HPC Workshop

Aug 2, 2012–Three Bioinformatics students were selected to participate in the High Performance Computing Summer Institute at the Virginia Bioinformatics Institute at Virginia Tech. This 2-week intensive course was directed towards eligible undergraduates, graduate students and postdocs interested in further developing their expertise in biology relevant high performance and data intensive computing field.

During the course, participants attended lectures and discussions by leading field members, including academic and industrial affiliates, and worked on a group research project with 3 other course participants.

The participating UD students were: Erin Crowgey, a Master’s student in Bioinformatics & Computational Biology; Modupe Adetunji, a Master’s student in Bioinformatics & Computational Biology; and Dan Nasko, a Doctoral student in Bioinformatics & Systems Biology.

The advent of less expensive genome sequencing techniques has accelerated the need to store, communicate, and manipulate large genomic data sets. Modupe’s and Nasko’s research team worked to develop a pipeline for sequence data compression, using a centroid based compression algorithm that takes large-scale short-read sequencing data as input and compresses them from clustering methods. Crowgey’s research team developed an automated pipeline to identify novel genetic variants in next generation sequenced human genome data.

“It was an intellectually stimulating and intense course. I really enjoyed being handed a fresh project and seeing how far we could get in 2 weeks, utilizing the Virginia Bioinformatics Institute’s high performance computing cluster (Shadowfax)”, said Nasko. “Working with researchers from other institutions and companies was a great pleasure as well. Overall, a worthwhile experience.”