Cytoscape: Mapping Relationships

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Posted by Ike Washington
Feb 19, 2008 at 12:10 PM

Anyone interested in social network analysis, in visually mapping relationships between individual actors in a given situation, should check out Cytoscape:
- http://www.cytoscape.org/

Don’t let its pitch put you off: it’s easy to adapt to uses other than a “bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.”

I’ve used Rationale and Mindmanager Pro 6 for this kind of work - figuring out, and laying out on the page so that it’s obvious to me, the elements within a set, figuring out, and laying out on the page so that it’s obvious to me, the boundaries of the set.

Alternatives? Without paying the big bucks charged for software like this aimed at, say, the intelligence community? Without messing around with clunky software aimed at academics? Rationale enforces a strict hierarchy on data - items can link from parents to children only. Not much use here. Mindmanager allows weak links to be drawn across hierarchies. And with its filters is actually quite good - at least for my limited needs in this area. I’m just not that keen on Mindmanager after spending far too much on upgrades over the years. I haven’t tried Flying Logic - looks good for this.

But all these three, and I suppose other standard mapping apps, can’t provide the kind of analysis Cytoscape provides.

Cytoscape Strengths:
- open source
- designed for specific aim: visualising and analysing network data
- industrial strength, thousands of nodes, compared to, say, Mindmanager
- good search/filtering
- in development, large academic development team
- fairly mature: v2.52, v1 - 2002
- easy to use
- isn’t at all clunky (unlike many of its academic competitors)
- well documented
- expandable through plug-ins
- good community

Cytoscape Weaknesses:
- created for needs of a specific scientific community
- to get full value, need to invest some time in understanding theory behind social network analysis
- doesn’t export as html or text pdf (though there is a plug-in which claims to do this, doesn’t work for me)
- can’t link nodes to files or websites
- panning depends on middle clicking which I don’t properly have on my laptop

Ike

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