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Date

Attendees


  • Beyers, Matthew (NIH/NCI) [C]

  • Rajesh, Anand, Chris Kinsinger, Deepak Singhai, Erika, Gilberto Fragoso, Henry Rodriguez, John, Karen Ketchum, Michael Holck, Mike MacCoss


Agenda

  • Ongoing work  
    • Data release - production deployment later today
      • HNSCC from CPTAC3
      • Lung Cancer dataset of Academia Sinica - from ICPC, MacCoss 
      • Release of Simplified study identifiers and external references - now in stage
    • Support
      • Clustergram tutorial video
  • Portal and workspace related improvements  
    • Workspace usability improvement 
  • Next data sets / releases in pipeline
    • LSCC from CPTAC3 (July)
    • PDA from CPTAC3
    • LUAD confirmatory from CPTAC3   
    • APOLLO
    • Georgetown lung dataset
    • Organoid dataset from PNNL
  • Other items
  • NCI Updates
  • New schedule for NCI-PDC call - move to a bi-weekly meeting
  • Update of ongoing PDC development
    • Release - May 13
      • New data released - CPTAC3 HNSCC and Academia Sinica LUAD
      • New PDC identifiers
    • discussion on composition of Advisory committee
  • Input/Feedback from stakeholders 

Discussion items

TimeItemWhoNotes

Data releaseRajesh
  • HNSCC from CTPAC3 and Lung cancer Academia Sinica went out.  New simplified study identifiers and external references now in production.

Advisory BoardMike MacCoss
  • 5-6 individuals
  • Want to ask Sam Payne to stay on - provided guidance on metadata and how to use data from a data scientist perspective.  Also familiar with CPTAC and working in proteomics for a long while.  Currently at Brigham Young.  Uses proteomics in his undergraduate data science teaching.  Shares feedback and criticism openly.  Present and active at Advisory Board past meetings.
  • Want someone else on signal processing and tool development.  Alexi Nashivsky.  Working with SBG on tools there.  Can provide feedback on what's working and what's not.  University of Michigan.  Will provide plenty of constructive criticism - very open with feedback.
  • Want some representation from Proteomic Exchange.  Eric Deutch from ISB or Juan Antonio Visano at EBI (UK).  Visano may feel less threatened by PDC.  Open to suggestions.  Ask one first?  Chris has had interactions with both.  Chris working more closely with Visano most recently.  Can't recommend one over the other.  Eric a little less engaged.  Eric at ISB could be a connection for collaboration.  Will reach out to Eric first since it's logistically easier.  Henry wants google doc with names - Mike will provide.
  • Want someone with clinical/cancer genomics background.  Mandy Polvich or Karen Rodman.  Mandy may feel like she's got too much on her plate.
  • Want someone from outside the US system.  Yuju Chen from Academia Sinica.  Might be a logistical challenge with time zone difference.
  • Henry doesn't want to call it Advisory Board.  Call it Scientific Committee instead.

External InteractionsRajesh

Share more about Philopher, ISB, PRIDE next call.

Henry wants interaction plan/schedule with external folks.  John will schedule call with Rajesh - need to discuss timing and how it fits within the rest of CRDC.  Erika/Rajesh/John will have call.  Erika wants concrete milestones defined for external interactions.




Sarah Gosling - looking to build tools for PDC workspace.  Chris heard from her.



Henry expects Daily Stats from the portal.  John suggests page views on agenda and overlay milestone events (data release, email blast, conference).  Added as agenda item to above call with Erika/Rajesh/John.



Henry asks how much we should be storing non-cancer proteomic data.  Open discussion question.  Chris suggests it be more open to data other than cancer.

Action items

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