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!


2 thoughts on “Network Analysis with Cytoscape Tutorial

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  1. Hello Tom.

    Firstly let me thank you very much for your incredibly informative (and useful) blog.

    I have been trying to dabble with networks recently but I haven’t really been getting anywhere. I came across your tutorial today and it is by far the most useful guide I’ve found for archaeologists.

    I have a few issues, though. I see (from the pictures) that the guide was written using version 3.0.1 whereas the latest version is 3.2.1. As such, there seems to be various things that no longer work they way they might have previously. For example, I keep getting ‘duplicate column name found’ when trying to import the “network_attributes” table.

    Do you have any suggestions for how I might get around this problem, or have a link to a more recent tutorial elsewhere?

    Thank you again!

  2. Hi Matt,

    Thanks for your kind comment, really delighted that the tutorial is useful for you.

    It does indeed work with an older version of Cytoscape and I will sadly not update the tutorial anymore (you reminded me that I should put a note about this in the tutorial document). This because the cytoscape updates come quite fast and often are quite significant. Whilst I am moving on to other software. In April I will make a new tutorial for archaeologists available, using Visone for exploratory network analysis for archaeologists. See keep an eye open for that.

    Concerning the ‘duplicate column name found’ problem. I am on a research trip this month without Cytoscape access. But sometimes this happens when you try to upload the same attributes files twice because it failed the first time. In that case, just start with a completely new project. It could also be that the unique ID given to the network table you upload first is the same as the unique ID given to the attribute table you add second. In that case, try to unselect the relevant columns when uploading them or see if there are any options concerning this in the upload dialog box. Or it could be that this has something to do with selecting the wrong primary key column in the attribute table (the column that will link the attribute data to the network data you uploaded earlier). Try to ensure you match up the correct columns.

    Sorry I cannot be of anymore help. Please stay in touch. Further feedback very much appreciated, I will update the tutorial with your comments as you send them in.



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