This course focuses on computational algorithms and methods used in the study of the genome including hidden Markov models, coalescent simulations, phylogenetic reconstruction, and models of nucleotide substitution. The prerequisite is MCBI 118 or permission of instructor.
Aims of the course:
Learn key algorithms used in genome analysis.
Gain some experience using and manipulating genomic data.
Instructor. Prof. Eliot Bush, bush at hmc dot edu.
Office hours: Tuesdays 2:30-4:30. I'll also be happy to meet at other times, just email me.
Location and time. Lectures will be Tuesdays and Thursdays 1:15-2:30 pm in Shan 2425.
There will be occasional selected readings which will be linked off the web page.
Homework 50%
Exam 25%
Paper presentation 15%
Participation 10%
Homework will include a mixture of practical problems (often with an evolutionary emphasis), and problems involving the implementation of algorithms. We will be doing this in Python. It will generally be given out on Tuesdays, and be due at 5 pm the following Tuesday.
Homework will be posted on the schedule of the course web page.
Collaboration on homework. Unless otherwise specified, homework problems are individual. You are allowed (and encouraged) to discuss the problem with other students or with me. However your solution must be your own. You are not allowed to use the internet, or other copying of files except those provided by the course material. If in doubt, ask me. All students enrolled in this course are bound by the HMC Honor Code. More information on the HMC Honor Code can be found in the HMC Student Handbook.
Late policy.
You start the course with a "late budget" of 72 hours. These late hours can be used to turn an assignment in up to 24-hours after the deadline. When you turn an assignment in after the deadline, you will automatically be charged from your late budget. These late hours are cumulative over all homework assignments for the course. Late hours cannot be used for the exam or traded to other students.