CPSC 536A - Bioinformatics Course, Spring 2002

[General Info] · [Course Outline] · [Course Projects] · [Grading] · [Assignments] · [Resources]

General / Administrative Information

Course number / title: 536A (201): Topics in Algorithms and Complexity - Bioinformatics
Catalogue number: 21053

Time: Mon 9:30-11:00, Wed 9:10-10:40 (changed time slot for Wed!)
Room: CISR 304

Instructors: Anne Condon / Holger Hoos

[Current official information on graduate courses in 2001/02 term 2 can be found here]

Course Description:

Bioinformatics involves the application of computational methods in order to address problems in molecular biology. This course will provide a graduate introduction to algorithms and their applications in bioinformatics. Topics in molecular biology that will motivate the algorithmic content of the course include: sequence alignment, phylogenetic tree reconstruction, prediction of RNA and protein structure, gene finding and sequence annotation, gene expression, and biomolecular computing.

Graduate students in computer science, or from the biological sciences who already have background in programming and algorithm design, are welcome to take this course. Because the course involves a significant project, a solid background in computer programming. Students should also be comfortable with mathematical reasoning, such as can be obtained in a college level course in Mathematics or Statistics. Background in discrete mathematics or in probability theory is especially relevant to the course content.

Class assignments will familiarize students with biological data and tools for understanding this data and will help students gain a solid understanding of principles for design and analysis of algorithms. Some assignments will be involve use and extension of software tools, and others will involve written studies of algorithms and their analysis. Class projects will bring together students with different backgrounds to apply ideas from the course to a problem in molecular biology.

Preliminary Course Outline

Module 1: Introduction and Basics (hh; 1.5wk)

Module 2: Sequence Alignment (hh; 1.5wk)

Resources: [BSA:2]

Module 3: Phylogenetic Trees (ac/hh; 1.5wk)

Module 4: RNA and Protein Structure (ac+hh; 1.5wk)

Module 5: Gene Finding and Motif Discovery (ac; 2wk)

Module 6: Gene Expression Analysis and Regulatory Networks (hh; 1.5wk)

Module 7: Biomolecular Computing (ac; 1.5wk)

Other Topics (not to be covered this time):

Algorithms / approaches to be covered:

Course Projects

Students are expected to select and complete a course project according to the following timetable:

01/15 sample project descriptions are now available
01/22 students form groups and select project
02/04 students submit project proposal
03/04 students submit progress report
04/02 students submit final report
04/17, 10:00-16:00 CPSC53A Bioinformatics Mini-workshop 2002 (project presentations)

Students should work in groups of two or three, preferably combining different background and expertise in each team. Each project team must have at least one, preferably two CS graduate student members. The project proposals and reports will be reviewed and evaluatated according to standard criteria for research proposals / research papers.

Since we intend to combine the final reports into a proceedings volume for the mini-workshop, they need to be formatted uniformly. Please follow the layout and formatting of this sample text as closely as possible. We recommend to use LaTeX for preparing the final document (in which case you can use the source of the sample text as a template for your report). Final reports should be submitted as PostScript or PDF files via e-mail to hoos@cs.ubc.ca.


Final grades will be determined from the following components:


01/07 - due 01/14 Reading assignment: Douglas Hofstadter, The Genetic Code: Arbitrary? (available from the Reading Room)
01/16 - due 01/23 Reading assignment: Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis, Chapter 2, Section 2.3 (available from the Reading Room)
01/23 - due 01/30 Reading assignment: Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis, Chapter 6, Section 6.4 (available from the Reading Room)
01/30 - due 02/06 Assignment 1 (covers Modules 1+2)
02/12 - due 02/27 Assignment 2 (covers Module 3)
03/25 - due 04/08 Assignment 3 (covers Module 4+5)



Papers / online articles:

Courses / course materials on the web:

Resource lists on the web

Bioinformatics tools / software / databases

last update 02/01/15, hh