Peer Review

DNA Subway

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Overall Rating:

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Overview:: The DNA Subway is a project of the iplantcollaborative in connection with the Dolan DNA Learning Center. The DNA Subway has two lines one is a workflow with a series of programs that can be used to analyze a genomic DNA sequence to identify genes and other genomic features, such as repeats. The final product of this line is an annotated sequence. The second line uses an annotated sequence to find gene families by searching multiple finished genomes, doing multiple sequence alignments, and creating phylogenetic tress of the genes. Thus, a student using this can go through many of the common steps used in genomics to analyze a new DNA sequence.
Type of Material:: This is an interactive site that allows users to upload and save their own projects.
Recommended Uses:: In-class activity, collaborative/team homework
Technical Requirements:: Users must be able to use a web-browser with a Java plugin. An email address is needed to save projects.
Identify Major Learning Goals:: Students will learn to generate DNA sequence annotations, conduct phylogenetic analyses, and analyze Next-Generation Sequencing data.
Target Student Population:: Upper-level undergraduate biology, plant science or genetics courses
Prerequisite Knowledge or Skills:: Students should have a strong familiarity with basic terminology and concepts related to DNA, genetics and so forth (5', 3', promoter regions, etc)

Rating:

Strengths:

The DNA subway provides a deep-dive into genomic analysis, covering a great deal of information and allowing students to apply the material
The content is well organized and follows good pedagogy

Concerns:

Material is not entirely self-contained; most students will need some context and/or a demonstration from faculty in order to use and interpret the tool.

Rating:

Strengths:

This tool would be very easy to integrate into assignments or class activities, as it’s hands-on and provides fast results
The concepts build on one another and allow students to
“Background” section provides an overview of the material needed to understand the tool
Free training is offered to educators

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Concerns:

Navigation is not entirely intuitive. For example, the navigation menu is at the bottom of the tool. In the “background” section, it is easy to miss the “next” button on each page. In some cases there is no easy way to get back “home” other than using your browser’s navigation buttons.
Although you can use the tool as a guest, saving your work requires creating an account and password as well as providing a reasonable amount of information (e.g. first & last name, email, city, state and institution)
Information is difficult to understand without a background in genetics or biology

Other Issues and Comments:: iPlant code is released using this standard BSD license, which is an Open Source Initiative-approved license. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of the iPlant Collaborative, BIO5, The University of Arizona, Cold Spring Harbor Laboratory, The University of Texas at Austin, nor the names of other contributors may be used to endorse or promote products derived from this software without specific prior written permission.
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