This page presents complete lecture notes for modules 1 and 3, plus a couple of notes for module 2.
Course lectures.
| LEC # |
TOPICS |
| Module 1: Phylogenetic Inference (PI) (Instructor: Prof. Alm) |
| 1 |
Course Overview
Introduction to Phylogenetic Inference; Case Studies; Phylogenetic Trees; Quick Review of Recursion (PDF)
|
| 2 |
Review of UPGMA; Purpose of Phylogenetics; Newick Notation (PDF) |
| 3 |
Phylogenetic Trees: Overview, Possible Trees
Python®: Trees; Data Structure, Parsing Function (PDF)
|
| 4 |
Parsimony; Sankoff Downpass Algorithm (PDF) |
| 5 |
Downpass (cont.); Fitch's Up Pass (PDF) |
| 6 |
Up Pass (cont.) (PDF) |
| 7 |
Parsimony (cont.); Overall Strategy; Maximum Likelihood (ML); Jukes-Cantor; Evolutionary Model (PDF) |
| 8 |
Greedy Algorithm for Trying Trees
Review (PDF)
|
| 9 |
Exam 1
|
| Module 2: Molecular Modeling / Protein Design (MM/PD) (Instructor: Prof. Alm) |
| 10 |
Introduction to The Protein Design Problem. What Makes Proteins Fold? Entropy (PDF) |
| 11 |
MM/PD Lecture 2 |
| 12 |
MM/PD Lecture 3 |
| 13 |
Dihedrals, Build Order (PDF) (Courtesy of Mike Yee. Used with permission.) |
| 14 |
MM/PD Lecture 5 |
| 15 |
MM/PD Lecture 6 |
| 16 |
MM/PD Lecture 7 |
| 17 |
MM/PD Lecture 8 |
| 18 |
Exam 2 |
| Module 3: Discrete Reaction Event Network Modeling (DRENM) (Instructor: Prof. Endy) |
| 19 |
When to Use Computational Methods vs. Exact Methods; The Physics Model Underlying Exact Methods (PDF) |
| 20 |
Physics Model Underlying Exact Methods (cont.); Using Physics Model to Compute When a Reaction will Take Place. (PDF) |
| 21 |
Review of How Physics Model Leads to Computational Method; The Complete Computational Method (Gillespie's Direct and First Reaction Methods) (PDF) |
| 22 |
Difference Between Reaction Rate and Reaction Propensity; Achieving Faster Computation (PDF) |
| 23 |
Next Reaction Method Algorithm; Application to Genetic Memory (Latch) (PDF) |
| 24 |
Review of Key Concepts (PDF 1) (PDF 2) |
| 25 |
Exam 3 |