Chapter 1 Overview and Learning Objectives

There is a growing need for undergraduate students to learn cutting-edge concepts in genomics data science, including performing analysis on the cloud instead of a personal computer. This lesson aims to introduce a mutant detection bioinformatics pipeline based on a publicly available genetic sample of SARS-CoV-2. Students will be introduced to the sequencing revolution, variants, genetic alignments, and essentials of cloud computing prior to the lab activity. During the lesson, students will work hands-on with the point-and-click Galaxy interface on the AnVIL cloud computing resource to check data, perform an alignment, and visualize their results.

1.1 Activity Context

Course Audience

Undergraduate biology majors
Graduate students with less exposure to bioinformatics

Course Prerequisites

Layman understanding of genetics (understanding of DNA, genes, trait inheritance)
Some previous exposure to the central dogma of molecular biology

Class Type

Lab
Computer-based

Class Size

1-50

Lesson Duration

20-30 minute pre-lab lecture
3 hour lab for undergraduate students
1 hour lab for graduate students
Additional short lecture modules

Assessment Type

Short answer questions at each lab stage

1.2 Learning Objectives

Learning objectives for this activity come from the Genetics Core Competencies:

Gather and evaluate experimental evidence, including qualitative and quantitative data
Generate and interpret graphs displaying experimental results
Critique large data sets and use bioinformatics to assess genetics data
Tap into the interdisciplinary nature of science