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Installing Cytoscape on Ubuntu



Installing cytoscape on Ubuntu

Cytoscape is a software for the easy visualization of complex networks [1-3]. In this article, we will install Cytoscape on Ubuntu.

Prepare your system

Let’s update and upgrade the system first.

Open the terminal (Ctrl+T) and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading Cytoscape

Change to the directory where you wish to download the software.

$ cd Downloads/

$ sudo wget

Installing Cytoscape

Provide access permission to the downloaded installer.

$ sudo chmod u+x

Running Cytoscape

You can look for Cytoscape in the Ubuntu start menu or run it via terminal using the following command:

$ Cytoscape &


  1. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., … & Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research13(11), 2498-2504.
  2. Kohl, M., Wiese, S., & Warscheid, B. (2011). Cytoscape: software for visualization and analysis of biological networks. In Data mining in proteomics (pp. 291-303). Humana Press.
  3. Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L., & Ideker, T. (2011). Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics27(3), 431-432.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.