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DNA Subway: Making Genome Analysis Egalitarian

Published: 13 July 2014 Publication History

Abstract

DNA Subway bundles research-grade bioinformatics tools, high-performance 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.

References

[1]
Sharp, P.A., Sugden, B., and Sambrook, J. (1973). Detection of two restriction endonuclease activities in Haemophilus paainfluenzae using analytical agarose-ethidium bromide electrophoresis. Biochemistry 12(16): 3055--63.
[2]
DNA Learning Center. Unpublished survey data.
[3]
National Human Genome Research Institute. www.genome.gov/sequencingcosts/.
[4]
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., and Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-Seq experiments with TopHat and Cufflinks. Nat. Protocols 7(3): 562--78.
[5]
FASTX-Toolkit. http://hannonlab.cshl.edu/fastx_toolkit/.

Cited By

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  • (2025)De Novo Leaf Transcriptome Assembly and Metagenomic Studies of Coast Live Oak (Quercus agrifolia)Applied Microbiology10.3390/applmicrobiol50100245:1(24)Online publication date: 22-Feb-2025
  • (2024)Improved species assignments across the entire Anopheles genus using targeted sequencingFrontiers in Genetics10.3389/fgene.2024.145664415Online publication date: 19-Sep-2024
  • (2024)Analysis of DNA Barcodes Using DNA SubwayDNA Barcoding10.1007/978-1-0716-3581-0_34(551-560)Online publication date: 30-Apr-2024
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Information

Published In

cover image ACM Other conferences
XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment
July 2014
445 pages
ISBN:9781450328937
DOI:10.1145/2616498
  • General Chair:
  • Scott Lathrop,
  • Program Chair:
  • Jay Alameda
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

In-Cooperation

  • NSF: National Science Foundation
  • Drexel University
  • Indiana University: Indiana University

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 13 July 2014

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Author Tags

  1. cold spring harbor
  2. dna subway
  3. education
  4. fastx toolkit
  5. green line
  6. iplant api
  7. iplant collaborative
  8. red line
  9. rna seq
  10. rna seq data
  11. undergraduate

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  • Research-article
  • Research
  • Refereed limited

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XSEDE '14

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XSEDE '14 Paper Acceptance Rate 80 of 120 submissions, 67%;
Overall Acceptance Rate 129 of 190 submissions, 68%

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Cited By

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  • (2025)De Novo Leaf Transcriptome Assembly and Metagenomic Studies of Coast Live Oak (Quercus agrifolia)Applied Microbiology10.3390/applmicrobiol50100245:1(24)Online publication date: 22-Feb-2025
  • (2024)Improved species assignments across the entire Anopheles genus using targeted sequencingFrontiers in Genetics10.3389/fgene.2024.145664415Online publication date: 19-Sep-2024
  • (2024)Analysis of DNA Barcodes Using DNA SubwayDNA Barcoding10.1007/978-1-0716-3581-0_34(551-560)Online publication date: 30-Apr-2024
  • (2022)The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National ForestMicroorganisms10.3390/microorganisms1006121810:6(1218)Online publication date: 14-Jun-2022
  • (2022)Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxiaBioTech10.3390/biotech1101000111:1(1)Online publication date: 14-Jan-2022
  • (2019)Apollo: Democratizing genome annotationPLOS Computational Biology10.1371/journal.pcbi.100679015:2(e1006790)Online publication date: 6-Feb-2019
  • (2018)A course‐based undergraduate research experience investigating the consequences of nonconserved mutations in lactate dehydrogenaseBiochemistry and Molecular Biology Education10.1002/bmb.2111546:3(285-296)Online publication date: 7-Mar-2018
  • (2017)High-protein paternal diet confers an advantage to sons in sperm competitionBiology Letters10.1098/rsbl.2016.091413:2(20160914)Online publication date: 15-Feb-2017
  • (2016)JBrowse: a dynamic web platform for genome visualization and analysisGenome Biology10.1186/s13059-016-0924-117:1Online publication date: 12-Apr-2016
  • (2015)Finding function in the unknownProceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)10.1109/BIBM.2015.7359834(1098-1099)Online publication date: 9-Nov-2015

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