Bioinformatics Main Page

BCH441 - Bioinformatics

Welcome to the BCH441 Course Wiki.

These wiki pages are provided to coordinate information, activities and projects in the introductory bioinformatics course taught by Boris Steipe at the University of Toronto. If you are not one of my students, you can still browse this site, however only users with a login account can edit or contribute or edit material. If you are here because you are interested in general aspects of bioinformatics or computational biology, you may want to review the Wikipedia article on bioinformatics, or visit Wikiomics. Contact boris.steipe(at)utoronto.ca with any questions you may have.

The Course

BCH441H1F is the undergraduate course code.
BCH1441H1F is the cross-listed course code for graduate students.

Organization

Dates

The course will be next held in the Fall Term - September to December 2012.

Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00

Tutorial sessions: Mondays, 12:00 to 13:00 for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.

Location

MSB 2173 (Medical Sciences Building)

General

See the Course Web page for general information.

We are recommending Understanding Bioinformatics, Zvelebil & Baum, Garland 2008 as a background textbook for the course. (buy used at AbeBooks)

This is an electronic submission only course; but if you must print material, you might consider printing double-sided. Learn how, at the Print-Double-Sided Student Initiative.

Grading and Activities

Activity	Weight (Undergraduates)	Weight (Graduates)
5 Assignments	15 marks (5 x 3)	10 marks (5 x 2)
5 In-class quizzes	35 marks (5 x 7)	25 marks (5 x 5)
Open project	7 marks	5 marks
"Classroom" participation	3 marks	3 marks
Graduate project		17 marks
Final exam	40 marks	40 marks
Total	100 marks	100 marks

Activity	Weight (Undergraduates)	Weight (Graduates)
9 In-class quizzes	35 marks (9 x 6)	25 marks (9 x 5)
Open project	18 marks	18 marks
"Classroom" participation	8 marks	8 marks
Graduate project		9 marks
Final exam	20 marks	20 marks
Total	100 marks	100 marks

A note on marking

It is not my policy to adjust marks towards a target mean and variance (i.e. there will be no "belling" of grades). I feel strongly that such "normalization" detracts from a collaborative and mutually supportive learning environment. If your classmate gets a great mark because you helped him with a difficult concept, this should never have the effect that it brings down your mark through class average adjustments. Collaborate as much as possible, it is a great way to learn. However I may adjust marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.

Assignments

Assignment 5 has been posted.
Due Monday, Dec. 5.

Temporary links for material

Lecture slides 2012

None yet.

Lecture slides 2011

• 01 - Introduction to the course (pdf, 6.1 MB)
• 02 - Sequence Data (pdf, 4.6 MB)
• 03 - Structure Data (pdf, 13.6 MB)
• 04 - Sequence Analysis I (pdf, 8.6 MB)
• 05 - Sequence Analysis II (pdf, 3.1 MB)
• 06 - Interpreting Protein Structure (pdf, 6.6 MB)
• 07 - Structural Domains (pdf, 5.8 MB)
• 08 - Genome Sequencing (pdf, 1.4 MB)
• 09 - Genome Annotation (pdf, 4.2 MB)
• 10 - Homology I: Principles (pdf, 2.6 MB)
• 11 - Homology II: Optimal Sequence Alignment (pdf, 2.6 MB)
• 12 - Homology III: BLAST (pdf, 2.6 MB)
• 13 - Homology IV: Multiple Sequence Alignment (pdf, 4.3 MB)
• 14 - Predicting Protein Structure I: Homology Modeling (pdf, 2.3 MB)
• 15 - Phylogenetic Analysis I (pdf, 3.3 MB)
• 16 - Phylogenetic Analysis II (pdf, 1.0 MB)
• 17 - Comparative Genomics
• 18 - Computational Systems Biology
• 19 - Statistics and Exploratory Data Analysis (pdf, 3.4 MB)
• 20 - Structure Prediction II: ab initio Prediction (pdf, 10.0 MB)
• 22 - Outlook: Computational Systems Biology (pdf, 2.4 MB)

A selection of Lecture recordings of the 2011 course is available.

Add this material

• Quantitative evolution: signals of recent change and selective pressure

 

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