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- Join Policy Restricted
- Created 08 May 2017
Using DNA Subway to Analyze Sequence Relationships
Version 1 published October 18, 2017
This is a 120-minute bioinformatics lab in which students will learn how to use the DNA Subway Blue Line workflow to determine the species of an organism using a DNA sequence.
Incubator Details
Statement from the author (Jason Williams):
Review for accurate science is always welcome. I would like folks who are actively teaching in the undergraduate space to "kick the tires" and see if this is viable as a short, self-contained bioinformatics lesson. It may be useful to add additional formative questions (and answers for faculty). May also be useful to extend some sections (e.g. have students work on NCBI BLAST site). I'd also like to focus on the following goals:
- Review the technical or scientific content of the activity.
- Identify pedagogical strategies for making it more student-centered, inquiry focused, or promoting active learning.
- Having others pilot the lesson and get their feedback on what worked and what didn’t.
Statement from the managing editor (Liz Ryder):
This Learning Resource is a nice introduction to the bioinformatics of barcoding. It includes an introduction to a number of different bioinformatics tools (BLAST, multiple alignment, phylogenetic trees). It addresses a conservation question -- a little different from more biomedical applications that often introduce these tools. It also teaches about cleaning DNA -- showing students the important point that sequence data are not perfect.
I feel the resource is an excellent start, but would benefit from:
- Some small additions and clarifications
- An example to illustrate interpretation of phylogenetic trees a bit more.
- It would be great to have an answer sheet for teachers, and perhaps a separate assessment / quiz.
- A short motivating scenario leading into the lab instructions would be helpful.
I'm sure other group members will have additional suggestions.
Incubator start and end times:
This incubator will run from November 13 through December 18, 2017.
QUBES Liaison: Sam Donovan
Licensing Information
All NIBLSE Incubators are under Creative Commons licensing. The default license for Incubators is the Attribution-ShareAlike 4.0 International license. This license allows for sharing of adaptations of the work, as longs as all adaptations are shared alike. It also allows for commercial use of the work. Learn more at the Creative Commons website.
Authorship Information
During the Learning Resource Incubator process a small group of faculty work on improving and supporting the use of existing bioinformatics lessons. Prior to the start of the incubator, the author addresses their expectations around participant authorship. Below are the author's expectations around contributions and authorship.
- Contributions to the teaching resource:
- I plan to list each of the incubator personnel who actively participate as contributors.
- Authorship of the primary teaching resource:
- I plan to include incubator participants who make a significant intellectual contribution to the primary teaching resource as a co-author.
- Authorship of derivative or customized materials:
- I plan to support others if they are interested in customizing these materials for use in other course contexts or with other student audiences.