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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

While the server is undergoing disaster recovery, please do not use this Wiki. Data may be arbitrarily outdated.
Contact Boris Steipe for all matters of urgency. September 25. 2011

Organization

Dates

Lectures: Monday and Thursday, 12:00 to 13:00

Tutorial sessions: Mondays, 13:00 to 14:00   for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.

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 a target average for the class ("Belling"). 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 section is currently under construction.

I n t r o d u c t i o n
#	Date	Lecturer	Topic	Handout	Book	Note
1	Mon. Sept 8	Steipe	Organisation and Orientation	Introduction	Ch 1, 2	-
A b s t r a c t i o n s
#	Date	Lecturer	Topic	Handout	Book	Note
2	Thu. Sept 11	Steipe	Sequence abstraction and sequence databases	Sequence data	Ch 3	Assignment 1 to be handed out
3	Mon. Sept 15	Steipe	Protein Structure Data	Structure data	-	-
A n a l y s i s
#	Date	Lecturer	Topic	Handout	Book	Note
3	Thu. Sept 18	Steipe	Sequence properties	Raw lecture PDF	Ch 4.9, 11, 12	-
4	Mon. Sept 22	Steipe	Sequence Analysis and Bioinformatics methods	Raw lecture PDF	-	-
5	Thu. Sept 25.	Steipe	Interpreting protein structure	Raw lecture PDF	-	Assignment 1 due First quiz in class Assignment 2 to be posted
12	Thu. Oct 23.	Steipe	Structural domains	Raw lecture PDF	-	Assignment 3 due
6	Mon. Sept 29	Steipe	Homology I: the principles	Raw lecture PDF	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	Lecture slide PDFs (2.4 MB)	-	-
H o m o l o g y
#	Date	Lecturer	Topic	Handout	Book	Note
9	Thu. Oct 9.	Steipe	Lecture: Homology II: Sequence alignment	Raw lecture PDF		Assignment 2 due Assignment 3 to be posted
10	Thu. Oct 16	Steipe	Lecture: Homology III: Fast sequence database searches	BLAST	Ch. 5	-
11	Mo. Oct 20	Steipe	Homology IV: Multiple sequence alignment	Multiple Sequence Alignment	Ch. 6	Second quiz in class (13:00 tutorial time slot)
18	Thu. Nov 13	Steipe	Homology modeling and structure prediction (Part 1)	Raw lecture PDF	-	-
19	Mon. Nov 17	Steipe	Homology modeling and structure prediction (Part 2)	Raw lecture PDF	-	Assignment 4 due. Fourth quiz in class: 13:00 in tutorial time slot. Assignment 5 to be posted.
P h y l o g e n y
#	Date	Lecturer	Topic	Handout	Book	Note
13	Mon. Oct 27	Steipe	Phylogenetic analysis I	Raw lecture PDF	Ch. 7,8	Third quiz in class, 13:00 in tutorial time-slot
14	Thu. Oct 30	Steipe	Phylogenetic analysis II	Raw lecture PDF	Ch. 7,8	-
15	Mon. Nov 3	Parkinson	Comparative genomics	Lecture slide PDFs (1.6 MB)	Ch. 9.8, 10.8	-
17	Mon. Nov 10	Steipe	Human population genomics	Raw lecture PDF	-	Assignment 4 to be posted
I n t e r a c t i o n s
#	Date	Lecturer	Topic	Handout	Book	Note
20	Thu. Nov 20	Wodak	Gene regulation (Part 1)	Lecture slide PDFs (2.1 MB)	Ch. 15	-
21	Mon. Nov 24	Wodak	Gene regulation (Part 2)	-	-	-
22	Thu. Nov 27	Wodak	Functional annotation	Lecture slide PDFs (10.6 MB)	Appendix A	-
23	Mon. Dec 1	Wodak	Metabolic networks	Lecture slide PDFs (3.1 MB)	Ch. 17.1	Assignment 5 due Fifth quiz in class: 13:00 in tutorial time slot
24	Thu. Dec 4	Parkinson	Computational systems biology	Lecture slide PDFs (3.4 MB)	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
• 2008 course feedback

 

Contents related

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