Say Hello to Bio
OLCF attends Bio-IT in effort to recruit underrepresented field
OLCF User Support Specialist Fernanda Foertter paid a visit to the annual Bio-IT conference in Boston, Massachusetts to try to connect with a traditionally underrepresented group in high-performance computing (HPC).
“The conference provided a good opportunity to reach out to a community that is underrepresented at our center,” said Foertter. “We need to learn what this community’s needs are, and how we can cater to those needs.”
Besides meeting with potential users, Foertter also met with the OLCF’s industry partners Cray and NVIDIA. Specifically, Foertter had discussions with four of both Cray and NVIDIA’s development teams dedicated to application porting in an effort build up collaboration with domain experts at the OLCF.
The conference, which took place from April 29 to May 1, hosted more than 2,500 participants from the life sciences, healthcare, pharmaceutical, and IT industries representing more than 30 countries.
In addition to reaching out to the larger bioinformatics community in an effort to get them more engaged in HPC, Foertter also met with representatives from the joint MIT/Harvard Broad Institute and MIT’s McGovern Institute for Brain Research, both leading institutes in the life sciences.
The conference featured 13 conference tracks, including “Software Development,” “Data Visualization and Exploration Tools,” and “Clinical Genomics.” All of these tracks were available alongside 16 preconference workshops, including “Genome Assembly and Annotation,” “Data Visualization in Biology,” and “Big Data Analytics.”
Joining Foertter on the trek to Boston were OLCF Director’s Discretionary Program users Bhanu Rekepalli and Tae-Hyuk Ahn, each of who presented their work from Titan at the conference.
Rekepalli uses his time on Titan to bridge the gap between the rate of data generation in life sciences and the speed and ease at which biologists and pharmacists can study this data. His application, based on NCBI BLAST, finds regions of similarities between biological sequences, can be used to infer functional and evolutionary relationships between sequences as well as help identify member of gene families.
Ahn uses the Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance and Taxonomic Profiling algorithm, or Sigma, algorithm for metagenomic sequencing, or the sequencing of genomic samples directly from an environment. Specifically, Ahn uses this novel sampling technique as a form of biosurveillance to pinpoint possible pathogenic sources, such as the recent E. Coli outbreak, in shorter timeframes than conventional methods.
“Bio is playing catch up when it comes to HPC. Only recently have their needs grown beyond workstations and small clusters,” said Foertter. “We are excited for the opportunity to help advance this domain with significant HPC resources.”