Install Cytoscape
Cytoscape homepage
current version 3.10.2
Install Cytoscape
Download the current version for your computer system: WinPC or macOS. Your browser should recognize your computer type and direct you to the correct download page. For example, Windows 11 (Fig 1).
Figure 1. Screenshot Cytoscape download page for Microsoft Windows 11 operating system.
Note that Cytoscape’s install file will also install a Java Development Kit, which is needed for Cytoscape to run. As usual, trust the default instructions and allow the installation to proceed. The last page of instructions will be a page that says Finish.
Close the page and start Cytoscape. If you followed the defaults, then you installed a desktop startup icon (Fig 2).
Figure 2. Cytoscape desktop startup icon.
After starting the app, you will see a splash screen (Fig 3)
Figure 3. Cytoscape splash screen
Once the app has launched, you’ll see this starter window (Fig 4).
Figure 4. Screenshot of Cytoscape’s starter window.
plugins
Base Cytoscape can do many things, but the power of the platform is that users write specialized extensions to make the software do more. The recommended plugins we need for Systems Biology are listed on your CANVAS assignment pages. For an example, we use the Social Network plugin to gain familiarity with working with Cytoscape.
Install and run app plugin
To install apps, start Cytoscape, then from menu bar select
Apps > App store > Show App Store
Find the search box and start typing the name of the app, e.g., Social. Enter (return), and your browser should navigate to the app.cytoscape.org web page and the desired app should be visible.
Click the app link to bring up the app’s install page; you may download the plugin install file, or press the install button and allow Cytoscape to add the app.
Once the app has been installed, it’s good practice to restart Cytoscape.
To start using an app, from the menu bar select Apps and select your plugin from the dropdown menu (Fig 5).
Figure 5. Screenshot Apps menu
More about Cytoscape
Online user manual at https://manual.cytoscape.org/en/stable/index.html
Kohl, M., Wiese, S., & Warscheid, B. (2011). Cytoscape: software for visualization and analysis of biological networks. Data mining in proteomics: from standards to applications, 291-303.
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.
Su, G., Morris, J. H., Demchak, B., & Bader, G. D. (2014). Biological network exploration with Cytoscape 3. Current protocols in bioinformatics, 47(1), 8-13.
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