Topics in Computational Biology and Genomics

{MCB, PMB, BioE}{c146, c246}

University of California, Berkeley Spring 2005

“Instruction and discussion of topics in genomics and computational biology. Working from evolutionary concepts, the course will cover principles and application of molecular sequence comparison, genome comparison & functional annotation, and phylogenetic analysis.”

4 Units

Instructors.

Steven E. Brenner
Assistant Professor, Plant & Microbial Biology
Affiliated Assistant Professor, Molecular & Cell Biology, Bioengineering
Faculty Scientist, Lawrence Berkeley National Laboratory

Michael B. Eisen
Staff Scientist, Lawrence Berkeley National Laboratory
Assistant Adjunct Professor, Molecular & Cell Biology

Both may be reached by email to profs@c246.lbl.gov

Teaching assistant.

Liana Lareau lfl@compbio.berkeley.edu

Class meetings.

Tuesday and Thursday, 11:00-12:30 in 241 Cory.
Weekly discussion section: Friday 10:00-12:00, 102 Wurster.
Attendance is required.

Prerequisites.

Bioengineering 142, Computer Science 61B, or equivalent ability to write programs in Java, Perl, C, or C++; Molecular and Cell Biology 100, 102, or equivalent; or consent of instructor.

Core specialization (Bioengineering).

B (Bioinformatics and Genomics) and D (Computational Bioengineering). It also fulfills biological content.

Core requirement (Molecular and Cell Biology).

This course can fulfill a core course requirement for the graduate program in G&D in the Department of Molecular and Cell Biology by petition.

Textbook.

Durbin R., Eddy S., Krogh A., Mitchison G. Biological Sequence Analysis. Cambridge: Cambridge UP, 1998.

Literature articles found on the course website: http://c246.lbl.gov

Assigned readings must be completed before the class for which they are assigned.

Optional Additional References.

These books provide additional introductory references to the core topics that will be discussed in the course. Copies will be placed on reserve in the Biosciences Library.

Lesk, A.M. Introduction to Bioinformatics. Oxford: Oxford UP, 2002.

Hall, B.G. Phylogenetic Trees Made Easy. Sinauer Associates, 2001.

Koonin E.V., Galperin M.Y. Sequence – Evolution – Function: Computational Approaches in Comparative Genomics. Kluwer Academic Publishers, 2002.

Sebutal J.C., Meidanis J. Introduction to Computational Molecular Biology. Brooks/Cole Pub Co, 1997.

Grading.

25% homework
20% midterm exam
20% project
25% final exam (+ resurrection from midterm exam)
10% class participation

Membership.

The six different “versions” of the class. The versions listed in different departments are identical. You may sign up for any version.

The undergraduate c146 & graduate c246 versions have the same lectures. However, for the graduate version, students will be required to do additional questions on homework problem-sets and to prepare a paper presentation for the class section.

Auditors are welcome if space allows. Auditors are expected to participate fully in the class

Homework.

Homework will typically be assigned in class on Tuesdays, and it will be due by email to by 5pm the following Monday. Homework should be submitted electronically to the GSI and should be in plaintext, Word or PDF. Identical paper copies must be turned in at the beginning of class on Tuesday. Where verbal responses are required, they must be in cogent standard written English.

Oral discussion of the class and homework is encouraged. However, all homework questions must be answered in writing alone and must be fully understood. You must also list all the people with whom you discussed the question.

Homework received between 5pm Monday and 11am Tuesday will be penalized by 10 percent. After that, an additional 10 percent will be deducted for each day late, and no credit will be given for problems that have been discussed in class.

The lowest scoring homework will not be included in your grade calculation.

Computer access.

Programs may be written on any computer in Perl, C, C++, or Java.

Class notes.

For lectures given with PowerPoint, the instructor’s presentation will be placed on the course website following class.

This class will use the scribe system. Failure to adhere to the following requirements will impact the student’s class participation grade. One student (“scribe”) will be designated to take notes each week, while another (“reader”) will review these notes for accuracy and work with the scribe to correct any errors or omissions. The scribe must provide notes to the reader by the following lecture. By the lecture thereafter, the reader must submit the notes by email to the teaching assistant. All notes must be electronic so they may be placed on the website.

Office hours.

Office hours for Steven Brenner will be 5:30-7:00pm on Mondays in Koshland Hall 461East; office hours for Michael Eisen will be by appointment. Any changes in office hours will be announced.

Project.

Pairs (or for exceptionally complex projects, triples) of students will undertake a substantial research project, creating new computational biology methodologies or performing a significant genomic analysis. The final project will be presented at a class poster session and written up as a brief (roughly 3 page) report. Electronic versions of both the poster and report must be submitted, along with supplementary information including figures, references, datasets, and custom software.

Website.

The course website is http://c246.lbl.gov. Consult the page regularly for homework, class notes, and updated information.