BIO4ST1 - Bioinformatics
Syllabus (Spring 2023)
Course Description: This course is an introduction to the methods used to analyze large datasets in biology. This course equips students with the mathematical and computing skills necessary to analyze large datasets. No prior experience in biology or computing is assumed. Students will be led and supported to design and implement algorithms for analyzing bioinformatic data in the R language. The datasets used in this class will be drawn from research conducted in the fields of biotechnology, health, and medicine. Students will design a group project that investigates a topic of their own interest and applies the skills they learn to a broader societal, environmental, or ethical issue.
Content covered in this course is relevant to exploring human and viral genomes, CRISPR, and genetic modification of organisms. Students will engage in technical analyses associated with these topics and will also be encouraged to consider the ethical implications of such work, weighing the benefits to society against the risks of interfering with the natural world.
Course Timeline and Notebooks
| Class Meeting | Before Class | During Class | After Class |
|---|---|---|---|
| 1 | Review Syllabus Attempt Software Setup |
Introduction and Software Setup | Homework 1 – Complete Software Setup |
| 2 | Setup a GitHub Account | My First Repo and Commit | Homework 2 – Make a Commit to Your Repository |
| 3 | Starter Notebook (html, qmd) | Tidy Analyses in R (html, qmd) | Homework 3 - Commit Your Tidy Analsis to Your Repository |
| 4 | From Description to Inference | ||
| 5 | Simulation-Based Inference (html, qmd | ||
| 6 | Look at Available Data Sets | Generating Hypotheses | Homework 4 – Generate Hypotheses |
| 7 | Exploratory Analysis And Reporting | Homework 5 – Write Partial Abstract, Introduction, and Exploratory Analysis | |
| 8 | Inference And Reporting | Homework 6 – Test Your Hypotheses and Describe the Results | |
| 9 | GitHub Pages and Publishing | Work on GitHub Pages Page | Homework 7 – Publish Your Report to Your GitHub Page |
| 10 | The Genome and Bioinformatics | ||
| 11 | Accessing Group Repository | Intro to R for Bioinformatics (html, qmd) | |
| 12 | An Introduction to Replication | ||
| 13 | Replication Origin, Part I (html, qmd) | ||
| 14 | Replication Origin, Part II (html, qmd) | Homework 9 – Replication Origin Project Check-In | |
| 15 | Replication Origin, Part III (html, qmd) | ||
| 16 | Replication Origin, Part IV (html, qmd) | Homework 10 – Replication Origin Project Check-In | |
| 17 | Replication Origin, Part V (html, qmd) | ||
| 18 | Finish and Recap Replication Origin Projects | Project I Due | |
| 19+ | Final Projects | Final Projects | Final Projects |