BIOEN 488/588
Computational Protein Design
Autumn 2013

Class Time and Place

Lecture: Mondays, 12:30 - 1:50 pm and Wednesdays, 1:30-12:50 pm
Labs: Fridays 11:30-3:30pm (11:30-2:30 or 12:30-3:30)
Location: BIOE N140

Instructor

Valerie Daggett
Office: Foege N310B
Email: daggett@u.washington.edu

Teaching Assistants

Chin Jung Cheng (Jonathan)
Email: chengc2@uw.edu

Labs

Labs will be held weekly in BIOE N140, the Bioengineering Advanced Computer Lab. Weeks 1-5 will be spent working on 5 1-week labs, each of which will help familiarize you with computational biology tools. Each lab will be due at the beginning of lab the following week. Weeks 6-10 will be spent working on a project which will depend on which class the student is enrolled in. Week 10 will be presentations.

Project

488 Students: The final 5 weeks of lab will be a design lab that incorporates the tools from the first set of labs but is more self directed. You will have 5 weeks to complete the project and prepare a final paper in journal format. There will be no presentation, but you are expected to attend your classmates' presentations.

588 Students: The final 5 weeks of lab will be spent working on a project of your design. You come up with the topic, research it and make sure it is feasible. The topic needs to be approved by the instructor. You will have 5 weeks to work on the project and prepare a final paper in journal format and presentation describing your project and the results. During the final week of class you will be spent presenting your findings to your classmates.

Grading

Assignments
4 Lab Progress Reports plus one Final Report
1 Project (488: Paper; 588: Paper and Presentation)
1 Literature Review Paper Presentation

Distribution
Lab Reports: 30%
Project: 50%
Participation: 10%
Literature Review: 10%