NGS Bioinformatics Workshop

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Workshop on "Challenges in accelerating Next-Gen Sequencing (NGS) bioinformatics"

September, 25, 2013, Washington DC, in conjunction with ACM-BCB 2013


There is a vital need and present opportunity to develop a community-based collaborative software infrastructure that aims to accelerate the design, implementation, optimization, and dissemination of a wide variety of NGS-enabled codes tuned for accelerator-based systems, as well as methodologies, education and training materials. The goal of this workshop is to explore these research challenges, both from a computer science as well as an applications perspective, and to develop a community research agenda, including identifying requirements and best practices, establishing community cases and bench marks, identifying software frameworks tools, and creating community forums for exchange of ideas and artifacts. Among the questions we will address are:

  • What are specific data-intensive problems with the best opportunities for future computing platforms?
  • 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?
  • What unique, common, and missing software infrastructure is needed to achieve sustained innovation in tackling each of these grand challenge problems?
  • What are common hurdles to developing accelerated applications and sustainability issues for NGS-enabled applications tools developers (eg. distribution channels, keeping up with changing platforms, fast shifting domain needs, etc.)?
  • What support mechanisms should an S2I2 provide domain researchers to accelerate scientific progress? What are the best practices for incorporating novel computing technologies?
  • What organizational structure and interactions best suit the scientists working toward these grand challenges? How should the resources of the S2I2 assist in achieving this goal?

This workshop is part a broader NSF Sustainable Software Innovation Institute Conceptualization project entitled "Software Infrastructure for Accelerating Grand Challenge Science with Future Computing Platforms", supported by the NSF BIO and CISE directorates. This multi-institutional project (PIs: Viktor Prasanna - USC, Manish Prashar - Rutgers, David Bader - GA Tech) is focused on supporting sustainable software for data-intensive and inter-disciplinary problems that may be enabled by graph algorithms. Applications made possible by high–throughput sequencing technologies is one target application area in this conceptualization phase. The outcomes of this workshop will be summarized in a publicly available report and incorporated into our proposal for a S2I2 Implementation award in FY 2014 ([NSF SI2 Program]).


  • Location: DoubleTree by Hilton Bethesda, Washington DC, in conjunction with ACM-BCB 2013
  • Room: Ballroom D
  • Time and Date: 1:30 - 5:30PM, Wednesday September 25th 2013
  • For more information, contact Shel Swenson, Future Computing Platforms S2I2 Project Manager
  • Link to collaborative notes


1:30 - 2:15 -- Opening Remarks and Introduction: “Leveraging future computing platforms to accelerate data-intensive grand challenge Problems” Speakers include Viktor Prasanna, Yogesh Simmhan, Inanc Birol, and Anton Nekrutenko

2:15 - 2:30 -- Coffee Break

2:30 - 3:30 -- Breakout Session 1: Exploring specific NGS-enabled applications with opportunities for graph abstractions and future computing platforms (Facilitator: Shel Swenson)

3:30 - 3:45 -- Breakout Session 1 Reports

3:45 - 4:00 -- Coffee Break

4:00 - 5:00 -- Breakout Session 2: Challenges and solutions in developing sustainable accelerated NGS bioinformatics applications (Facilitator: Rich Vuduc)

5:00 - 5:15 -- Breakout Session 2 Reports

5:15 - 5:30 -- Outline Report and Concluding Remarks: Shel Swenson


Goals and Detailed Agenda

Workshop Report


  • Don Adjeroh (West Virginia University)
  • Giuseppe Agepito (Magna Graecia University of Catanzaro, Italy)
  • Srinivas Aluru (Georgia Institute of Technology)
  • Carlos Arana (UT Southwestern Medical Center)
  • Inanc Birol (University of British Columbia)
  • Paul Bodily (Bringham Young University)
  • Shamid Bokhari (Algopath LLC)
  • Mario Cannataro (Magna Graecia University of Catanzaro, Italy)
  • Umit Catalyurek (Ohio State University)
  • Mark Clement (Bringham Young University)
  • Nan Deng (Wayne State University)
  • Mikhail Dozmorov (Oaklahoma Medical Research Facility)
  • Nathan Edwards (Georgetown University)
  • Rudi Eigenmann (National Science Foundation)
  • Pietro Hiram Guzzi (Magna Graecia University of Catanzaro, Italy)
  • Li Jia (SIAC - Frederick, Inc)
  • Julia Jiao (SIAC - Frederick, Inc)
  • Seugnhwa Kang (Pacific Northwest National lab)
  • Manjula Kasoji (SIAC - Frederick, Inc)
  • Carl Kingsford (Carnegie Mellon University)
  • Paul Medvedev (Penn State University )
  • Nate Olson (National Institute of Standards and Technology)
  • Julie Petereit (University of Nevada, Reno)
  • Mihai Pop (University of Maryland)
  • Alex Pothen (Purdue University)
  • Viktor Prasanna (University of Southern California)
  • Steven Salzberg (Johns Hopkins University)
  • Han Si (SIAC - Frederick, Inc)
  • Yogesh Simmhan (University of Southern California)
  • Shel Swenson (University of Southern California)
  • Haibao Tang (J. Craig Venter Industries)
  • Rich Vuduc (Georgia Institute of Technology)
  • May Wang (Georgia Institute of Technology)
  • Daifeng Wang (Yale University)
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