Symposium on Application Accelerators in High-Performance Computing (SAAHPC)

Call for Papers: Special Track on Rapid Development of Accelerators for the Biological Sciences

Recent advances in biology and biomedicine have stimulated a vast and increasing demand for computational power. The volume of data produced by high-throughput experimental technologies, as well as the demands of computationally modeling biological and biochemical phenomena, tax the capacity of today's general-purpose multiprocessors.  Biologists can benefit greatly from the availability of computational accelerators that exploit technologies such as GPUs, reconfigurable hardware, and other specialized processors.  Scaling up such accelerators promises to deliver supercomputer-level computational power to even small biological labs.

To design accelerators that have a significant impact on the biosciences, the computer science community must revolutionize the way accelerated applications and their underlying hardware are developed and deployed. Application development cycles of months or years are too slow to keep pace with the rapid progress of discovery.  Moreover, bioinformatics programmers are unlikely to build applications for architectures whose use requires highly specialized programming or architectural knowledge (i.e., parallel computing or hardware design). 

For this track within SAAHPC, we invite papers that describe new or proposed techniques, systems, and infrastructure to increase the speed, agility, and flexibility with which accelerators can be deployed in bioscience applications.  Contributions of interest may include, but are not limited to:

• methods for automatically translating high-level computation specifications, either imperative or declarative, into efficient accelerator implementations;
• libraries and parameterized accelerator designs that can rapidly implement a family of computations;
• infrastructure to rapidly interface accelerators with software front-ends, or to create full hybrid systems;
• deployment and validation of biocomputing applications on widely supported accelerator platforms.

Application areas of interest within biology include:

• analysis of DNA, RNA, and protein sequences;
• models of evolution, at all levels from sequences to populations;
• molecular dynamics, reaction kinetics, and other models of biochemical processes;
• systems biology, especially modeling and inference of gene regulatory networks;
• biological signal and image acquisition and analysis;
• neurological modeling and brain mapping.

Submissions can come in two forms: 

1. Regular submissions will be peer-reviewed and, if accepted, published in IEEE's SAAHPC Proceedings. These may be either short papers of up to 4 pages for poster presentation, or long papers of up to 10 pages for oral presentation.
2. Position papers (up to 4 pages for either poster or oral presentation) will be editorially reviewed and, if accepted, published on the conference web site.  If you are submitting a position paper, please so indicate in the comments section of the submission form.

Track Chairs: Jeremy Buhler, Roger Chamberlain, & Mark Franklin, Department of Computer Science & Engineering, Washington University in St. Louis
Submission deadline: May 11, 2012
Acceptance notification: June 13, 2012
Final papers due: June 27, 2012
Conference dates: July 10-12, 2012