DNA Subway: Making genome analysis egalitarian

Uwe Hilgert, Sheldon McKay, Cornel Ghiban, Mohammed Khalfan, David Micklos, Jason Williams

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Abstract

DNA Subway bundles research-grade bioinformatics tools, highperformance computing, and databases into easy-to-use workflows. Students have been "riding" different lines since 2010, to predict and annotate genes in up to 150kb of raw DNA sequence (Red Line), identify homologs in sequenced genomes (Yellow Line), identify species using DNA barcodes and construct phylogenetic trees (Blue Line), and examine RNA sequence (RNA-Seq) datasets for transcript abundance and differential expression (Green Line). With support for plant and animal genomes, DNA Subway engages students in their own learning, bringing to life key concepts in molecular biology, genetics, and evolution. Integrated DNA barcoding and RNA extraction wet-lab experiments support a variety of inquiry-based projects using student-generated data. Products of student research can be exported, published, and used in follow-up experiments. To date, DNA Subway has over 8,000 registered users who have produced 51,000 projects. Based on the popular Tuxedo Protocol, the Green Line was introduced in January 2014 as an easy-to-use workflow to analyze RNA-Seq datasets. The workflow uses iPlant's APIs (http://agaveapi.co/) to access high-performance compute resources of NSF's Extreme Scientific and Engineering Discovery Environment (XSEDE), providing the first easy "on ramp" to biological supercomputing.

Original languageEnglish (US)
Title of host publicationProceedings of the XSEDE 2014 Conference
Subtitle of host publicationEngaging Communities
PublisherAssociation for Computing Machinery
ISBN (Print)9781450328937
DOIs
StatePublished - Jan 1 2014
Event2014 Annual Conference on Extreme Science and Engineering Discovery Environment, XSEDE 2014 - Atlanta, GA, United States
Duration: Jul 13 2014Jul 18 2014

Publication series

NameACM International Conference Proceeding Series

Other

Other2014 Annual Conference on Extreme Science and Engineering Discovery Environment, XSEDE 2014
CountryUnited States
CityAtlanta, GA
Period7/13/147/18/14

Keywords

  • Cold spring harbor
  • DNA subway
  • Education
  • Fastx toolkit
  • Green line
  • Iplant api
  • Iplant collaborative
  • Red line
  • Rna seq
  • Rna seq data
  • Undergraduate

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

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  • Cite this

    Hilgert, U., McKay, S., Ghiban, C., Khalfan, M., Micklos, D., & Williams, J. (2014). DNA Subway: Making genome analysis egalitarian. In Proceedings of the XSEDE 2014 Conference: Engaging Communities [70] (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/2616498.2616575