User Brainstorm Session

Date: Friday, July 18, 2008 Leads: Allan Kuchinsky, Alex Pico, Gary Bader


Cytoscape users and developers will brainstorm and discuss aspects of Cytoscape. The goal of this session is to listen to the users to find out ways of improving Cytoscape.

The Evolution Game


Cytoscape Break out Evolution Game Ideas:

Gary: Red Group
1) Biggest Problem: biologists trusting the data, Barbara, look at it need to know
where it is from, or if producing it in cytoscape, want p values i.e don't know how to trust the data
2) how to use: Interactivity, increasing interactivity to solve problems. 
Cytoscape needs to be more interactive, ie. more views, change like SpotFire
updating one view updates all views, 
combining data, common features from multiple sources, places it in context, possible scripting
3) outreach, grow the community how? Increase the number of users

John: Blue Group
1) things break/more to relationships than a line, need to score....interactive
   better illustrations, nice pictures, publication quality
   Batch mode, workflow mode
2) Too focused on genomics...we like mass spec/interacting with complexes
   work in instrumentation
3) Identify plugins, find them rank them 
   Web delivery
1) Developer oriented.. API lack of modularity, lacking tests, documentation
2) Nature in/visualize/write it out...would like to send it out to another programme
   "data providence"
3) Knowledge navigator, apple vision... computers like in 2011, cytoscape 3000.0
video tutorials...cytoscape consortium vision on how should it be used...
Treys vision: Nurse/clinician/ wall view of network...patients cell...clinician plugs in data
cytoscape outputs right treatment, given genotype given available drugs....
Pfizer, robots putting chemicals on plates, technician, wall display of network, and says there is the hub
disturb that node, 3D structure design structure..  
in summary "Medical Application of Cytoscape"
Input from Bruce would be useful

1) Developer heavy/ API clarify/simplify/documenting benifit new devolopers and plugin interopolity to form 
pipelines of plugins....Single best practice approach to getting at object
Just prune/document/scooter presention would help quite a bit
Combine documentation (Jeremey Hancock) community documention, if it was easier to document
2) intergate resources gene stuff in one place you can visualize to allow for interuptation
3) collecting user feed back/usability some mechanism , more often, workflows that people want for new techniques stay on top 
   sexy visualisations, plug in "processing" visualisation styles...
   "User Perspective"

1) Ease of use, strange terms with scary words more friendly, more documentation, step by step guides
   with screenshots of unexpected, we don't like webstart need it to work better
2) Gene expression with ineraction data, with visualisation, preprocessing done outside of cytoscape
3) Easter Egg secret set of keys for PacMen

Further Discussion
Usability peeve
1. Multiple versions: Cytoscape 2.3 and 2.1 needed just to teach the course!

2. Need a simple tutorial for outreach for different communities
: PlugIn's don't work all the time
functionality disappears across versions, and users don't know where it has gone

4. Webstart, deployment of it...
Barriers to success, plugins, adding data after started, 
Rigid, unwieldy, 
Getting it to start in the same application rather than many windows
5. Vizmapper filters buggy.... hard to replicate errors

6.Consistency through versions, plugins break....
how to remove old versions of plugins without losing statistics

7. backward compatibility

8. if pipeline breaks cytoscape gets the blame

9. Users freak out....Before Release: clean up code and debugging messages before release

10 lack of web interface -> not going to work for scooters groups....
   need cutting edge right now.... social networking....
11. Presentation don't work/ 1024x768; considered minor but annoying and hard to
        1)side panel too big can't be made smaller
        2)webservices and table importer fits on screen, but if open the advance 
          settings leads to problems, too much information...
12. Destroy Network -> Delete Network (positive transference)
13. rotate slider is clunky should be more direct manipulation
14. Undo option...does something expected and can't get back...redo...
    Redo doesn't redo?
15. Does it make sense to have one size fits all.... difficult to handle hyper-edges
    need other visualisation engine?
16. Lossless Graph compression, with CPU costs (GOOD IDEA LIGHT BULB)
+ Data structures that use the hard drive, secondary storage
17. Layout menu is scary! part of network, but only want to modify part by part
        Data panel only shows selected, need secondary selection option...

1. Tutorials, stable that we can download across machines 
   wrapped up in a webstart with plugins that you can teach with
   Gene Expression/ChipChip do enrichment, find transcription factors
   Current Tutorials not really geared towards biologists, currently feature orientated
   "Bio orientated" / "Task Orientated" Collecting them from current users
   Easy method for uploading them? Test tutorials in a course/real life experience
   NB not developer input, need course instructor needs. 
   Open Helix, curriculum service. they would charge us... 
   (ISB Course, running 4 years) need method for feed back 
   Orientate better website for Developers/Users/Press, role oriented like university
   Should we target conferences rather than responding to requests i.e proactive rather than reactive

2. Vignettes, short how to tutorials, could be web based...or screen capture, or video
   update tutorials before release
3. bug reporting should be easier? Need light weight method. bugs don't get reported, people time short
   e.g. vizmapper bug, hard to report but would be too good to know. 
   Ask user if they want to report crash/exception/ -> Scooter does it for Chimera.
   and it works really well.
4. Pitch to head of labs, Executive summary of capabilities. what it can do
   like the two minute summary's that websites use to sell new productives
5. Upto date publication list..GenMapp :Real time highwire search, and link to that result page.
                               Chimera, do the same, cherry picked so it looks very busy,
   Would be good for cytoscape, lots of publications and pictures....
6. Screen Grab, to report errors? Fogbugz does it....very easy...
   Want to be able to tell the user if it has been reported already and what the fix is.
7. Development is closed to non-core developers. Read access would be useful, design decisions should
   be made on open lists. Or move to use the Wiki to avoid flood of emails. Needs to clean up wiki
   or New Wiki!!
8. LinkedIn/Facebook group? 

9. No press package on the website. Not accessible.

CytoscapeRetreat2008/Brainstorm (last edited 2009-02-12 01:04:01 by localhost)

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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