CMDB Quantitative Biology Lab 2025

Logistics

  • 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-answers repository

Schedule

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

Project Work

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

CMDB Quantitative Biology Bootcamp 2025

Logistics

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

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 - 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!