Schedule
Week 1: Introduction to Computational Biology
- Aug. 27
- Lecture: Introduction to Computational Biology
- In-class discussion: Prior knowledge of computational biology
- Aug. 29
- Lecture: Introduction to R
- Handout: Intro to R, operators, variable assignment, and vectors
- Lab: Initial R exercises
- Laptop poll: Click here
- Week 1 resources
Week 2: Random Numbers and Probability Distributions
- Sept. 03
- Sept. 05
- Week 2 Resources
- Office Hours: 12-3pm on WEDNESDAY, LSB 127A (Come here for help with setting up your laptop if you need it).
- Improved description of PMF and CDF: This will be useful for Thursday, hope this is a better explanation than my first one
- Course laptop survey
Week 3: Simulating Evolution using For Loops
- Sept. 10
- Pre-Lab Quiz
- Lecture: Simulating evolution using for loops
- Handout: For loops
- Coding assignment: Programming Project 1 - Simulating Evolution
- Sept. 12
- Pre-Lab Quiz
- Programming Project 1 Canvas submission page
- Programming Project 1 Rubric
- Week 3 Resources
- Office hours, Monday Sept. 9 12pm-3pm. LSB 127A
Week 4: Game Theory and Conditional Statements
- Sept. 17
- Lecture: Conditionals, custom functions,and game theory
- Worksheet: Conditional statements and functions
- Handout: Coding the Hawk-Dove game
- Sept. 19
- Pre-Lab Quiz
- Lecture: Effective coding strategies
- Coding assignment: Programming Project 2 - Game Theory
- Programming Project 2 Rubric
- Programming Project 2 Canvas Submission Page, due Sept. 26 at 1:30pm
- Week 4 Resources
- Office hours, Monday Sept. 16 12pm-3pm. LSB 127A
Week 5: Tensors and lists
- Sept. 24
- Review day, no materials needed
- Sept. 26
- Lecture: Tensors and lists
- Pre-Lab Quiz
- Handout: Tensors and lists
- Week 5 Resources
- Office hours, Monday Sept. 23 12pm-3pm. LSB 127A
- Coding Quiz 1, due Oct. 1st, 1:30pm
- Practice Quizziz quiz
Week 6: Individual-Based Simulations
- Oct. 1
- Oct. 3
- Handout: Plots
- Week 6 Resources:
- Office hours, Monday Oct. 1st 12pm-3pm. LSB 204
- Coding Quiz 2, due Oct. 8th at 1:30PM
- Programming Project 3 - Individual-Based Simulations
- SeedDispersal.R
Week 7: Midterm Prep and Bootstrapping/Permutations
- Oct. 8
- Lecture: Game Theory Results and Review
- Oct. 10
- Lecture: Permutations and Bootstrapping
- Handout: Permutations and Bootstrapping
- Week 7 Resources
- Office hours, Monday Oct. 7 12pm-2pm. LSB 127A
- Coding Quiz 3, Due Oct. 15th at 1:30pm
Week 8: Midterm
- No class meetings this week
- Week 8 Resources
- Office hours, Monday Oct. 14 12pm-3pm. LSB 127A
- Midterm, due Friday 10/18 at 11:59PM
Week 9: Numerical Optimization
- Back to meeting in person this week
- Oct. 22
- Lecture: Updates and Permutation Practice
- Handout: Permutation-based genetic association test
- Oct. 24
- Pre-Lab Quiz
- Lecture: Numerical Optimization
- Code: GoldenSearch.R
- Data: CountData.txt
- Week 9 Resources
- Office hours, Monday Oct. 21 12pm-3pm. LSB 127A
Week 10: Numerical Optimization cont.
- Oct 29
- Handout 1: Reading data and data frames
- Handout 2: While loops
- Data: CherryTrees.txt
- Oct 31
- Programming Project 4 - Computational statistics exercises
- Programming Project 4 Rubric
- beetleBirths.txt
- Week 10 Resources
- Office hours, Room got scalped, shoot me an email if you have a question instead!
- Course survey
Week 11: Linear models
- Nov 5th
- Lecture: Linear models
- Handout: Linear models in R
- Nov 7th
- Lecture: Penalized regression for feature selection
- Handout: Packages and LASSO regression
- Week 11 Resources
- Office hours, Monday Nov. 4th 12pm-3pm. LSB 127A
- Course survey
Week 12: Genome wide association mapping
- Nov 12th
- Lecture: Genome-wide association mapping
- Programming Project 5, due Nov. 21 1:30PM
- Programming Project 5 Rubric
- Programming Project 5 Data
- Nov 14th
- Week 12 Resources
- Office hours, Monday Nov. 11th 12pm-3pm. LSB 127A
- Programming Project 2 working functions: working_PP2_functions2.R
- Code to run the above functions: RunPP2Contest.R
Week 13: Introduction to bioinformatics
- Nov 19th
- Nov 21st
- Week 13 Resources
- Office hours, Monday Nov. 18th 12pm-3pm. LSB 127A
Week 14: Random Forests
- Week 14 Resources
- We aren’t meeting, but you’ll have a small assignment for the break
- Assignment Canvas page
- Blog post
- StatQuest video
Week 15: Neural Networks