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Identifying Cancer DNA Changes With XSEDE Resources

Identifying Cancer DNA Changes With XSEDE Resources

The scientific field of bioinformatics has for the past five years relied on increasingly larger data sets for new and innovative research. With few in the field trained in computer science, many groups, like the University of Pittsburgh Cancer Institute, have turned to XSEDE for help.

"Nobody in my group is really an expert in IT or computer science. We're trained in bioinformatics," says Uma Chandran, co-director of Cancer Bioinformatics Services at the Institute. "We've been very fortunate to have the Pittsburgh Supercomputing Center (PSC) next door, and through them, the XSEDE resources that we found out about. And it's really saved us a tremendous amount of work having to learn it ourselves."  

Her group participates in the Cancer Genome Atlas project, which aims to use computational bioinformatics to find all of the genomic changes that might inform why a patient got cancer, as well as how they might respond to therapy. There's also the potential to create better predictive markers for cancer.

Chandran said the project has benefitted greatly from XSEDE's Extended Collaborative Support Services (ECSS). ECSS Consultant Alex Ropelowski at PSC helped her group.

"The consultants have installed all the bioinformatics tools. Helped us troubleshoot installation, running the tools. And have trained my analysts in running them. Without that human support, we wouldn't have been able to use XSEDE services even if they were available," Chandran said.