Hilgert, U., McKay, S., Ghiban, C., Khalfan, M., Micklos, D., Williams, J. (July 2014) DNA Subway: Making genome analysis egalitarian. ACM International Conference Proceeding Series . Association for Computing Machinery, Article number 70. ISBN 978-145032893-7
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. Copyright 2014 ACM.
| Item Type: | Book |
|---|---|
| Additional Information: | Meeting Abstract |
| Uncontrolled Keywords: | Cold spring harbor DNA subway Education Fastx toolkit Green line Iplant api Iplant collaborative Red line Rna seq Rna seq data Undergraduate |
| Subjects: | educational material bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes Publication Type > Meeting Abstract Investigative techniques and equipment > assays > whole genome sequencing |
| CSHL Authors: | |
| Communities: | Dolan DNA Learning Center |
| Depositing User: | Matt Covey |
| Date: | 13 July 2014 |
| Date Deposited: | 22 Aug 2014 21:04 |
| Last Modified: | 06 Feb 2018 16:24 |
| URI: | https://repository.cshl.edu/id/eprint/30719 |
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