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 translation performed automatically. Suggestion: provide generalized database wrappers.

GenMapp to provide 'back-page' functionality to multiple databases for Cytoscape. Much of this can come from Ensemble, which has become very efficient for data base provision. GenMAPP would provide a Gene database.

General User Interface Issues

lots of confusion with the menu system. typically they scan the menus from right to left to relocate menu options. Suggestion: move more things to right-click menu and simplify global menu.

not enough feedback in operations like selection or filtering; in import operations, make clear when the import is done.

some ambiguity, can close a task bar and an import will still work.