Carrie L. Ganote
ABSTRACT
One of the challenges to adoption of HPC is the disjunction between those who need it and those who know it. Biology (specifically, genomics) is a growing field for computational use, but the typical biologist does not have an established informatics background. The National Center for Genome Analysis Support (NCGAS) aids users in getting past the initial shock of the command line and guides them toward savvy cluster use. NCGAS is initiating a push to become domain champions alongside Oklahoma State's Brian Cougar. Our position at IU gives us a close relationship with XSEDE and we already fulfill a role in pushing users toward XSEDE resources when our local clusters are ill-suited to the job. We currently act as liaison between biologists and Jetstream, IU and TACC's research computing cloud. Typical issues include: Software installation; Software usage - what parameters do I choose, and how do I interpret the results; Batch job submission; Understanding how queues and job handlers work; Data movement, Spinning up VMs on Jetstream We will discuss how we have structured our support, and illustrate our impact on XSEDE resources.
- 2016. The Cost of Sequencing a Human Genome-National Human Genome Research Institute. https://www.genome.gov/sequencingcosts/.Google Scholar
- Richard D. LeDuc, Le-Shin Wu, Carrie L. Ganote, Thomas Doak, Philip D. Blood, and Matthew Vaughn. 2013. National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery. ACM Press. Google ScholarDigital Library
- Zachary D. Stephens, Skylar Y. Lee, Faraz Faghri, Roy H. Campbell, Chengxiang Zhai, Miles J. Efron, Ravishankar Iyer, Michael C. Schatz, Saurabh Sinha, and Gene E. Robinson. 2015. Big Data: Astronomical or Genomical? PLOS Biology 13, 7 (July 2015), E1002195.Google ScholarCross Ref
- Craig A. Stewart, William K Barnett, Matthew W. Hahn, and Michael R. Lynch. 2015. ABI Development: National Center for Genome Analysis Support. PTI Technical Report PTI-TR15-009 (December 2015).Google Scholar
Index Terms
- A Voice for Bioinformatics
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