National Center for Genome Analysis Support (NCGAS) use and development of Tripal Genome Browsers on XSEDE’s Jetstream

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Date
2018-01-14
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Plant and Animal Genomics 2018
Abstract
The National Center for Genome Analysis Support (NCGAS) helps the biological community analyze, understand, and make use of the vast amount of genomic information now available. To this end, NCGAS develops and supports genome browsers for several genomics projects, using Tripal as its front end for the last year. Since the adoption of Tripal, we’ve modified some of the tools to develop features our users find useful. We will introduce our groups’ projects and give a demo of these tools in our browsers. These tools include: 1) Modifications to tripal_blast module to link blast reports to external JBrowse sites through URL manipulation—allowing visualization against potentially any browser with publicly available data with which to build a blast database. 2) A GUI based web tool to spin up new JBrowse instances, with on-the-fly GUI-based track addition/removal, which allows for more flexible community visualization. 3) Finally, we will demo the virtual machine image built on the XSEDE cloud (Jetstream) with Tripal, JBrowse, and these tools installed - allowing for free genome browser hosting with minimal command line use. It is our hope that these tools will reduce the learning curve required to make use of Tripal genome visualization tools.
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NCGAS, Jetstream, Genome Browsers
Citation
Sanders, S., C. Ganote, B. Papudeshi, and T. Doak. (2018). National Center for Genome Analysis Support (NCGAS) use and development of Tripal Genome Browsers on XSEDE’s Jetstream. Plant and Animal Genomics 2018, San Diego, CA. Retrieved from http://hdl.handle.net/2022/21898
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