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CMDB Quantitative Biology 2024
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CMDB Quantitative Biology Bootcamp 2024

Logistics

Prep Work:

  1. Part 1
  2. Part 2

R chapters to read before class:

  1. Workflow Basics
  2. Data Visualization
  • 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 - 9:30 Welcome Small Groups Small Groups Small Groups
9:30 - 11:00 Unix, git, R Explore text files w/ Unix Python Indexing, Arrays Linear Regression
11:00 - 12:00 Exercise Exercise Exercise Exercise
12:00 - 1:00 Lunch Lunch Lunch Lunch
1:00 - 1:30 Small Groups Small Groups Small Groups Small Groups
1:30 - 3:00 Plotting w/ ggplot2 Parsing files w/ Python Python Dictionaries Multiple testing, power analysis
3:00 - 3:15 Break Break Break Break
3:15 - 5:15 Exercise Exercise Exercise Exercise

CMDB Quantitative Biology Lab 2024

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, Carnegie Rose Auditorium
  • 10:00 - 12:30 pm, Fridays
  • Assignments must be submitted within one week to your qbb2024-answers repository

Schedule

Week Date Instructor Topic Resubmission Deadline
1 9/13 Mike Schatz Genome assembly 10/4
2 9/20 Mike Sauria Genome Content 10/13
3 9/27 Rajiv McCoy Variant discovery and genotyping 10/20
4 10/4 Frederick Tan Project Work + HPC Demo N/A
5 10/11 Mike Sauria Bulk RNA-seq, PCA, & Clustering 11/01
6 10/18 N/A Departmental Retreat N/A
7 10/25 Rajiv McCoy Bulk RNA-seq, PCA, & Clustering 11/15
8 11/1 Frederick Tan Single cell RNA-seq Analysis with Bioconductor 11/22
9 11/8 Frederick Tan Project Work + Notebooks Demo N/A
10 11/15 Mike Sauria Image processing 12/02
11 11/22 Frederick Tan Image Classification 12/13
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Project Work

Resources

Useful Goodies

Unix and Git

Python

Helpful Documentation (external links)