Syllabus for Math 5233, Mathematical Foundations of Bioinformatics

This page will be updated throughout the semester.

Instructor: Marshall Hampton

Office: 172 SCC

Email: mhampton at d.umn.edu (preferred contact method)

Telephone: 726-6329

Office hours: MWF 10-11, Tu 11-1, and by appointment.

Class homepage: http://www.d.umn.edu/~mhampton/m5233s11.html

Lecture/Lab Times and Locations: 3 - 3:50 pm, M, W, F (1/18 - 5/06). On Mondays we will be working in a computer lab (H 470), on Wednesdays and Fridays we will be in Chem 251.

Prerequisites: Any two of the following: Biol 5233, Math 3355, CS 1511, Stat 3611, or equivalents. Please come see me if you have any questions about the preparation required for this course. Since Biol 5233 has not been offered recently, other biology coursework in genetics and biochemistry is acceptable.

Textbook: Bioinformatics and Molecular Evolution, by Paul Higgs and Teresa Attwood. Blackwood Publishing, ISBN-13: 978-1405106832.

Topics: The official course description is "Mathematical, algorithmic, and computational foundations of common tools used in genomics and proteomics. Topics include: sequence alignment algorithms and implementations (Needleman-Wunsch, Smith-Waterman, BLAST, Clustal), scoring matrices (PAM, BLOSUM), statistics of DNA sequences (SNPs, CpG islands, isochores, satellites), and phylogenetic tree methods (UPGMA, parsimony, maximum likelihood). Other topics will be covered as time permits: RNA and protein structure prediction, microarray analysis, post-translational modification prediction, gene regulatory dynamics, and whole-genome sequencing techniques." One thing not mentioned there that I would like to at least briefly cover is hidden Markov models (HMMs). We will be using the programming language Python as our primary computational tool, with the biopython module. All of the software we will be using is free.

Exams: There will be a midterm Wednesday, March 23rd, and a final exam. The final is 4 - 6 pm, Monday, May 9th.

Projects: There will be several projects and presentations for small groups.

Grading: You will be evaluated in a variety of ways: homework/labs, class participation (including worksheets) and presentations, and exams. The labs and class presentations will be the primary factors for determining grades (roughly 70%, each exam about 15%).

Assignments and labs: Most of the assignments will be either readings or group lab assignments. Labs will mostly be done using the computational platform Sage. Sage can be accessed through a browser at either https://rudolph.d.umn.edu:8000/ or https://rigel.d.umn.edu:8000/. You can access that off campus if you are on a VPN connection (see this for how to get on a VPN).

• The first lab will be done individually, and is due January 31st. Lab links: rudolph and rigel. (You need to make an account on the server to edit this copy.)
• Reading assignment: read the first two chapters of the textbook before the lab on the 24th of January. The main goal is that you understand the basic biological background in those chapters. We will not cover sections 2.5 and 2.6 from Chapter 2.
• Reading assignment: read chapter 4 of the textbook by February 2nd.
• The second lab will be done in groups, and is due February 14th. Lab links: rudolph and rigel.
• The third lab will be done in groups, and is due as a class presentation on Wednesday, February 23rd. Lab links: rudolph and rigel.
• Reading assignment: read chapter 6 of the textbook by February 21st.
• Optional, recommended reading: Sean Eddy's primer on dynamic programming (Pubmed ID 15229554).
• Optional, recommended reading: S.R. Eddy's primer on BLOSUM matrices.
• The fourth lab is due Friday, March 11th. Lab links: rudolph and rigel.
• The fifth lab will be done individually, and is due Monday, March 11th. Lab links: rudolph and rigel.
• The sixth lab is on the Altschul-Karlin Blast statistics, and is due Friday, April 8th. Lab links: rudolph and rigel.
• Assigned reading: Chapter 7 in our text (alignment scores and statistics).
• Dynamic programming problem from Project Euler. Write a program to find the answer. Extra credit but very highly recommended - if you can do this, you will understand dynamic programming much better.
• Assigned reading: Understanding Evolutionary Trees by Ryan Gregory. There's a more informal blog summary which provides a good summary.
• Assigned reading: Chapter 8 in our text (phylogenetic methods).
• The seventh lab is on computing phylogenies, in particular mammalian phylogenies. It is due Friday, April 15th. Lab links: rudolph and rigel.
• The eighth lab is on finding patterns in proteins and DNA. It is due Friday, May 6th. Lab links: rudolph and rigel.
• Practice final exam.

Student Conduct Code: see the full description at http://www.d.umn.edu/assl/conduct/code/.

Policy statement: The University of Minnesota is committed to the policy that all persons shall have equal access to its programs, facilities, and employment without regard to race, religion, color, sex, national origin, handicap, age, veteran status, or sexual orientation.

Disabilities: An individual who has a disability, either permanent or temporary, which might affect his/her ability to perform in this class should contact the instructor as soon as possible so that he can adapt methods, materials and/or tests as needed to provide for equitable participation.