Diff for "CytoscapeRetreat2006/Hackathon/HackathonNotes"

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. Need some structuring of plugins. Perhaps another look at menu items to see if all types of plugins can be handled by a small set of menu items.

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.

Advanced User workarounds

For one user who wanted to view conditional edges, he: 1. used Cytoscape to generate GML, hen used script to construct PDB file from GML, the cmpared PDB files with ta molecular modeling viewer.

Another user had plugin that specified node by name, node is fetched from a larger network, with right-click menu user can extend network with first neighbors. Node border indicates if there are any neighbors not shown. Use edge typoe to reference publication documenting interactions. Visual properties are assigned using edge classes.

users choosing not to update their Cytoscape installation

many users at ISB still run Cytoscape 1.X

why? key plugins no longer compatible with core. Changes to input file specs. Other changes to key concepts, not always obvious.

Brainstorming/Prototyping workshop

30 minutes of open brainstorming, followed by construction with screen shots, markers, post-it notes.

include users that are already familiar with the process.

main categories: filtering/selection/attributes, data import/export/management, installation and architecture, graph layout, combining multiple networks and multiple heterogeneous networks.

brainstorming ideas: dynamic filtering, global network annotation, integration w/ public dbs, multiple heterogeneous networks, multi-level analysis (e.g. motifs/domains in the proteins of the network).

multi-level network (network, protein complex, protein, domain, peptide, GO term). Nodes replaced by corresponding domains. Similar domains merged into one node.

Conclusions

ideas are simple but not communicated clearly

simplify the process of improt

simplify visual property management, even if it means losing some flexibility

integrate plugins more closely with the core.