New tutorials on network analysis with Cytoscape

The Cytoscape interface, featuring a pane on the left with buttons and a graph diagram on the right
I find the Cytoscape interface more intuitive than Gephi’s, although in both cases, you need to have a basic understanding of key NA terms.

For some reason I got it into my head to write a bunch of tutorials on using Cytoscape for network analysis. They’re now all up on Github. (I’ve been moving to Github for tutorials because they’re easier to update there.)

I started writing these for the students in my spring-quarter class and, even though the class is over, I’ve been adding to them compulsively. They’ll take you from zero to an interactive, web-based network graph, with stops along the way for projecting a two-mode network to a one-mode network and working with node attributes. (If you don’t know what any of that stuff means, they explain that, too.)

There’s a bit of a Gephi-versus-Cytoscape battle right now among people who do network analysis. I actually started out on Cytoscape, only because I found it slightly more intuitive, and switched to Gephi when I discovered most people used that. But in recent years, I’ve had a really hard time dealing with Gephi. First, there was the Legendary Java Problem, and although the new version is purportedly more stable, I actually just cannot get it to work on my Mac and have frankly kind of lost the will to keep trying.

Cytoscape is Fine. It’s designed for scientists, really, and other people who care very much about statistical measures of networks, which to be honest, I don’t really care that much about. (I don’t think most humanists trust these measures anyway, so I don’t see much point in hammering on them.) I find Cytoscape’s web service, CyNetShare, to be pretty janky-looking, but … you can interact with the network diagram, so that’s good, I guess.

To be honest, I’ve been slowly making the switch from Gephi/Cytoscape/etc. to R’s igraph package, and to D3 for displaying networks on the web, just because they’re so much nicer looking. One thing I like about Cytoscape is that after you’ve measured various aspects of your network, you can export JSON that’s set up specifically for D3’s popular force-layout network.

When I was visiting Stanford last winter, I got to see a preview of a network analysis tool that the Humanities + Design team is building, and I really liked the way they placed the emphasis on exploration and discovery, rather than statistical measures. I’ll be looking forward to seeing the release of that tool (I think it’s called Idiographic?), since I do feel that humanists have different interests when it comes to networks than scientists or social scientists.

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