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BCH441 - Bioinformatics

Welcome to the BCH441 Course Wiki.

This is our main tool to coordinate information, activities and projects in University of Toronto's bioinformatics course BCH441. If you are not one of our 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

I am in the process of repairing the original course Wiki and many of the pages are still arbitrarily outdated. Please don't use pages other than those that are linked directly from here.
Contact Boris Steipe for all matters of urgency. November 11. 2011

Organization

Dates

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

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

• 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
• 21 - Gene regulation
• 22 - Metabolic Pathways

Lecture recordings

• Thursday, 15. September 2011: Lecture 02 (Sequence data) (mp4, 16.4 MB)
• Monday, 19. September 2011: Lecture 03 (Sequence data cont.; Structure Data) (mp4, 17.2 MB)
• Thursday, 22. September 2011: Lecture 04 (Structure data cont.; Sequence Analysis I) (mp4, 16.9 MB)
• Monday, 26. September 2011: Lecture 05 Sequence Analysis I cont. & II (mp4, 15.3 MB)
• Thursday, 29. September 2011: Lecture 06 Sequence Analysis II cont. & Analysis of structure (mp4, 15.6 MB)
• Monday, 3. October 2011: Analysis of Structure (cont.) (mp4, 18.3 MB)
• Thursday, 6. October 2011: Lecture 07 Protein Structural Domains (mp4, 16.3 MB)
• Thursday, 13. October 2011: (Parkinson)
• Monday, 17. October 2011: (Parkinson)
• Thursday, 20. October 2011: Lecture 10 Homology I: Principles (mp4, 19.4 MB)

• Monday, 24. October 2011: Lecture 11 Homology II: Optimal Sequence Alignment (mp4, 12.4 MB)
• Thursday, 27. October 2011: Lecture 12 Homology III: BLAST (mp4, 16.8 MB)
• Monday, 31. October 2011: Lecture 13 Homology IV: Multiple Sequence Alignment (mp4, 22.7 MB)
• Thursday, 3. November 2011: Lecture 14 Predicting Protein Structure I: Homology Modeling (mp4, 18.7 MB)
• Thursday, 10. November 2011: Lecture 15 Phylogenetic Analysis I: Principles (mp4, 16.7 MB)
• Monday, 14. November 2011: Lecture 16 Phylogenetic Analysis II (mp4, 18.5 MB)
• Thursday, 17. November 2011: Lecture 17 Comparative Genomics (Parkinson)
• Monday, 21. November 2011: Lecture 18 Computational Systems Biology (Parkinson)
• Thursday, 24. November 2011: Lecture 19 Exploratory Data Analysis (mp4, 20.0 MB)

• Monday, 28. November 2011: Lecture 20 Protein structure prediction II: ab initio (Quiz 4)
• Thursday, 1. December 2011: Lecture 21 Gene Regulation
• Monday, 6. December 2011: Lecture 22 Metabolic Pathways (Quiz 5)
• Virtual Monday, 7. December 2011: Exam review