InstallationΒΆ

  1. Install Cytoscape

  • Download and install the latest version of Cytoscape at cytoscape.org.

Note

Cytoscape minimum version 3.8 is required for this version of MCODE.

If you want to run MCODE on older versions of Cytoscape, the App Manager (see below) should show the latest compatible version of MCODE.

  1. Install MCODE

2.1. Automated Installation (via the App Manager)

  • Open Cytoscape.

  • In the main menu select Apps > App Manager.

  • In the App Manager select MCODE in the list of all apps and click the Install button.

Note

MCODE can also be installed from the Cytoscape App Store.

2.2. Manual Installation

  • Download the MCODE jar file from the Cytoscape App Store, where you have two options:

    1. Click the Download button on the MCODE app page to get the latest version.

    2. Go to the Release History section and click on the specific version you want to download.

  • Copy the downloaded jar file (e.g. mcode-app-2.0.0.jar) to your [...]/CytoscapeConfiguration/3/apps/installed directory.

  • Check that MCODE appears in the Apps menu of Cytoscape. It may take a few seconds for the app to load up and appear in the menu. If it still does not appear, the most common causes are:

    1. You placed the MCODE jar file in the wrong directory.

    2. You may have one or more newer versions of MCODE already installed, in which case you just need to delete all the other mcode-[...].jar files you find in the installed directory.

    3. The downloaded version is not compatible with the running version of Cytoscape.