CSE 801: Computational Science for Evolutionary Biologists

Instructors: C. Titus Brown, ctb@msu.edu; Randy Olson, olsonran@msu.edu.

Overview

CSE 801, fall 2013, 3 credits.

Class time: 3-4:30pm EST on Wednesday, from Sep 25th, 2013 to December 4, 2013.

MSU location: 1455A BPS (BEACON classroom).

UW location: Kane hall, Kane 019 (note: starts at noon PST).

This course will run from 9/25/12 - 12/4/12 (on a mixed UW/MSU schedule) and will be offered by videoconference at remote BEACON locations, as part of the BEACON Center collaborations. Please, no sitting in without doing the work.

Prerequisites: graduate standing in the natural sciences and/or engineering, OR permission of instructor. (An override is required to enroll for this course at MSU; 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/.


Course information:

Performing research in 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, evolutionary modeling, 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.

In addition to teleconferenced lectures and discussion, we will be providing classroom lectures via YouTube and e-mail discussion.

The learning objectives for this course include the following:

  • Students will be able to analyze spreadsheet-style data, using the Python programming language in the IPython Notebook
  • Students will implement agent-based models for evolutionary modeling;
  • Students will be able to perform basic short-read sequencing data analysis, including mapping, assembly, and visualization;
  • Students will know how to organize input data, programs, and results for computational reproducibility and data publication;

Pre-course workshops

A mandatory pre-course "zero-entry" workshop will help everyone work through installation and setup issues, as well as cover basic introductory concepts.

At MSU this workshop will take place on Sep 23rd and 25th, from 1-5pm.

At UW, this workshop will take place on the weekend of Sep 28th and 29th, from noon to 5pm.


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