01-overview.Rmd

```{r, include = FALSE}
ottpal::set_knitr_image_path()
```

# 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](https://anvilproject.org/) cloud computing resource to check data, perform an alignment, and visualize their results.

## 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

## Learning Objectives

Learning objectives for this activity come from the [Genetics Core Competencies](https://genetics-gsa.org/education/genetics-learning-framework/):

- 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