Biochemistry and Molecular Biophysics Graduate Group

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BMB 627 - Computer Programming for Biophysicists and Biochemists

Spring, even-numbered years (1/2 semester, 1/2 credit)

Course Directors: Kim Sharp and Greg Van Duyne

Number of Lectures: 12

Description: An introductory course on programming and algorithms with an emphasis on applications to biophysics; Brief lectures followed by extensive hands on programming

Prerequisites: Familarity with Unix recommended

Course materials: Handouts, examples of programs on electronic medium

Course requirement: Students attend brief introductory lectures on topics, followed by hands on programming

How students are evaluated: Evaluation of programs written for homework and for final project.

Topics:

Introduction to Unix, text editing
Introduction to Python
Elements of programming: Control structures
Elements of programming: Data structures
Elements of programming:
Special cases/end conditions
Elements of programming: I/O
Numerical/computational programming
Handling, parsing of database files
Algorithms: Sampling, random and Monte Carlo
Algorithms: Integration
Algorithms: Optimizations
Algorithms: Geometry operations