The National Center for Genome Analysis Support (NCGAS) has received a joint five-year, $4 million resource improvement grant from the National Cancer Institute. The grant is a partnership with the Broad Institute of MIT and Harvard, the lead institution, and the Center for Information Services and High Performance Computing (ZIH) at Technische University in Dresden. The partnership’s goal is to advance cancer research.
Researchers at the Broad Institute and Hebrew University developed the software, known as Trinity. It produces high-quality RNA sequence assemblies used by scientists studying gene expression. These RNA sequence assemblies allow scientists to know which genes are active within any living creature.
NCGAS, along with ZIH, will continue to optimize key Broad software and make it available to the cancer research community on IU cluster computers, NCGAS director Bill Barnett said.
The work funded by the grant will result in cancer researchers having more comprehensive assemblies of cancer genomic data, and access to bioinformatics resources to rapidly obtain those assemblies. The goal is for these expanded research capabilities to lead to an improved understanding of cancer biology and ultimately to more effective cancer treatments.
So far, Trinity has quadrupled in speed since the collaboration began in 2011. "By optimizing Trinity, researchers can now do four times as much science," Barnett said. "The Broad Institute continues to improve their software and Indiana University will continue to optimize it to make it run more efficiently."
The grant has annual benchmarks over the course of the five years, with work being continually refined. "It will be a constant cycle of code improvement, optimization, then delivering new software for researchers to use on systems we support for them," Barnett said.
Code optimization will include improvements to run-time performance, memory usage, CPU usage, and storage usage, particularly using High Performance Computing (HPC) machines, said Robert Henschel, NCGAS’ Scientific Applications and Performance Tuning manager. "We keep the quality of the software high while being more efficient using computational resources, like supercomputers," Henschel said.
Cancer research is new territory for NCGAS, Barnett said.
"This grant is important for us because it allows us to serve a community that we haven’t been able to before," Barnett said. "And it allows us to continue working with the premiere genomic medicine institute in the country. IU and the Broad Institute are leaders who can collaborate and leverage each other’s expertise. And it’s important that the result will be in advancing therapies for treating cancer."
The mission of the National Center for Genome Analysis Support is to enable the biological research community of the US to analyze, understand, and make use of the vast amount of genomic information now available. NCGAS focuses particularly on transcriptome- and genome-level assembly, phylogenetics, metagenomics/transcriptomics, and community genomics.
About the Broad Institute of MIT and Harvard
The Eli and Edythe L. Broad Institute of Harvard and MIT was launched to empower creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community.
Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over 100 private and public institutions in more than 40 countries worldwide.