[hpc-announce] Call for Papers: HPCA Workshop on Accelerator Architecture in Computational Biology and Bioinformatics workshop (AACBB-2018)

Jishen Zhao jishen.zhao at ucsc.edu
Sat Dec 2 01:44:22 CST 2017

[Apologies if you receive multiple copies of this message.]

*Accelerator Architecture in Computational Biology and Bioinformatics
workshop (AACBB-2018)*

*In conjunction with 24th IEEE International Symposium on High-Performance
Computer Architecture (HPCA-2018)*

*Vienna, Austria, February 24, 2018*

Conference website         http://hpca2018.ece.ucsb.edu/

Submission link               https://easychair.

Submission deadline        Friday, December 15, 2017

Over the last decade, the advent of high-throughput sequencing techniques
brought an exponential growth in biosequence database sizes. With increased
throughput demand and popularity of computational biology tools, reducing
time-to-solution during computational analysis has become a significant
challenge in the path to scientific discovery.

Conventional computer architecture is proven to be inefficient for
computational biology and bioinformatics tasks. For example, aligning even
several hundred DNA or protein sequences using progressive multiple
alignment tools consumes several CPU hours on high performance computer.
Hence, computational biology and bioinformatics rely on hardware
accelerators to allow processing to keep up with the increasing amount of
data generated from biology applications.

In a typical application, dominant portion of the runtime is spent in a
small number of computational kernels, making it an excellent target for
hardware acceleration. The combination of increasingly large datasets and
high performance computing requirements make computational biology prime
candidate to benefit from accelerator architecture research. Potential
directions include 3D integration, near-data processing, automata
processing, associative processing and reconfigurable architectures.

This workshop will focus on architecture and design of hardware
accelerators for computational biology and bioinformatics problems. We plan
to present and discuss a variety of acceleration techniques,
accelerator architectures
and their implications on the development of computational biology.

*Submission guidelines:*

Interested authors are encouraged to submit papers (2-5 pages) through
EasyChair: https://easychair.org/conferences/?conf=aacbb2018.

The full version should be a PDF file in HPCA24 submission format. For
formatting instructions please refer to: http://hpca2018.ece.ucsb.

*List of topics:*

   - Impact of bioinformatics and biology applications on computer
   architecture research
   - Bioinformatics and computational biology accelerator architecture and
   - 3D memory-logic stack based accelerators
   - Automata processing in bioinformatics and computational biology
   - Associative processing in bioinformatics and computational biology
   - Near-data (in-memory) acceleration bioinformatics and computational
   biology applications
   - Emerging memory technologies and their impact on bioinformatics and
   computational biology
   - Embedded and reconfigurable architectures
   - Field programmable logic based accelerators
   - Bioinformatics and computational biology-inspired hardware/software

*Program Committee:*

   - Ananth Kalyanaraman, WSU
   - Bertil Schmidt, University of Mainz
   - Can Alkan, Bilkent University
   - Engin Ipek, University of Rochester
   - Jason Cong, UCLA
   - Mattan Erez, UT Austin
   - Mircea Stan, UVA
   - Onur Mutlu, ETH/CMU
   - Ran Ginosar, Technion
   - Srinivas Aluru, GT
   - Yuan Xie, UCSB

*Invited speakers:*

   - Onur Mutlu, ETH/CMU
   - Ananth Kalyanaraman, WSU
   - Can Alkan, Bilkent University
   - Bertil Schmidt, University of Mainz
   - Srinivas Aluru, GT

All questions about submissions should be emailed to Leonid Yavits (
yavits at technion.ac.il) or Roman Kaplan (sromanka at campus.technion.ac.il)

Jishen Zhao

Assistant Professor
Computer Engineering Department
University of California, Santa Cruz
Office: Engineering 2, Room 217
Email: jishen.zhao at ucsc.edu
Homepage: https://users.soe.ucsc.edu/~jzhao/
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