Workshop on Parallel Software Libraries for Sequence Analysis (pSALSA)

Workshop on Parallel Software Libraries for Sequence Analysis (pSALSA)

In conjunction with the ACM Conference on Bioinformatics, Computational Biology and Health Informatics

Wednesday, September 9, 2015
Gerogia Tech Global Learning Center, Atlanta, GA

Click here for technical program

Call for Participation

High-throughput DNA sequencing instruments are capable of generating terabytes of sequencing data in a single experiment at a cost that is affordable on a routine basis. Analyzing such data is fundamental to many applications including genome resequencing, de novo genome sequencing, transcriptome sampling, metagenomics, and population diversity studies. The rate and volume of data generation is exposing the limitations of serial bioinformatics software. Effective exploitation of high performance computing technologies including multicores, accelerators, cluster and cloud computing platforms can bridge this critical gap.

The goal of this workshop is to bring together a community of bioinformatics researchers interested in development of parallel algorithms and high performance computing software for high-throughput DNA sequence analysis and its myriad applications. In particular, this workshop focuses on community-driven development of parallel software libraries to enable the bioinformatics community to more easily exploit high performance computing technologies. Development of such libraries is feasible because bioinformatics applications often rely on a common core of index and data structures – for e.g., look up tables, suffix trees/arrays, de Bruijn graphs etc. Such libraries have proved enormously useful in other application domains (e.g. BLAS libraries for scientific computing), and similar efforts are currently underway in other application domains (e.g. parallel graph libraries).

This workshop is aimed at bringing together like-minded researchers who are interested in contributing to the development of such libraries, or application scientists who are interested in driving the creation of such libraries and using them. We plan to sustain the momentum by periodically hosting additional meetings to assess progress, develop common community abstractions and standards, and make future plans. The workshop is held in conjunction with the ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), and the Workshop on Algorithms for Bioinformatics (WABI) both of which run from September 9-12. Workshop registration is through ACM-BCB and automatically provides access to both the events in addition to the workshop. We encourage workshop attendees to take advantage of these meetings. Limited travel support is available through an NSF-NIH Big Data grant. If you need travel support, please contact Yongchao Liu (

Workshop Registration

Advance registration and discounted hotel reservation deadline: August 5, 2015

Register for the workshop here.
Hotel reservation is available here.

Workshop Organizers

Srinivas Aluru, Georgia Institute of Technology
Yongchao Liu, Georgia Institute of Technology

Workshop Sponsors: