To facilitate communication, deadlines and point allocations for the assignments associated with this course are provided in Table 1.1. Please see here for more information on each assignment. All assignments should be submitted on Google Drive.
| Assignment | Points | Date | Time |
|---|---|---|---|
| Mini-Report 1 | 25 | 02/02/24 | 5 PM MT |
| Mini-Report 2 | 25 | 02/21/24 | 5 PM MT |
| Mini-Report 3 | 50 | 03/29/24 | 5 PM MT |
| Group Lab presentation | 50 | 04/26/24 | 9 AM MT |
| Group Lab report | 150 | 04/26/24 | 5 PM MT |
The tentative timetable for this course is available in Table 2.1. The instructor wants to warn students that he might adjust the timetable to accommodate any needs. However, in case of changes, the instructor will make sure to contact enrolled students to keep them posted.
| WeekID | Date | Weekday | Topic | Homework/Deadlines | |
|---|---|---|---|---|---|
| 1 | 2024-01-10 | Wednesday | CANCELLED (snow day) | ||
| 1 | 2024-01-12 | Friday | CANCELLED (snow day) Syllabus / Chapter 1 |
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| 2 | 2024-01-17 | Wednesday | ON ZOOM Chapter 1 | ||
| 2 | 2024-01-19 | Friday | ON ZOOM Chapter 2 / Mini-Report 1 | ||
| 3 | 2024-01-24 | Wednesday | Chapter 2 / Mini-Report 1 | Review material from Chapter 2 and watch video on Sanger sequencing | |
| 3 | 2024-01-26 | Friday | Mini-Report 1 / Journal Club: Pub. #1 | Read the Giant panda publication for Journal Club (on Google Drive) using the following resources: How to read a scientific paper and How to (seriously) read a scientific paper | |
| 4 | 2024-01-31 | Wednesday | Chapter 3 | ||
| 4 | 2024-02-02 | Friday | Chapter 3 / Mini-Report 2 | Turn-in Mini-Report 1 (by 5PM MT) | |
| 5 | 2024-02-07 | Wednesday | Mini-Report 2 / Mini-Report 3 - Introduction |
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| 5 | 2024-02-09 | Friday | Mini-Report 3 - PART1 |
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| 6 | 2024-02-14 | Wednesday | Mini-Report 3 - PART 2 |
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| 6 | 2024-02-16 | Friday | Mini-Report 3 - PARTS 2 | TBD | |
| 7 | 2024-02-21 | Wednesday | Mini-Report 3 - PARTS 2-3 |
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| 7 | 2024-02-23 | Friday | Mini-Report 3 - PART3 | TBD | |
| 8 | 2024-02-28 | Wednesday | Mini-Report 3 - PART3 | Do the following tasks associated with Mini Report 3 - Part 3: 1. Complete MSA analysis in MEGA; 2. Install the ape R package (see section 4.13.7.1); 3. Download RAxML data from Google Drive (DNA_barcoding > 04_Data_analyses > Phylogenetic_analyses > RAxML_analysis) | |
| 8 | 2024-03-01 | Friday | Mini-Report 3 - Work on Reports | Produce Figures for Mini-Report 3 as shown in section 4.13.7.3 | |
| 9 | 2024-03-06 | Wednesday | Mini-Report 3 - Wrap-up and Q&A; Group accounts & Introduction to Linux OS |
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| 9 | 2024-03-08 | Friday | Chapter 4 - Introduction and Chapter 4 - PART 1 | Install FileZilla | |
| 10 | 2024-03-13 | Wednesday | Chapter 4 - PART 1 |
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| 10 | 2024-03-15 | Friday | Chapter 4 - PART 1: Step 4 - What’s “in” the reads | Complete bioinformatic analyses all the way to the end of section 6.8.7.3.5 | |
| 12 | 2024-03-27 | Wednesday | Chapter 4 - PART 1: Complete step 4 and work on step 5 | ||
| 12 | 2024-03-29 | Friday | Chapter 4 - PARTS 1-2: Complete PART 1 - step 5 and run de novo genome assembly analysis (PART 2) | Challenge & Turn-in Mini-Report 3 (by 5PM MT) | |
| 13 | 2024-04-03 | Wednesday | Chapter 4 - PARTS 2-3 - Complete PART2 and perform the genome assembly quality analysis described in PART3 | Make sure that your de novo genome assembly analysis is completed | |
| 13 | 2024-04-05 | Friday | Complete Chapter 4 & Introduction to group lab report | Read Melton et al. (2021) | |
| 14 | 2024-04-10 | Wednesday | Mining genome: Modules 1 and 2 | ||
| 14 | 2024-04-12 | Friday | Mining genome: Modules 3 and 4 | ||
| 15 | 2024-04-17 | Wednesday | Mining genome: Group work | ||
| 15 | 2024-04-19 | Friday | Mining genome: Group work | ||
| 16 | 2024-04-24 | Wednesday | Mining genome: Group work | ||
| 16 | 2024-04-26 | Friday | Mining genome - Oral group presentations | Turn-in lab reports (upload on Google Drive by 5PM MT) |