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 https://github.com/cytoscape/cytoscape/releases/download/3.7.2/Cytoscape_3_7_2_unix.sh

Installing Cytoscape

Provide access permission to the downloaded installer.

$ sudo chmod u+x Cytoscape_3_7_2_unix.sh

Running Cytoscape

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

$ Cytoscape &

---

References

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 research, 13(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. Bioinformatics, 27(3), 431-432.