Notes from Interview with researcher, University Dept. Pharmaceutical Chemistry

15th February, 2006

Interviewers: Chris Workman, Allan Kuchinsky

What do you use Cytoscape for?

Primarily for protein interaction networks. Visualize data from protein arrays. Visualize networks and find hubs. She expressed a desire to be able to customize Cytoscape but because she is not a programmer, feels some what helpless to do so.

How long have you been using Cytoscape?

6 to 7 months.

What would be the most helpful for learning how to use Cytoscape?

Expand the online tutorial. She found that the current one was not comprehensive enough to demonstrate the more powerful functionalities. Filters not described and some filter definitions and applications are difficult (e.g. topology filter not easy to use). Wished the tutorial would touch on advanced features more. The topic of an expanded tutorial came up at least 3 different times during our conversation.

What new features would you like to see?

Has trial of Pathway Assist and liked how it showed enrichment in particular organelle or cellular compartment without having to do very much. Allow public network databases to be loaded.

What features are confusing or annoying?

Didn't understand what SetEditor was meant to do. Didn’t know how to use gene expression matrix files or GO server. Struggled with setting up visual styles and quit using them because it seemed “dubious” (hidden actions and behaviors of visual styles made her uncomfortable). We asked if a wizard would be helpful for setting up a visual style and her response was very positive. Not clear how to import BioPAX files. She also had problems with saving and restoring visual styles, “you think you save it but it’s not there”.

Which features do you use a lot?

Use selection features a lot, e.g. select from file, select first neighbors of selected nodes. For layout, uses yFiles organic. Hadn’t tried spring embedded layout (wasn’t sure what this does). Uses network rotation and scaling. Also uses Toggle Overview a lot. Found cyto-panels helpful and uses them a lot. Somewhat as a surprise to Allen and I, she uses help feature. She didn’t find the help content to be any different than what was on the web-site though.

What plugins do you use?

BiNGO to look at gene function. Network analyzer plugin has been helpful. Found Agilent Literature Search plugin and cPath plugin too difficult to install and use (Allen plans to follow up with her regarding the Literature Search plugin). PathBLAST is not easy to install or use(I told here new versions were coming soon). Has down loaded a lot of other plugins and found that most were straight forward.

“BiNGO is really good because it is explained well.” Plugin examples should walk the user through a relevant problem.

Filters are useful once she had them figured out (i.e. had Gary Bader help her get started with them). Not difficult after that though.

Should there be any pre-defined filters then?

Might be nice to have a filter that would select the essential genes? It would be nice to highlight these genes. (This would require genetic data for particular species.) Also wanted to be able to color nodes based on gene function (We mentioned that this is possible with GO annotation and the vizMapper.)

How do you run Cytoscape?

Clicks on a cytoscape.BAT

Have you noticed any difference in performance with the newer version?

Didn't notice that version 2.2 was faster. Network loading is "very fast" on 3K nodes 12K edges.

She would like to contact someone about developing the tutorials. She is also starting to work with human interaction networks and, in general, would want more content (species bundles). Want to use Cytoscape as it is easier to use than GenMAPP.

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Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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