Syllabus

Course Meeting Times

Lectures: 2 sessions / week, 1.5 hours / session

Recitations (Optional): 1 session / week, 1 hour / session

Prerequisites

You will be most effectively prepared to take this subject if you have previously taken the following subjects:

Description

This course focuses on computational and experimental analysis of biological systems across a hierarchy of scales, including genetic, molecular, cellular, and cell population levels. The two central themes of the course are modeling of complex dynamic systems and protein design and engineering. Topics include gene sequence analysis, molecular modeling, metabolic and gene regulation networks, signal transduction pathways and cell populations in tissues. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling.

Grading

ACTIVITIES PERCENTAGES
Exam 1 20
Exam 2 20
Protein Networks Project 20
Protein Design Project 20
Final Exam 20
Problem Sets 0

Problem sets are not turned in or graded, although problems sets and answer keys from previous years are provided for your reference. Optional study problems are posted for each section. We strongly encourage the completion of study problems, as they provide a direct metric of your understanding of the material in the course and also serve as practice problems for the exams.

We adhere to the Institute guidelines to determine final grades, and use the full range of grades, from "A" to "F".

If you have questions about problems that you got wrong on the exams or design projects, or if you think you have been graded incorrectly, you are welcome to discuss your questions with any member of the staff. However, if you have concerns about your overall grade for the course, you must speak to either Professor Fraenkel or Professor White. The teaching assistants are not authorized to discuss projected or final course grades.

Software

MATLAB® is used in the Modeling of Cellular Systems and Protein Networks Project sections of the course; Python, PyMOL and PyRosetta are used in the Modeling and Manipulating Biomolecular Interactions and Protein Design Project sections. If you are a student or teacher, you may be able to register for an educational-use-only PyMOL license.