This Incubator is now Completed, but please feel free to look around. You can view the Publication version in the NIBLSE Learning Resource Collection. If you are interested in revising or extending these materials, please contact NIBLSE.
This resource involves downloading RNAseq data sets from NCBI SRA and using Galaxy tools to identify differentially expressed genes (in this case Arabidopsis roots +/- nematode infection). Students are introduced to all major computational steps in RNAseq data analysis, including the concept of computational pipelines/workflows.
Statement from the author (Matt Escobar):
The author identified the following as the most appropriate steps to focus on during the Incubator:
- Review the technical or scientific content of the activity.
- Identify pedagogical strategies for making it more student-centered, inquiry focused, or promoting active learning.
Right now there isn't much flexibility in the exercise to explore program options or alternative tools. It's very detailed and step by step. This is good because the students are able to follow it as a tutorial and I walk around the room to help, but I would like for the students to get a better idea of how changing programs or settings can change results.
Statement from the managing editor (Bill Morgan):
Following discussion, the managing editor and submitting author prioritized the following desired outcomes for the incubator:
- Review of the technical/scientific content by an RNA-seq expert. This includes a general review of the workflow procedure, suggestions to explain outputs to students, and recommendations for other data sets to include as alternatives.
- Develop supporting documentation to allow adaptation by other instructors. In addition to teaching and pedagogical notes, this might include additional background information to use the learning resource in multiple advanced biology courses.
- Consider the proper balance between a highly directed tutorial with detailed instructions and a more open-ended activity that requires students to select among available options.
Incubator start and end times:
This Incubator will run from mid-July to late August with biweekly meetings.
QUBES Liaison: Sam Donovan
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.