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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 4 has been posted. Due, Monday November 17th. 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...

• Glossary
• Mutation Data Matrices
• Amino acids

 

Resources

Course related

• The Course Web site.
• The Course Google Group.
• Netiquette for the Group mailing list
• Previous Exam_questions
• 2007 course feedback

 

Contents related

• The VMD tutorial
• A Stereo Vision tutorial
• MetaDatabase
• NAR January-2008 Database issue
• NAR July-2008 Web server issue