CSE 891: Computational Science for Evolutionary Biologists

Instructor: C. Titus Brown, ctb@msu.edu.

TA: Art Covert, covertar@gmail.com.

Overview

CSE 891, fall 2011, section 002. Tu/Th 2:20-3:40pm Eastern time zone. MSU location: 1455A BPS (BEACON classroom). The first class meets Thursday, 9/1.

U Idaho contact: James Foster, foster@uidaho.edu

Class mailing list: cse891@lists.idyll.org

This course will run from 9/1/11 - 12/8/11 (the Michigan State schedule) and will be offered by videoconference at UW Seattle, U Idaho, and UT Austin as part of the BEACON Center collaboration. Please, no auditing.

Two 80 minute lectures (3 credits).

Prerequisites: graduate standing in the natural sciences and/or engineering, OR permission of instructor. (An override is required to enroll for this course; please send the your full name and PID to the instructor.)

This course is offered as part of the BEACON NSF Science and Technology Center, http://beacon.msu.edu/.

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Course information:

Doing biology increasingly requires computational skills and quantitative reasoning abilities. This course will introduce students to computational thinking and practice through an intensive scripting and programming regimen, built around a series of models and data sets from evolutionary and molecular biology. During this course we will introduce the Python programming language, scripting and pipelining, simulations, and data analysis.

This course is intended for graduate students with little or no previous programming experience. There are no prerequisites other than a strong background in at least one of evolution, ecology, genetics, or molecular biology. Enrollment by permission of instructor only.


Objectives: At the end of the course, you will have gained basic programming skills in Python, been exposed to a variety of biology & evolution research that uses computation, and learned how to use iPads to facilitate distance collaboration.

Course structure: Class will consist of group exercises, lectures on various topics, and student presentations. Most weeks, there will be programming homework as well as a paper or two to read, digest, and answer questions on.

Homework and grading: Individual homeworks will be graded on a P/F basis. Homeworks will contribute evenly to 80% of the final grade, i.e. ~20 homeworks each worth 4%. In class presentation (also P/F) will contribute the final 20%. Attendance will count for the same as homework, although absences can be arranged in advance. Group or collaborative work is allowed and encouraged on homework, although students must each hand in homework and are individually responsible for their solutions.

Materials: Most of the course will use materials developed by the instructor, which will be placed on the Web. All such course materials will be made available under a Creative Commons license (CC-BY-SA 2.0), use/reuse OK but attribution required. There is no required textbook, but students may find "Practical Computing for Biologists" (Haddock/Dunn) useful reference material.

Attendance: Attendance is generally required, especially since there will be in-class group projects.

Office hours: There are no set office hours for Dr. Brown. If you make an appointment with him, he is located on MSU campus in BPS 2228(c). His Skype ID is c.titus.brown, and his FaceTime ID is 'titus@idyll.org'.

Art Covert is available 1-4pm Central time, at UT Austin. His Skype ID is covertspartan.

Lab of Genomics, Evolution and Development / ctb@msu.edu