This page presents complete lecture notes for modules 1 and 3, plus a couple of notes for module 2.
| 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 |
