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.

lots of menu items that don't do anything unless some conditions are met. Suggestions: disable menu items when input conditions are not met. Would want a library of tools that handles enabling/disabling of menu items.

Vizmapper intimidates new users

"Calculators" and "Map attributes" reflect programmer thi;nking, not user thinging. Suggestion: provide direct controsl tying attribute values to visual properties.

"Define", "Delete", "Duplicate" visual style scares users

Filters

Everybody wants them but no one -- not one -- ahve been suggessful with them. Incremental laytering of filters (a la topological filter) natural for Computer types, but not for biologis.

Search/filtering are similar. Cytoscape design should reflect tis.

Graph Layout

Every single user was comfortable with graph layout est

Unresolved use case: how to represent a conditional edge -- advanced user studying closely-related networks, certain edges exist in only some experiments. Some sort of visual filter might be useful. Or use some gradation via translucency.

Plugin architecture

users not aware of plugins: suggestion: incorporate some plugin documentation into manual. Or provide something along the lines of "eclipse update".

users not comfortable installing JAR files. Suggestion: provide template install scripots.

users find the separation of "core" and "plugin" strange. It's all Cytoscape. Suggestion: break the convention that plugins use plugin menu.

Suggestion: have a plugin management system that maintains information about the plugin and handles loading of plugins.

Suggestion: use the term "Extension" rather than "plugin". Mimic foxfire's handling of plugins. Have a "search for new features" capability.

Suggestion: provide feedback about what plugins (and versions of them) are loaded.