Intro to DNA Subway
The Basics of DNA Subway
DNA Subway is an educational bioinformatics platform developed by CyVerse. It bundles research-grade bioinformatics tools, high-performance computing, and databases into workflows with an easy-to-use interface. “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).
By combining bioinformatics with a wet-lab ‘hook,’ we are able to offer educators a path to supporting a variety of inquiry-based learning experiences using student-generated data. Products of student research can be exported, published, and utilized in follow-up experiments. Examples from The Urban Barcode project http://www.urbanbarcodeproject.org/ and RNA-Seq for the Next Generation project http://www.rnaseqforthenextgeneration.org/ highlight how DNA Subway can be leveraged for distributed science and course-based research experiences. DNA
- Navigate to the DNA Subway homepage http://dnasubway.iplantcollaborative.org/
- Enter your username and password and click 'Log In' OR click 'Enter As Guest' to use Subway without credentials
- You will arrive on a 'My Projects' page that contains a list of existing projects, and previous projects (registered users only).
Key DNA Subway Features
'Research Grade' software
DNA Subway uses the same open-source bioinformatics tools used by researchers. See a complete list of the tools provided in the Subway pipelines: http://dnasubway.iplantcollaborative.org/about/resources.html
Cyberinfrastructure for Analysis and Data Storage
DNA Subway is part of the CyVerse cyberinfrastructure. Users don't have to pay to store data or conduct analyses - even for large projects like RNA-Seq which require large data storage and are analyzed using high-performance computing.
Registered user and Guest user account types
DNA Subway supports two modes of use
- Registered Users: Registered users have their worked saved, and can return to projects in progress at any time. It is encouraged that each student register for their own account, especially if they will be using Subway for several class periods or over the length of a project.
- Guest Users: Guest users will not have their worked saved beyond a single DNA Subway session. They are also disallowed from using one of the gene predictors (FGenesH) in the genomic annotation pipeline (Red Line).
Tip: To Register: Click on the the 'Register' link on the DNA Subway Homepage or register for a CyVerse account (Register at https://user.cyverse.org/ and then request access at https://user.cyverse.org/dashboard/
Sample Datasets and reference data
All Subway lines accept user data and also have sample data that can be immediately used to create a project.
- Red Line: Genome Annotation - Samples of plant and animal genomes that can be used in annotation projects.
- Yellow Line: TARGeT Search for transposons and other DNA Sequences - Several model plant genomes
- Blue Line: DNA Barcoding and Phylogenetics - Sample sequence from plant, animal, fungal, and bacterial barcoding regions; human mitochondrial DNA sequence
- Green Line: RNA-Seq for differential expression - Sample high-throughput reads from RNA-Seq experiments.
Public and private projects
- DNA Subway projects are private by default, but can be shared by making them public. Public projects are searchable and are a great way to share data or present analysis for grading in a classroom project.