CPSC 445/545 - Algorithms for Bioinformatics

[General Info] · [Course Outline] · [Course Calendar] · [Course Projects] · [Grading] · [Assignments] · [Resources]
Latest news (01/21): The CPSC 545 Mini-Workshop (with project presentations) will be held today - details can be found on the workshop web page.

General / Administrative Information

Course number / title: 445 (101) / 545 (101): Algorithms for Bioinformatics

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]

Course Description:

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.

Course Projects (CPSC 545 only)

General Information

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

09/20 sample project descriptions are now available
09/27 students form groups and select project
10/12 students submit project proposal as PDF files via e-mail to Holger. (A sample project proposal is now from here - this is an actual project proposal from last year's CPSC 545.)
11/04 students submit progress report
11/29 students submit final report as PDF file via e-mail to Holger. (A sample project report is now from here - this is an actual project report from last year's CPSC 545.)
01/21 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.

Preparation and Submission of Final Reports

Since we intend to combine the final reports into a proceedings volume for the mini-workshop, they need to be formatted uniformly. Please use LaTeX for preparing your final report and use this
sample text as a template (PDF of the sample text available here). Final reports have to be submitted as PDF files and complete sources via e-mail to hoos@cs.ubc.ca by Thu, 05/01/13, 9:00 PST.

Preparation and Format of Workshop Talks

Each paper will be assigned a 40min slot, at least 10 minutes of which are intended for discussion. An overhead projector as well as an LCD projector will be available in the workshop room. Presenters who want to use the LCD projector need to provide their own laptop.

CPSC 545 Mini-Workshop 2005 "Algorithms for Bioinformatics"


Student evaluation and grading will differ between CPSC 445 and CPSC 545.

CPSC 445 Student Evaluation and Grading:

CPSC 545 Student Evaluation and Grading:

Note: Homework assignments for CPSC 445 will be considerably more extensive than those for CPSC 545.



Lecture notes:
Background reading:

last update 05/01/07, hh