| title | layout |
|---|---|
CMDB Quantitative Biology 2025 |
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- Syllabus
- Announcements
- This one day a week course builds upon the foundations of Quantitative Biology Bootcamp, reinforcing and expanding upon mathematical and computational methods for analysis of biological data.
- In person, Carnegie Rose Auditorium
- 10:00 - 12:30 pm, Fridays
- Assignments must be submitted within one week to your
qb25-answersrepository
| Week | Date | Instructor | Topic | Due Date | Resubmission Deadline |
|---|---|---|---|---|---|
| 1 | 9/12 | Frederick Tan | Genome Content | 9/19 | 10/3 |
| 2 | 9/19 | Frederick Tan | Sequence Alignment | 9/26 | 10/10 |
| 3 | 9/26 | Rajiv McCoy | Variant Discovery and Genotyping | 10/10 | 10/24 |
| 4 | 10/3 | Frederick Tan | Project Work + HPC Demo | ||
| 5 | 10/10 | Rajiv McCoy | Linear Regression | 10/20 | 10/31 |
| 6 | 10/17 | Departmental Retreat | |||
| 7 | 10/24 | Mike Sauria | Unsupervised Learning | 10/31 | 11/14 |
| 8 | 10/31 | Rajiv McCoy | Multiple Testing | 11/7 | 11/21 |
| 9 | 11/7 | Rajiv McCoy | Project Work + Bootstrap and Permutation Demo | ||
| 10 | 11/14 | Mike Sauria | Sequence Alignment | 11/21 | 12/5 |
| 11 | 11/21 | Mike Schatz | Genome Assembly | 12/1 | 12/12 |
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See Project Work Guide for more details
| Deadline | Assignment | Reference |
|---|---|---|
| 9/19 | Project Topics | Submission Form |
| 9/22 - 26 | Instructor/TA Feedback | Timeful |
| 10/3 | Proposal | |
| 10/24 | Check-in #1 | |
| 11/7 | Peer Review | Sign Up |
| 11/14 | Check-in #2 | |
| 12/5 | Final Presentation | Shared Drive |
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Prep Work: zero-to-python Software Carpentry
- Syllabus
- Four day intensive bootcamp to introduce students to fundamentals in quantitative and computational biology
- NO other classes, meetings, lab work, lab meetings, etc.
- In person, Carnegie Rose Auditorium
- Please arrive by 8:45am ET
- Lunch and an afternoon snack will be provided
All times in ET
Resources for each day (links for assignment, any relevant recordings or slides, etc.) will be linked in the schedule below
| Time | Tuesday | Wednesday | Thursday | Friday |
|---|---|---|---|---|
| 9:00 - 10:00 | Welcome | Python file IO | Git Setup | R - base |
| 10:00 - 11:00 | Laptop orientation | Python dictionaries | Git Practice | R - tidyverse |
| 11:00 - 12:00 | Python datatypes & functions | Assignment | Catch Up | Assignment |
| 12:00 - 1:00 | Lunch | Lunch | Lunch | Lunch |
| 1:00 - 2:00 | Python conditionals, strings, & lists | Assignment cont. | Mini project | Assigment cont. |
| 2:00 - 3:00 | Python loops | Unix | Mini project cont. | R - ggplot2 |
| 3:00 - 4:00 | Assignment | Python scripts | Small group review | Assignment |
| 4:00 - 5:00 | Assignment cont. | Assignment | Small group review | Finished! |
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