Network Analysis with Cytoscape Tutorial

visEver wanted to learn network analysis on your own but thought it’s just a bit too scary? Many friends and colleagues I talk to about networks sure seem to feel this way. Well, network analysis does not have to be difficult or scary at all. There are many free network software platforms out there and many of them have a user-friendly interface. I decided to make a tutorial I have been using for a few years now publicly available, in the hope that it can be of interest and help to some.

In this tutorial you will learn how to create, visualise and analyse networks using Cytoscape, and how to export the results of these analyses. This practical is conceived as an introduction to exploratory network analysis for the Humanities, using an archaeological/geographical example. Moreover, the resource includes a list of introductory bibliography and software. Have a look at my resources page to download the tutorial. Good luck!

Cytoscape plugins

The authors of Cytoscape, a software platform for the analysis and visualisation of networks, have just published an overview of Cytoscape plugins in Nature Methods. Although many of these plugins might be most relevant for biological networks, there might be some original and useful Humanities applications to be developed as well. The overview covers 152 plugins, that should be plenty for the more creative among us to explore and play around with.

Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.

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