CMDB Quantitative Biology Bootcamp 2023

Logistics

Prep Work:

  1. Part 1
  2. Part 2
  3. Part 3
  • Syllabus
  • Class Notes
  • 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, UTL 398
  • Please arrive by 8:45am ET
  • Lunch and an afternoon snack will be provided

  • Answers to Student Questions

Schedule

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 - 12:00 The Unix Shell Python: numpy and matplotlib Python: While, If, Functions Review and advanced topics
12:00 - 1:00 Lunch Lunch Lunch Lunch
1:00 - 3:00 Python Introduction Git Python: Dictionaries Assignment: the Wright-Fisher Model
3:00 - 3:15 Break Break Break Break
3:15 - 5:00 File Parsing in Python Git and Plotting: RNAseq Data Dictionaries: .gff Files Assignment: the Wright-Fisher Model

CMDB Quantitative Biology Lab 2023

Logistics

  • Syllabus
  • 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, BLC 5015
  • 10:00 - 12:30 pm, Fridays
  • Assignments must be submitted within one week to your qbb2023-answers repository

Schedule

Week Date Instructor Topic Resubmission Deadline
1 9/15 Rajiv McCoy Linear regression |
2 9/22 Mike Schatz Genome assembly |
3 9/29 Dylan Taylor Sequence alignment |
4 10/6 Mike Sauria ChIP-seq |
5 10/13 Rajiv McCoy Variant calling |
- 10/20 No Class Retreat |
6 10/27 Rajiv McCoy GWAS |
7 11/3 Mike Sauria Single-molecule sequencing and DNA modifications 11/27
8 11/10 Mike Sauria 3D Genome |
9 11/17 Rajiv McCoy Bulk RNA-seq 12/8
- 11/24 No class Thanksgiving Break |
10 12/1 Rajiv McCoy Data Visualization |
11 12/8 Mike Sauria Single-cell RNA-seq 12/15