Abstract Detail

Education and Outreach

Using the Google Cloud Platform and Fungal Genomes to teach Undergraduate-Level Bioinformatics.

Bioinformatics skills are an important component of undergraduate biology and botanical education. Educators seeking to provide marketable skills for students entering the job market or applying for graduate school may especially want to emphasize experience working with genome-scale data in a command line environment. However, many universities, especially primarily undergraduate institutions, do not host substantial compute resources and students may not have reliable personal computers. Even with sufficient compute resources, using whole-genome plant datasets may prove too large a task given the time frame for classes. In this talk I will share a series of tutorials I created for an undergraduate bioinformatics class that were designed specifically for a Linux-based Virtual Machine running on the Google Cloud Platform. All analyses use long-read, whole-genome sequence data from lichens, and the tutorials use data from multiple organisms in the lichen symbiosis. Skills covered included bash, blast, samtools, genome assembly, genome annotation, multiple sequence alignment, and phylogeny building. Both qualitative and quantitative student learning outcomes were substantial at the end of the course. All of the tutorials, both for initial set-up of the class for the instructor and activities for the students, are available on GitHub.

1 - Eastern Washington University, Biology, 258 Science Building, Cheney, WA, 99004, United States

Keywords:
genomics
Nanopore
Data analysis
Long read sequencing
Quantitative Literacy
Curriculum.

Presentation Type: Oral Paper
Number: EO2004
Abstract ID:389
Candidate for Awards:None