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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

Assignment 1 has been posted.

You should start with the stereo assignment right away since you have to practice daily. Don't run out of time on the assignments. And remember: there will be a quiz.

Organization

Dates
Monday and Thursday, 12:00 to 13:00
Optional tutorial sessions will be offered as the need arises, most likely on Mondays, probably from 13:00 to 14:00.
First class: Monday, September 8. 2008
Location
MSB 2173 (Medical Sciences Building)

See the Course Web page for general information.

We are recommending Understanding Bioinformatics, Zvelebil & Baum, Garland 2008 as a background textbook for the course. (amazon, UofT Bookstore)

Grading and Activities

Activity Weight
(Undergraduates)		 Weight
(Graduates)
5 Assignments (drop 1) 16 marks (4 x 4) 12 marks (4 x 3)
5 In-class quizzes (drop 1) 32 marks (4 x 8) 20 marks (4 x 5)
Group project 10 marks 6 marks
Participation 2 marks 2 marks
Graduate project   20 marks
Final exam 40 marks 40 marks
Total 100 marks 100 marks

I will not adjust marks towards any target average for the class. If your classmate gets a great mark because you helped him with a difficult concept, this will have no bearing whatsoever on your own mark. Collaborate as much as possible, it is a great way to learn. The only times I will consider adjusting marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.

Lecture Schedule

This is the current schedule for 2008, but changes may be still be made if required.


# Date Lecturer Topic Handout Book
0 Mon. Sept 8 Steipe Organisation and Orientation - -


The objects of bioinformatics
# Date Lecturer Topic Handout Book
1 Thu. Sept 11 Steipe Sequence abstraction and sequence databases - Ch 3
Assignment 1 handed out
2 Mon. Sept 15 Steipe Protein Structure Databases - -
3 Thu. Sept 18 Steipe Bioinformatics methods - -


Analysis based on properties
# Date Lecturer Topic Handout Book
4 Mon. Sept 22 Steipe Sequence properties - Ch 4.9, 11, 12
5 Thu. Sept 25 Steipe Sequence Analysis - -
Assignment 1 due - First quiz in class - Assignment 2 handed out
6 Mon. Sept 29 Steipe Interpreting protein structure - Ch. 14
7 Thu. Oct 2 Parkinson Genome sequencing, genome browsers - Ch. 9, 10
8 Mon. Oct 6 Parkinson Genomes and genome structure - -


Analysis based on homology
# Date Lecturer Topic Handout Book
9 Thu. Oct 9. Steipe Homology I: the principles - -
Assignment 2 due - Second quiz in class - Assignment 3 handed out
10 Thu. Oct 16 Steipe Homology II: Sequence alignment - Ch. 4
11 Mo. Oct 20 Steipe Homology III: Multiple sequence alignment - Ch. 5
12 Mon. Oct 20 Steipe Homology IV: fast sequence database searches - Ch 6
13 Thu. Oct 23 Steipe Structural domains - -
Assignment 3 due - Third quiz in class - Assignment 4 handed out
14 Mon. Oct 27 Steipe Homology modeling and structure prediction - Ch. 13


Analysis based on conservation
# Date Lecturer Topic Handout Book
15 Thu. Oct 30 Steipe Essential concepts of probability and information theory - Appendix A
16 Mon. Nov 3 Parkinson Comparative genomics - Ch. 9.8, 10.8
17 Thu. Nov 6 NN Human population genomics - -
Assignment 4 due - Fourth quiz in class - Assignment 5 handed out
18 Mon. Nov 10 Steipe Phylogenetic analysis I - Ch. 7, 8
19 Thu. Nov 13 Steipe Phylogenetic analysis II - -
20 Mon. Nov 17 Steipe Protein structure motifs - -


Analysis based on context
# Date Lecturer Topic Handout Book
21 Thu. Nov 20 Wodak Gene regulation I - Ch. 15
22 Mon. Nov 24 Wodak Gene regulation II - -
23 Thu. Nov 27 Wodak Functional annotation - Appendix A
Assignment 5 due - Fifth quiz in class
24 Mon. Dec 1 Wodak Metabolic networks - Ch. 17.1
25 Thu. Dec 4 Parkinson Computational systems biology - Ch. 17



In depth...


 

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