Computation for biological engineers

Lectures: 2 sessions / week, 1 hour / session

20.180

There will be short assignments distributed at almost every lecture. We expect that all assignments will be turned in by midnight on the day they are due. You may discuss assignments with your classmates but we expect that you will submit your own work. Late assignments (up to one week late) will be given 1/2 credit; solutions for assignments will be posted at the posted due date. A family crisis or severe illness requiring attention from the infirmary and prohibiting you from all your coursework are acceptable reasons for missing an exam; every effort will be made to accommodate you in these exceptional circumstances. More information regarding academic integrity is available here.

The course is divided into three modules, with exams at the end of each module.

Module 1: Phylogenetic Inference (Lec #1-8)

Module 2: Molecular Modeling / Protein Design (Lec #10-17)

Module 3: Discrete Reaction Event Network Modeling (Lec #19-24)

Each module covers the following general topics:

Course Overview

Introduction to Phylogenetic Inference; Case Studies; Phylogenetic Trees; Quick Review of Recursion

Phylogenetic Trees: Overview, Possible Trees

Python®: Trees; Data Structure, Parsing Function

Greedy Algorithm for Trying Trees

Review

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