PathVisio 3: An Extendable Pathway Analysis Toolbox

Martina Kutmon*, Martijn van Iersel, Anwesha Bohler, T. Kelder, Nuno Nunes, A.R. Pico, Chris T. Evelo

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways. Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application. PathVisio can be downloaded from and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license ( It is implemented in Java and thus runs on all major operating systems. The code repository is available at The support mailing list for users is available on!forum/wikipathways-discuss and for developers on!forum/wikipathways-devel.
Original languageEnglish
Article numbere1004085
Number of pages13
JournalPLoS Computational Biology
Issue number2
Publication statusPublished - Feb 2015


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