Notes from Cytoscape Hackathon

Observations on Cytoscape Usability (Melissa)

Motivations: assess Cytoscape usability from biologists perspective, address stumbling blocks in the UI, assess biologists respeonse to vizmapper and filters.

Interviews with 9 users, conducted in workspace, presented in context of users' data and analyses, observed how users worked with software and explore new functionality.

Ran a brainstorming/prototyping workshop with users from usability studies, 2 groups, each group selected one topic to prototype with screen-dumps, post-its, etc. and were videotaped.

Issues raised were:

Documentation:

PDF-format manual too monolithic, HTML preferred

Online tutorials not used -- they want tutorials oriented around biological tasks, not software functionality

• Question: how does this fit with Cytoscape's being domain-neutral? Suggestion: have a top-level set of domain-specific tutorials, with pointers to more detailed software functionality tutorials.
• Issue: given the funding structure, is there enough incentive for groups to develop good documentation/tutorials? Suggestion: be creative in supplying a foundation that users can extend with Help documentation. Also, ISB may have some funding for this kind of work -- this should be brought up at the board meeting.
• Also, a glossary would be critical
• Suggestion: incorporate the tutorials more with the software

Data Import and Export

exporting data from Excel into Cytoscape is a big bottleneck.

PSI-MI now has an excel template that we could use when importing protein-protein interactions.

input file requirements not clearly understood

• suggestion: have the input dialog indicate what programs can be used to view the different types of data files

why don't users look at the sample data

• some examples too large to be viable -- unfortunately BIND_human and BIND_yeast show up first in the list of sample files. Suggestion: have a demo directory. GalFiltered files are quite useful, should appear first.

• Distinguish files created by people from those created by machines.
• ACTION ITEMS generate a demo directory
• users discouraged when they see examples from another domain. Suggestion: work with user community to expand the breadth of the examples. Suggestion: add wording to top-level Cytoscape description to make clear that Cytoscape supports multiple organisms.

Connectivity to External Databases

all users would benefit from improved connectivity for network and attribute data. Benefits: user doesn't have to search web for data, format translatio performed automatically. Suggestion: provide generalized database wrappers.