A voice for bioinformatics

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Date

2017-07-11

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Publisher

PEARC 2017

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.

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Keywords

NCGAS, services, bioinformatics

Citation

Ganote, C., S. Sanders, B. Papudeshi, P. Blood, T. Doak. (2017). A voice for bioinformatics. Presented at PEARC 2017, New Orleans, LA. Retrieved from http://hdl.handle.net/2022/21604.

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Except where otherwise noted, the contents of this presentation are copyright of the Trustees of Indiana University. This license includes the following terms: You are free to share -to copy, distribute and transmit the work and to remix -to adapt the work under the following conditions: attribution -you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work.

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Presentation

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