DNA Subway is an educational bioinformatics platform developed by CyVerse (formerly iPlant Collaborative - NSF #DBI–0735191). Subway bundles research-grade bioinformatics tools, high-performance computing, and databases into web-based, classroom-friendly workflows. “Riding” DNA Subway lines, students can predict and annotate genes in up to 150kb of DNA (Red Line), identify homologs in sequenced genomes (Yellow Line), identify species using DNA barcodes and phylogenetic trees (Blue Line), and examine RNA-Seq datasets for differential transcript abundance (Green Line).
The American Association for the Advancement of Science and other research and science policy groups have reached similar conclusions about reforming undergraduate Science, Technology and Engineering, and Math (STEM) education: 1) Focus on the first two years of college education is critical to recruiting and retaining STEM majors. 2) Foster conceptual understanding, higher level thinking, and practice of STEM rather than memorization of terms, facts, and techniques. 3) Adopt inquiry and student-centered approaches that begin with students’ own questions. 4) Increase opportunities for interdisciplinary and collaborative work. Subway promotes these principles by combining bioinformatics with wet-lab ‘hooks,’ offering educators a paths to using student-generated data in course-based research experiences (CURES).
Since 2010, Subway has supported more than 90,000 student projects, and longitudinal data documents 19,418 student exposures collected from undergraduate faculty trained at CyVerse ‘Genomics and Education’ and NSF Advanced Technological Education workshops. Student using Subway’s streamlined tools (e.g. ‘Red Line’ genome browsers) demonstrate increased confidence when using these tools in the same contexts as researchers (e.g. through online databases such as UCSC Browser). At the secondary level, high school students participating in research projects using Subway demonstrate comparable level of gains on attitudinal and behavioral measures to the aggregate results of undergraduate students assessed using the Survey of Undergraduate Research Experience (SURE).
Examples from The Urban Barcode Project (http://www.urbanbarcodeproject.org) and RNA-Seq for the Next Generation project (http://www.rnaseqforthenextgeneration.org) highlight how products of student research can be exported and utilized in follow-up experiments, including direct publication of sequence data to NCBI GenBank. DNA Subway is freely accessible at dnasubway.org.