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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 3 has been posted. Due, Monday October 27th. Enjoy!

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 Introduction Ch 1, 2


The objects of bioinformatics
# Date Lecturer Topic Handout Book
1 Thu. Sept 11 Steipe Sequence abstraction and sequence databases Sequence data Ch 3
Assignment 1 handed out
2 Mon. Sept 15 Steipe Protein Structure Data Structure data -
3 Thu. Sept 18 Steipe Sequence properties - Ch 4.9, 11, 12



Analysis based on properties
# Date Lecturer Topic Handout Book
4 Mon. Sept 22 Steipe Sequence Analysis - -
5 Thu. Sept 25. Assignment 1 due
First quiz in class
Steipe Lecture: Interpreting protein structure
 - -
Assignment 2 handed out
6 Mon. Sept 29 Steipe Homology I: the principles - Ch. 14
7 Thu. Oct 2 Parkinson Genome sequencing, genome browsers Lecture slide PDFs (1.8 MB) 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. Assignment 2 due
Steipe Lecture: Homology II: Sequence alignment
 - -
Assignment 3 handed out
10 Thu. Oct 16 Steipe Lecture: Homology III: Fast sequence database searches BLAST Ch. 4
11 Mo. Oct 20 Steipe Homology IV: Multiple sequence alignment Multiple Sequence Alignment Ch. 5
Second quiz in class (13:00 tutorial time slot)
Steipe - Ch 6
12 Thu. Oct 23. Assignment 3 due
Steipe Lecture: Structural domains
 - -



Analysis based on conservation
# Date Lecture
13 Mon. Oct 27 (Steipe) Phylogenetic analysis I (Book: Ch. 7,8)

Third quiz in class, 13:00 in tutorial time-slot

14 Thu. Oct 30 (Steipe) Phylogenetic analysis II (Book: Ch. 7,8)
15 Mon. Nov 3 (Parkinson) Comparative genomics (Book: Ch. Ch. 9.8, 10.8)
16 Thu. Nov 6 (Steipe) Quiz pickup, Human population genomics (Part 1)
17 Mon. Nov 10 (Steipe) Human population genomics (Part 2)

Assignment 4 to be posted.

18 Thu. Nov 13 (Steipe) Homology modeling and structure prediction (Part 1)
18 Mon. Nov 17 (Steipe) Homology modeling and structure prediction (Part 2)

Assignment 4 due.

Fourth quiz in class: 13:00 in tutorial time slot.

Assignment 5 to be posted.


Analysis based on context
# Date Lecturer Topic Handout Book
20 Thu. Nov 20 Wodak Gene regulation I - Ch. 15
21 Mon. Nov 24 Wodak Gene regulation II - -
22 Thu. Nov 27 Wodak Functional annotation - Appendix A
23 Mon. Dec 1 Wodak Metabolic networks - Ch. 17.1
Assignment 5 due
Fifth quiz in class: 13:00 in tutorial time slot
24 Thu. Dec 4 Parkinson Computational systems biology - Ch. 17



In depth...


 

Resources

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