RNA-Seq analysis used as a model of complex computing requirements in initiative to advance cloud computing

The MDI Biological Laboratory in Bar Harbor, Maine, has been awarded a grant to promote the shift to cloud computing among undergraduates and researchers at the 14 Maine educational and research institutions that comprise the federally funded Maine INBRE network, a program to strengthen biomedical research and research training in Maine.

The “cloud lab” program will address costs and time associated with analyzing the large, complex datasets that are being generated as a result of the advent of the genomic age. The volume and complexity of these datasets places a strain on the time and resources of researchers and institutions and inhibits the easy, rapid analysis and exchange of information among those at geographically distributed locations.

Maine students will be trained in RNA sequencing analysis using a generic workflow analysis module developed by Benjamin L. King, Ph.D., assistant professor of bioinformatics at the University of Maine and co-director of the Maine INBRE  Bioinformatics Core. The module will use data on antibiotic-resistant non-tuberculosis mycobacteria generated by Sally D. Molloy, Ph.D., also of the University of Maine.

The training module offers an example of how cloud computing can advance biomedical knowledge. Using the workflow, students can quickly identify genes associated with antibiotic resistance in non-tuberculosis mycobacteria. Such research could lead to the development of treatments that are effective against this type of infection, which can cause serious lung damage and is a growing health problem.

The module allows students to execute analyses at a keystroke that otherwise would have taken days and would only have been possible at institutions with high performance computing capabilities, King said. Though the generic module can be adapted to other research, future plans call for teaching students and researchers how to develop analysis workflows that are customized to their research needs.

“With cloud-based resources, students and researchers can basically build their own servers, design their own analysis pipelines and set up data storage just by typing a single command,” King said. “They don’t have to understand how the system works, they don’t have to compete with others for computing resources, and they aren’t limited on data storage. They can build whatever they need – it’s quite powerful.”

Source – MDI Biological Laboratory

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