Cytoscape Wiki2nd March, 2006
Interviewed by: Chris Workman and Mike Smoot
What do you use Cytoscape for?
Uses Cytoscape on windows.
Gene expression analysis - number crunching in genespring. Then import into Cytoscape. Network based on array experiments and sometimes human interactome.
Somewhat hard to get data from genespring into Cytoscape.
Building the network is not trivial. Finding identifiers is hard. You can lose data if your gene isn't in interaction database. An incorrect gene id will also cause problems. As many as 30% of genes can have problems.
What parts of system do you use? - Setting visual attributes, as opposed to editing networks. - Working with plugins. - Using filters.
Which plugins - Bingo, JActiveModules, GraphMerge (simple but very useful), Agilent lit search, searching cpath (but there are firewall issues), Interaction fetcher (only works sometimes because of firewall).
Doesn't think others (non-bioinformaticians or non-technical) would be able to use Cytoscape, very busy and not enough time to learn or use. Too steep a learning curve. Takes time to create networks suitable for analysis.
Once you learn it, it gets better.
Loading data at startup is a bit fiddly.
How do you run Cytoscape?
Double clicks on the icon to run.
Installation was pretty easy. Others found the install pretty straightforward as well. Needed a bit of help using plugins.
Apart from the "data" menu, the menus are ok.
Loves cytoPanels.
Some plugins create many attributes which makes finding them in VizMapper difficult.
How is the performance of Cytoscape?
Can be slow - 11000 nodes, 50000 edges. Can do analysis without visualizing whole network. Some plugins require view of network before plugin will work (either Bingo or MCode) which is a problem.
Uses most of the system features.
Would like to delete more than one network at a time. Has a lot of networks open at a time and to delete them takes a lot of clicking.
Some of the keyboard shortcuts don't work on Windows (e.g. F6).
Windows XP automatically saves the jar file as a .zip file. Actually changes the .jar to .zip which makes integrating plugins a bit more of a challenge.
Filters are slightly erratic. Attributes you want to filter on sometimes don't appear. Filters correctly come back when you close Cytoscape.