Welcome to the central hub for course organization in BIOL 497/597 – Genomics & Bioinformatics. This webpage consolidates all essential information related to assignment deadlines, the weekly schedule, and the typical structure of class meetings.
Here you will find:
This page serves as a single reference point to help you plan your semester, stay on top of coursework, and engage fully with both theoretical and applied aspects of genomics and bioinformatics.
To facilitate communication, deadlines and point allocations for all course assignments are provided in Table 2.1.
For more detailed information on each assignment, please see Assessments and Grading.
All assignments must be submitted via Google Drive.
| Assignment | Points | Date | Time |
|---|---|---|---|
| Mini-Report 1 | 25 | 2026-02-06 | 5 PM MT |
| Mini-Report 2 | 25 | 2026-02-20 | 5 PM MT |
| Mini-Report 3 | 50 | 2026-03-27 | 5 PM MT |
| Group Lab presentation | 50 | 2026-04-29 | 9 AM MT |
| Group Lab report | 150 | 2026-04-29 | 5 PM MT |
💡 Information
The tentative schedule for this course is provided in Table 3.1. Please note that the instructor may adjust our schedule to accommodate the course’s progress and students’ needs. Any changes will be communicated to enrolled students in a timely manner.
| Week | Date | Weekday | Topic | Homework | Completed |
|---|---|---|---|---|---|
| 1 | 2026-01-14 | Wednesday | Review Syllabus and start Chapter 1 | No homework | ✓ |
| 2 | 2026-01-21 | Wednesday | Complete Chapter 1 and start Chapter 2 | Review Syllabus and read giant panda publication using the following resources: How to read a scientific paper and How to (seriously) read a scientific paper | ✓ |
| 3 | 2026-01-28 | Wednesday | Chapters 1, 2 and Mini-Report 1 | Review material from Chapter 1 (up to slide 26) and watch the video on Sanger sequencing | ✓ |
| 4 | 2026-02-04 | Wednesday | Chapter 2 and Mini-Report 3 | Review material from Chapter 2 (up to slide 12) and read Ellestad et al. (2022) | ✓ |
| 5 | 2026-02-11 | Wednesday | Guest lecture and Mini-Report 2 | Work on Mini-Report 2 | ✓ |
| 6 | 2026-02-18 | Wednesday | Chapter 2 (lecture) (starting at slide 33) and Chapter 3 (lecture) and Mini-Report 3 - PART 1 | Study the Learning Outcomes and Structure sections of Mini-Report 3, and familiarize yourself with the content of Part 1. Install FinchTV on your computer. | ✓ |
| 7 | 2026-02-25 | Wednesday | Mini-Report 3 - PARTS 2 and 3 | Complete Mini-Report 3 - PART 1. Install R, RStudio and MEGA on your computer. | ✓ |
| 8 | 2026-03-04 | Wednesday | Complete Mini-Report 3 - PART 3 and work on individual report | Complete Mini-Report 3 - PARTS 2 and 3 (until the end of section 4.11.4) | ✓ |
| 9 | 2026-03-11 | Wednesday | Mini-Report 3 - Group Activity on Data Interpretation and Lab - Group Activity | Complete Mini-Report 3 - PART 3 and read Melton et al. (2021) for Lab group activity | ✓ |
| 11 | 2026-03-25 | Wednesday | Lab - Mining genome: Complete group activity, Remote Computing and Bash Tutorials, and bioinformatics analyses (modules 1 to 4) | Work on Mini-Report 3. If you have a Windows computer, can you please install Putty on your computer prior to class? I provide guidance on installation and how to set the software here (section 5.4). | |
| 12 | 2026-04-01 | Wednesday | Chapter 4 - Introduction and PART 1 and Mining genome: Group work | TBD | |
| 13 | 2026-04-08 | Wednesday | Chapter 4 - PART 1 | TBD | |
| 14 | 2026-04-15 | Wednesday | Chapter 4 - PARTS 2-3 | TBD | |
| 15 | 2026-04-22 | Wednesday | Complete Chapter 4 | TBD | |
| 16 | 2026-04-29 | Wednesday | Mining genome - Oral group presentations | TBD |
The weekly class structure is summarized in Table 4.1.
A typical class meeting is structured as follows:
During the first several weeks of the semester, class time will emphasize lectures and structured group activities to build foundational knowledge and skills. As the semester progresses, the course will gradually transition to primarily computer-based laboratory work, with increased emphasis on independent and applied problem-solving.
| Week | 9:00–9:50 a.m. | 9:50–10:05 a.m. | 10:05–11:45 a.m. | Completed |
|---|---|---|---|---|
| 1 | Syllabus and Chapter 1 (lecture) | BREAK | Chapter 1 - Group activity | ✓ |
| 2 | Chapter 1 (lecture) | BREAK | Chapter 2 - Group activity | ✓ |
| 3 | Chapter 1 (lecture) (starting at slide 27) | BREAK | Chapter 2 - Quiz (40 minutes) – Chapter 2 (lecture) (30 minutes) – Mini-Report 1 (30 minutes) | ✓ |
| 4 | Chapter 2 (lecture) (starting at slide 13) | BREAK | Mini-Report 3 - Group activity (1 hour 20 minutes) – Mini-Report 2 (20 minutes) | ✓ |
| 5 | Guest lecture (Dr Jim Beck – BSU Research Computing) | BREAK | Students work on Mini-Report 2 | ✓ |
| 6 | Chapter 2 (lecture) (starting at slide 33) and Chapter 3 (lecture) | BREAK | Mini-Report 3 - Introduction and Part 1 | ✓ |
| 7 | Mini-Report 3 - Part 2 | BREAK | Mini-Report 3 - Parts 2 and 3 until end of section 4.11.4 | ✓ |
| 8 | Mini-Report 3 - PART 3 focusing on running a Maximum Likelihood phylogenetic analysis and introducing the Newick tree format | BREAK | Mini-Report 3 - PART 3 focusing on building the Vanilla phylogenetic tree and working on individual report | ✓ |
| 9 | Mini-Report 3 - Group Activity on Data Interpretation | BREAK | Lab - Group Activity | ✓ |
| 11 | Lab - Mining genome: Complete group activity and Remote Computing and Bash Tutorials | BREAK | Lab - Mining genome: Bioinformatics analyses (modules 1 to 4) |