Supporting Bioinformatics Pipelines in an HPC Environment: Lessons Learned from the Pediatric Cancer Genome Project
MONDAY, JUNE 3RD, 2013, 2:00 – 3:00 PM
307 EBERLY HALL
ABSTRACT: Bioinformatics has become a highly influential field of investigation for the understanding of human disease. The Pediatric Cancer Genome Project (PCGP) is an unprecedented three-year effort to sequence and analyze the genomes of 600 pediatric cancer patients to identify genetic variations that give rise to childhood disease. Begun in 2010, it is a joint venture between St. Jude Children’s Research Hospital and Washington University in St. Louis and is the largest whole-genome sequencing of pediatric cancers ever conducted. This talk will describe the lessons learned in the High Performance Computing Facility at St. Jude while supporting the PCGP effort and describe the computational infrastructure developed in response to the unique challenges of the project. Opportunities and challenges for the HPC community to support future work in bioinformatics will also be discussed.
BIO: Antonio M. Ferreira received his Bachelor of Arts in Mathematics with a minor in Chemistry from Syracuse University in 1993. He went on to earn a Ph.D. in Physical Chemistry with Dr. Henry Kurtz at The University of Memphis specializing in theoretical studies of the nonlinear optical properties of materials. Following his graduate studies he worked as a postdoc with Dr. J. Vincent Ortiz at Kansas State University, where he developed electron propagator methods for the Gaussian quantum chemistry package. He returned to The University of Memphis in 2001 as a Visiting Assistant Professor in the Chemistry Department. During his time there he worked with staff at ORNL and PNNL on improvements to the NWChem software and his research efforts shifted toward the application of quantum chemical methods in drug design with Dr. Bob M. Moore of the University of Tennessee. In 2004, he joined the group of Dr. Donald Bashford in the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children’s Research Hospital in Memphis, Tennessee. He was promoted to Staff Scientist in the Structural Biology Department in 2006 and in 2010 became the manager of St. Jude’s High Performance Computing Facility. As manager of that facility he was responsible for architecting and deploying a major expansion of the institutional computing infrastructure to support the Pediatric Cancer Genome Project. He is currently working to leverage GPUs for genomics analysis with the Center for Integrative and Translational Genomics at the University of Tennessee Health Science Center.