Cytoscape Installation and Setup

Cytoscape is required for network visualization in the application. Ensure that Cytoscape is installed and running before launching the application. Follow the steps below to install Cytoscape on your operating system.

Installing Cytoscape

Linux

  1. Prerequisites: - Ensure Java 17 is installed:

    sudo apt update
sudo apt install openjdk-17-jdk
java -version

  2. Download Cytoscape: - Visit the Cytoscape Downloads page and download the latest .sh installer.

  3. Install Cytoscape: - Open a terminal and navigate to the folder containing the downloaded file. - Run the installer:

    sh Cytoscape_<version>_unix.sh

    • Follow the on-screen instructions to complete the installation.

  4. Launch Cytoscape: - After installation, run:

    cytoscape

  5. Troubleshooting: - If you encounter a Java error, ensure the correct Java version is set:

    export INSTALL4J_JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64

Windows

  1. Download Cytoscape: - Visit the Cytoscape Downloads page and download the .exe installer.

  2. Install Cytoscape: - Double-click the downloaded .exe file to start the installation. - Follow the on-screen instructions, choosing the default installation options.

  3. Launch Cytoscape: - Search for “Cytoscape” in the Start Menu and open it.

macOS

  1. Download Cytoscape: - Visit the Cytoscape Downloads page and download the .dmg file.

  2. Install Cytoscape: - Open the downloaded file and drag the Cytoscape icon into the Applications folder.

  3. Launch Cytoscape: - Open Cytoscape from the Applications folder. - If you encounter a security warning, go to System Preferences > Security & Privacy and allow Cytoscape to run.

Verifying Cytoscape Installation

  1. Launch Cytoscape and ensure it opens without errors.

  2. You should see the Cytoscape interface where you can load and manipulate networks.

Testing the Cytoscape Connection

To verify that the application can communicate with Cytoscape, run the following commands in R:

library(RCy3)
cytoscapePing()

If Cytoscape is running, you should see a message confirming the connection.

Important Notes

  1. Run Cytoscape Before the Application: - Ensure Cytoscape is open and running before starting the application.

  2. Supported Versions: - Use Cytoscape version 3.10.x or higher.