15th IEEE International Workshop on High Performance Computational Biology
Monday, May 23, 2016
Chicago, Illinois, USA

  In conjunction with the IEEE International Parallel and Distributed Processing Symposium

The Parallel Software Libraries for Sequence Analysis (pSALSA) session is on Sunday, May 22!
HiCOMB 2016 Program is now available!


HiCOMB 2016 Keynote Talk

The Big Challenges of Big Data in Bioinformatics

Alex Pothen, Purdue University

Abstract: With the advent of new genomic and proteomic technologies, biological scientists face the challenge of collecting, organizing, and analyzing big data sets. Examples include functional MRI data sets in neuroscience, transcriptomics data on micro-RNAs expressed in healthy and diseased cells, and high dimensional proteomic data obtained at the single cell level from flow cytometry experiments. Another challenge is to share human data in a way that protects the privacy of individuals. I will consider a few of these problems, and discuss our work on designing algorithms that can process these datasets efficiently. A few themes that emerge are the use of graph models to solve the problems, the power of approximation to make graph algorithms efficient, and the use of parallel computing to make the computations fast.

Speaker Biography: Alex Pothen is a Professor and Associate Head of Computer Science at Purdue University. He has led a pioneering research project in combinatorial scientific computing as the Director of the CSCAPES Institute funded by the U.S. Department of Energy. Alex’s research interests span combinatorial scientific computing, parallel computing, and bioinformatics. Alex received an undergraduate degree from the Indian Institute of Technology, Delhi, and a PhD from Cornell. He is an editor of the Journal of the ACM and the SIAM Review, and has served as an editor of SIAM Books and other journals. Alex has received a National Science Talent Scholarship, a Distinguished Alumnus award from IIT Delhi, and several best paper prizes. He has advised more than twenty PhD students and postdoctoral scientists.

Invited Talk

Parallel de novo Assembly of Complex Genomes via HipMER

Aydin Buluc, Lawrence Berkeley National Lab

Abstract: De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. I will first present distributed-memory parallelization of de Bruijn graph construction and traversal, which is a key component of most de novo genome assemblers. I will also talk about load-balancing techniques for repetitive genomes with highly skewed k-mer distributions. Then, I will briefly talk about merAligner, a highly parallel sequence aligner that implements a seed-and-extend algorithm. Since merAligner employs parallelism in all of its components, especially the seed index construction, it is particularly useful for aligning contigs to reads within the context of de novo genome assembly. I will also talk about other modules and their characteristics. Large-scale results on a Cray XC30 using grand-challenge genomes demonstrate efficient performance and scalability on thousands of cores. Overall, our pipeline accelerates Meraculous performance by orders of magnitude, creating unprecedented capability for extreme-scale genomic analysis. I will conclude by presenting some forward-looking ideas for parallel assembly of multi-terabyte sized metagenomic datasets.

HiCOMB 2016 Call For Papers

High-performance computing is an integral part of research and development in bioinformatics/computational biology and medical and health informatics. The large size and complexity of biological data sets, and inherent complexity of the underlying biological problems have collectively resulted in large run-time and memory requirements. The goal of this workshop is to provide a forum for discussion of latest research in developing high-performance computing solutions to data- and compute-intensive problems arising from all areas of computational life sciences. We are especially interested in parallel and distributed algorithms, memory-efficient algorithms, large scale data mining techniques, including approaches for big data and cloud computing, algorithms on multicores, manycores and GPUs, and design of high-performance software and hardware for biological applications.

The workshop will feature contributed papers as well as invited talks from reputed researchers in the field.

Topics of interest include but are not limited to:

This year, the HiCOMB workshop will also host multiple sessions specifically dedicated to parallel sequence analysis libraries. These sessions will be held on Sunday, May 22, and are continuation of the pSALSA workshop. The sessions will feature relevant contributed submissions from HiCOMB, multiple invited talks, and discussion. Consequently, we also seek paper submissions that focus on parallel Next-Generation Sequencing (NGS) bioinformatics.

Submission guidelines

Papers reporting on original research (both theoretical and experimental) in all areas of bioinformatics and computational biology are sought. Surveys of important recent results and directions are also welcome. Submission site is available on EDAS system. Submitted manuscripts may not exceed ten (10) single-spaced double-column pages using 10-point size font on 8.5x11 inch pages (IEEE conference style), including figures, tables, and references (see IPDPS Call for Papers for more details). All papers will be peer-reviewed by the technical program committee of the workshop. Accepted manuscripts will be considered for publication either at the HiCOMB main track or the pSALSA special track. The complete symposium and workshop proceedings will be distributed at the conference and will be submitted for inclusion in the IEEE Xplore Digital Library after the conference.

Important Dates

Workshop papers due:January 4, 2016   December 18, 2015
Authors notification:February 1, 2016
Camera-ready papers due:March 7, 2016

Workshop Co-Chairs

Srinivas Aluru
College of Computing
Georgia Institute of Technology
Atlanta, GA 30332, USA
Email:

David A. Bader
College of Computing
Georgia Institute of Technology
Atlanta, GA 30332, USA
Email:

Program Chairs

Ananth Kalyanaraman
School of Electrical Engineering and Computer Science
Washington State University
Pullman, WA 99164-2752, USA
Email:

Jaroslaw Zola
Department of Computer Science and Engineering
Department of Biomedical Informatics
University at Buffalo, SUNY
Buffalo, NY 14260-2500, USA
Email:

Program Committee


HiCOMB Archive

14th International Workshop on High Performance Computational Biology - HiCOMB 2015
13th International Workshop on High Performance Computational Biology - HiCOMB 2014
12th International Workshop on High Performance Computational Biology - HiCOMB 2013
11th International Workshop on High Performance Computational Biology - HiCOMB 2012
10th International Workshop on High Performance Computational Biology - HiCOMB 2011
9th International Workshop on High Performance Computational Biology - HiCOMB 2010
8th International Workshop on High Performance Computational Biology - HiCOMB 2009
7th International Workshop on High Performance Computational Biology - HiCOMB 2008
6th International Workshop on High Performance Computational Biology - HiCOMB 2007
5th International Workshop on High Performance Computational Biology - HiCOMB 2006
4th International Workshop on High Performance Computational Biology - HiCOMB 2005
3rd International Workshop on High Performance Computational Biology - HiCOMB 2004
2nd International Workshop on High Performance Computational Biology - HiCOMB 2003
1st International Workshop on High Performance Computational Biology - HiCOMB 2002