{"id":2053,"date":"2016-07-01T17:26:17","date_gmt":"2016-07-02T00:26:17","guid":{"rendered":"http:\/\/miriamposner.com\/blog\/?p=2053"},"modified":"2016-07-01T17:26:17","modified_gmt":"2016-07-02T00:26:17","slug":"new-tutorials-on-network-analysis-with-cytoscape","status":"publish","type":"post","link":"https:\/\/miriamposner.com\/blog\/new-tutorials-on-network-analysis-with-cytoscape\/","title":{"rendered":"New tutorials on network analysis with Cytoscape"},"content":{"rendered":"
\"The<\/a>
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.<\/figcaption><\/figure>\n

For some reason I got it into my head to write a bunch of tutorials on using Cytoscape<\/a> for network analysis. They’re\u00a0now all up on Github<\/a>. (I’ve been moving to Github for tutorials because they’re easier to update there.)<\/p>\n

I started writing\u00a0these\u00a0for the\u00a0students in my spring-quarter class and, even though the class is over, I’ve\u00a0been adding to them compulsively. They’ll take you from zero to an interactive, web-based network graph, with stops along the way for projecting\u00a0a 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.)<\/p>\n

There’s a bit of a Gephi-versus-Cytoscape battle\u00a0right 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\u00a0really<\/em> hard time dealing with Gephi. First, there was the Legendary Java Problem<\/a>, and although the new version<\/a> is purportedly more stable<\/a>, I actually just cannot get it to work on my Mac and have frankly kind of lost the will to keep trying.<\/p>\n

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\u00a0don’t see much\u00a0point in hammering on them.)\u00a0I find Cytoscape’s\u00a0web service, CyNetShare<\/a>, to be pretty janky-looking<\/a>, but … you can interact with the network diagram, so that’s good, I guess.<\/p>\n

To be honest, I’ve been slowly making the switch from Gephi\/Cytoscape\/etc.\u00a0to R’s igraph package, and to D3 for displaying networks on the web<\/a>, 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.<\/p>\n

When I was visiting Stanford last winter, I got to see a preview of a network analysis tool that the Humanities\u00a0+ Design\u00a0team<\/a> 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.<\/p>\n","protected":false},"excerpt":{"rendered":"

For some reason I got it into my head to write a bunch of tutorials on using Cytoscape for network analysis. They’re\u00a0now all up on Github. (I’ve been moving to Github for tutorials because they’re easier to update there.) I started writing\u00a0these\u00a0for the\u00a0students in my spring-quarter class and, even though the class is over, I’ve\u00a0been […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3,5],"tags":[286,339],"class_list":["post-2053","post","type-post","status-publish","format-standard","hentry","category-digital-humanities","category-tools","tag-cytoscape","tag-network-analysis"],"_links":{"self":[{"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/posts\/2053","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/comments?post=2053"}],"version-history":[{"count":5,"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/posts\/2053\/revisions"}],"predecessor-version":[{"id":2059,"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/posts\/2053\/revisions\/2059"}],"wp:attachment":[{"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/media?parent=2053"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/categories?post=2053"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/miriamposner.com\/blog\/wp-json\/wp\/v2\/tags?post=2053"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}