Time: Tue+Thu 9:30-11:00, first class: Tue, 04/09/07
Room: FSC 1611 (Forest Sciences Centre)
Instructor: Holger Hoos
TAs: Baharak Rastegari, Sanja Rogic
[Current official information on graduate courses in 2004/05 term 1 can be found here]
Bioinformatics involves the application of computational methods in order to address problems in molecular biology. This course will provide a 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 and senior undergraduate students in computer science, or from the biological sciences who already have a substantial background in programming and algorithm design, are welcome to take CPSC 445/545. Because the course involves a significant project, a solid background in computer programming is required. Background in discrete mathematics or in probability theory, such as can be obtained in a college level course in Mathematics or Statistics, is especially relevant to the course content. Students should also be comfortable with mathematical reasoning. Solid basic knowledge in molcular biology is required or will need to be ackquired during the course.
Note to undergraduate students interested in taking CPSC 445: Due to the interdisciplinary and advanced nature of the material covered, you should expect the course to be very challenging and time-consuming. It will probably involve more work per credit than most other courses you have taken. Also, due to the nature of the course offering (together with 545), enrollment is restricted to a small number of dedicated and exceptionally qualified students.
Class assignments will familiarise 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 involve the 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. Students in CPSC 445, the undergraduate version of the course, will work on smaller projects or project components and get additional homework assignments.
Students are expected to select and complete a course project according to the following timetable:
sample project descriptions are now available
students form groups and select project
students submit project proposal
as PDF files via e-mail to Holger.
(A sample project proposal is now from
- this is an actual project proposal from last
year's CPSC 545.)
students submit progress report
students submit final report
as PDF file via e-mail to Holger.
(A sample project report is now from
- this is an actual project report from last
year's CPSC 545.)
1/2 day mini-workshop (project presentations)
Students should work in groups of two or three, preferably combining different background and expertise in each team. The project proposals and reports will be reviewed and evaluatated according to standard criteria for research proposals / research papers.
CPSC 445 Student Evaluation and Grading:
CPSC 545 Student Evaluation and Grading: