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

Technical Program (Room 233)

8:15 – 8:30 Opening Remarks
8:15 – 8:30 Special guest: Sylvia Spengler, National Science Foundation
8:30 – 9:30 Keynote
8:30 – 9:30 Grand challenges in plant sciences: roles for NGS bioinformatics
Patrick Schnable, Iowa State University
9:30 – 10:00 Break
10:00 – 12:00 Section A
10:00 – 10:30 The Genome Assembly & Analysis Tool Box (GATB), a low-memory and efficient data structure for de Bruijn Graph applications
Guillaume Rizk, Institute for Research in IT and Random Systems (IRISA), France
10:30 – 11:00 Skyport - a multi-cloud scientific workflow system with Linux container orchestration to efficiently execute complex data-parallel bioinformatics pipelines
Wolfgang Gerlach, Argonne National Laboratory
11:00 – 11:30 Similarity detection in large sequence collections
Jaroslaw Zola, State University of New York at Buffalo
11:30 – 12: 00 Spaler: Spark and GraphX based de novo genome assembler
Umit Catalyurek and Anas Abu-Doleh, Ohio State University
12:00 – 13:30 Lunch
13:30 – 15:30 Section B
13:30 – 14:00 Scalable parallel algorithms for de novo assembly of complex genomes
Evangelos Georganas, University of California at Berkeley
14:00 – 14:30 Functional phylogenomics analysis of microbial genomics and metagenomics using high-performance computing
Chongle Pan, Oak Ridge National Laboratories
14:30 – 15:00 Exploring tens of thousands of RNA-seq samples with Rail-RNA
Ben Langmead, Johns Hopkins University
15:00 – 15:30 Parallel software libraries for high-throughput sequencing
Srinivas Aluru, Tony Pan and Patrick Flick, Georgia Institute of Technology
15:30 – 16:00 Break
16:00 – 17:30 Open Discussion