There are different ways to install PathVisio (also depending on the operating system). You can find instructions here:

Webstart Installation

Download the pathvisio.jnlp file, you will be asked how to open it. Please select “Java Webstart” (This should be the default). The application will be downloaded and PathVisio will be started.

Binary Installation

The binary and source files for PathVisio and the Webservice Client are released here: PathVisio release.
If you want to run PathVisio as a local Java application, download and extract pathvisio_bin-$version-$ file ($version and $revision get updated with every release).


On Windows, double-click on the pathvisio.bat file and PathVisio will be started.


Linux, please run the file and PathVisio will be started.


In Mac OSX press left command and double click the pathvisio.jar file. You will be prompted with a dialog informing that the jar was not downloaded from the MacOS app store. You can bypass  the command and run the jar.

The jar is signed with the Cytoscape certificate. If you wish you can confirm the authenticity of the file.

Homebrew Installation (MacOSX)

A brew for PathVisio is available from Homebrew. Before installing make sure you have the latest brews:
brew update
Then install PathVisio with:
brew install homebrew/science/pathvisio

Pathvisio is installed into /usr/local/bin.
PathVisio can be started with pathvisio from the terminal command line