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Computation for Biological Engineers >> Content Detail



Lecture Notes



Lecture Notes

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)

2Review of UPGMA; Purpose of Phylogenetics; Newick Notation (PDF)
3

Phylogenetic Trees: Overview, Possible Trees

Python®: Trees; Data Structure, Parsing Function (PDF)

4Parsimony; Sankoff Downpass Algorithm (PDF)
5Downpass (cont.); Fitch's Up Pass (PDF)
6Up Pass (cont.) (PDF)
7Parsimony (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)
10Introduction to The Protein Design Problem. What Makes Proteins Fold? Entropy (PDF)
11MM/PD Lecture 2
12MM/PD Lecture 3
13Dihedrals, Build Order (PDF) (Courtesy of Mike Yee. Used with permission.)
14MM/PD Lecture 5
15MM/PD Lecture 6
16MM/PD Lecture 7
17MM/PD Lecture 8
18Exam 2
Module 3: Discrete Reaction Event Network Modeling (DRENM) (Instructor: Prof. Endy)
19When to Use Computational Methods vs. Exact Methods; The Physics Model Underlying Exact Methods (PDF)
20Physics Model Underlying Exact Methods (cont.); Using Physics Model to Compute When a Reaction will Take Place. (PDF)
21Review of How Physics Model Leads to Computational Method; The Complete Computational Method (Gillespie's Direct and First Reaction Methods) (PDF)
22Difference Between Reaction Rate and Reaction Propensity; Achieving Faster Computation (PDF)
23Next Reaction Method Algorithm; Application to Genetic Memory (Latch) (PDF)
24Review of Key Concepts (PDF 1) (PDF 2)
25Exam 3

 








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