12859-015-0708-8|volume=16|issue=1 |page=267|pmid=26298294|pmc=4546821 |doi-access=free }}</ref>
==References== {{Reflist|30em}}
== External links == * {{Official website|http://www.pathvisio.org/}} * [https://twitter.com/PathVisio/ PathVisio on Twitter]
[[Category:Free bioinformatics software]] [[Category:Systems biology]] [[Category:Data and information visualization software]] [[Category:Mathematical and theoretical biology]] [[Category:Cross-platform free software]] [[Category:Free software programmed in Java]] [[Category:Software using the Apache license]]