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Genome center expands scientific reach with new services, partnerships

Cancer researchers, biologists, agriculture scientists: new NCGAS data analysis tools help all

BLOOMINGTON, Ind. — The National Center for Genome Analysis Support (NCGAS) has announced new services and partnerships to further support genome science and researchers working to study the diversity of life, cure disease, and improve farming around the world.

NCGAS is a collaboration led by the Indiana University Pervasive Technology Institute in partnership with the Texas Advanced Computing Center of the University of Texas, Austin; the San Diego Supercomputer Center of University of California, San Diego; and the Pittsburgh Supercomputing Center. NCGAS helps US researchers make sense of today’s vast amounts of genomic data. To that end, NCGAS has launched two new analysis tools:

  • The Trinity RNA-Seq portal, created in partnership with the Eli and Edythe L. Broad Institute of Harvard and the Massachusetts Institute of Technology, provides access to cancer genome analysis tools on a pipeline housed on IU’s Karst supercomputer. Funded by the National Cancer Institute, the portal has already been used by more than 50 cancer researchers.
  • The GenePattern software provides algorithms in a user-friendly environment for the analysis of genomics data for tens of thousands of researchers worldwide. This tool was created by the Broad Institute and funded by the National Institutes of Health. NCGAS is partnering with the Broad to provide a high performance public GenePattern server and optimize the algorithms for its use.

"Our partnership with NCGAS will enable us to expand the computational resources we are able to offer investigators, which is so critical in this big data era of biomedical science," said Jill P. Mesirov, who serves as associate director and chief informatics officer and director of computational biology and bioinformatics at the Broad Institute. "Moreover, we are working with NCGAS to optimize our most compute-intensive methods to reduce runtimes and speed up delivery of results to our users."

NCGAS services are also expanding. Based on user demand, the center is now rolling out a genome browser service that allows investigators to visualize entire genomes with annotated data, including gene prediction and other structural data. This is available remotely through web browsers and has been piloted on IU’s massive IQ-Wall, which allows comparison across many more genomes simultaneously.

In addition, NCGAS has named Keithanne Mockaitis, Ph.D., of Dow AgroSciences as its first visiting scientist. Mockaitis was an associate scientist in the IU biology department who has worked closely with NCGAS for years. In that role, she became known worldwide for her work on plant genomics, specifically economically important specialty crops such as the chocolate tree and the loblolly pine, a US industrial forest tree. In 2014, she and NCGAS staff hosted a workshop for her research collaborators, "Genomics in July: an introduction to genome discovery and analysis using next-generation sequencing data."

"NCGAS is a great place to get science done. I’m excited to engage with the center on these large plant genomics projects and to continue my work mentoring post-docs and students in the IU School of Informatics and Computing," said Mockaitis. "This new collaboration will allow me to continue my federally funded nonprofit work and maintain my engagement with basic science, which I love."

Whether it’s new staff members, new partnerships, or new tools, NCGAS is continuing its upward trajectory.

"The NCGAS service model, first funded by the National Science Foundation, is proving to be a valuable and much-needed asset to the research community. We have worked hard to be responsive to the needs of researchers, and we are excited about the possibilities for future growth that these new services and partnerships provide," said NCGAS Director Bill Barnett.