NGS Workshop

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Future Computing Platforms to Accelerate Next-Gen Sequencing (NGS) Applications

Boston, MA, May 19th, collocated with IPDPS 2013


The workshop has three main objectives:

  1. What are specific grand challenge problems in this area with the best opportunities for future computing platforms?
  2. How can graph algorithms and analytics best be leveraged to advance NGS applications? Can we identify algorithms of broad use and high-impact for NGS to accelerate on FCP?
  3. What organizational structure and interactions best suit the scientists working toward these grand challenges? What support mechanisms should an S2I2 provide domain researchers to accelerate scientific progress? What are the best practices for incorporating novel computing technologies?


  • Location: Hyatt Regency Cambridge, Boston, MA
  • Room: Paul Revere A
  • Dial-in access: (424) 203-8400 x410936#
  • On-site internet access
    • SSID: IPDPS 2013
    • Passcode: ipdps (case sensitive)
  • Link to collaborative notes


9:30  - 10:00 -- Set-up (load presentations), coffee and tea
10:00 - 10:15 -- Welcome and Introductions (Viktor Prasanna) ppt
10:15 - 10:45 -- FCP Presentation (David Bader) ppt
10:45 - 11:45 -- Participant Presentations (Facilitator: Jason Riedy)
                 -- Srinivas Aluru pptx
                 -- Thomas Brutnell pptx
                 -- Ion Mandoiu pptx
                 -- James Taylor 
                 -- Ben Langmead pdf
                 -- Mark Borodovsky 
                 -- Jaroslaw Zola 
                 -- Ananth Kalyanaraman pptx
11:45 - 12:30 -- Identify two or three use-cases and goals for break-out sessions (Facilitator: Shel Swenson)
                 (Use-cases will be specific data-intensive problems with the best opportunities 
                  for graph abstractions and future computing platforms -- ideally algorithms of 
                  broad use and high-impact for NGS to accelerate on FCP.)
12:30  -  1:30 -- Lunch (provided)
 1:30 -  3:00 -- Break out sessions (Facilitators: Shel Swenson, Yogesh Simmhan, and Manish Parashar)
                 For each problem identified at the end of the morning session, determine: 
                 -- What an FCP center could do that would help
                 -- Why a center vs additions to existing efforts?
                 -- Potential timeline
                 -- What other applications may benefit from these efforts?
                 -- Outline a report
 3:00 -  3:20 -- Break
 3:20 -  4:30 -- Discuss proposed center model (Facilitator: Yogesh Simmhan) pptx
 4:30 -  5:00 -- NSF Report Generation (Viktor Prasanna)


Goals and Agenda

Guidelines for Participant Presentations

Workshop Report (Draft)


Invited Participants:

  • Srinivas Aluru (Iowa State Univ.)
  • Mark Borodovsky (Georgia Tech)
  • Thomas Brutnell (Donald Danforth Plant Science Center)
  • Ananth Kalyanaraman (Washington State Univ.)
  • Ben Langmead (Johns Hopkins Univ.)
  • Ion Mandoiu (Univ. of Connecticut)
  • James Taylor (Emory Univ.)
  • Jaroslaw Zola (Rutgers Univ.)

FCP S2I2 Participants:

  • David Bader (Georgia Tech)
  • Manish Parashar (Rutgers Univ.)
  • Viktor Prasanna (Univ. of Southern California)
  • Jason Riedy (Georgia Tech)
  • Yogesh Simmhan (Univ. of Southern California)
  • Shel Swenson (Univ. of Southern California and Georgia Tech)
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