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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

Here are two tasks I would like you to get completed before the next class.

1. Please subscribe yourself to the Course Mailing List

2. Please download and install VMD

(follow the links above for more information).

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.

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
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	-	-
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	-	-
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	-	-
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	-	-
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
24	Mon. Dec 1	Wodak	Metabolic networks	-	Ch. 17.1
25	Thu. Dec 4	Parkinson	Computational systems biology	-	Ch. 17

In depth...

• Glossary
• Mutation Data Matrices

 

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

• A Stereo Vision tutorial
• MetaDatabase
• NAR January-2007 Database issue
• NAR July-2007 Web server issue