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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

Follow the link to read feedback from those who have taken this course before you..

• Fall 2007 feedback

I anticipate changes to the grading scheme, the schedule and the assignments. All changes will be posted here as they get decided on. Check back here in August.

The first session for the 2008 term will be held Monday, September 8., 12:00.
It is crucial that you make every effort to attend: we will be discussing access to the course Wiki, the mailing list and how groupwork will be organized.

Organization

Slowly gearing up for the 2008 Fall term ...

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.

Lecture Schedule

(This schedule is for orientation only, changes may be made at any time as the subject matter and the progress of the lecture requires. This is the old schedule for 2007 with the 2007 dates and will be rearranged and changed for 2008.)

Ongoing construction
Don't trust information below.

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

Sequences

2. Sequence Abstraction + Sequence Databases (Boris, Thursday, Sept. 13)
3. Sequence Properties (Boris, Monday, Sept. 17)
4. Sequence Analysis (Boris, Thursday, Sept. 20)
5. Homology I: the principles (Boris, Monday, Sept. 24)
6. Homology II: Sequence Alignment (Boris, Thursday, Sept. 27)
7. Homology III: Multiple Sequence Alignment (Boris, Monday, Oct. 1)
8. Homology IV: Fast Sequence Database searches (Boris, Thursday, Oct. 4)

Structures

9. Protein Structure Databases (Boris, Thursday, Oct. 11)
10. Interpreting Protein Structure (Boris, Monday, Oct. 15*)
11. Structural Domains (Boris, Monday, Oct. 15*)
12. Homology Modeling + Protein Structure Prediction (Boris, Thursday, Oct. 18)

(*) Double lecture (12:00 - 14:00) to make up for Thanksgiving, Oct 8.

Genomes

13. Genome Sequencing (John, Monday, Oct. 22)
14. Genomes (John, Thursday, Oct. 25)
15. Comparative Genomics (John, Monday, Oct. 29)
16. Phylogenetic Analysis (Boris, Thursday, Nov. 1)

Systems

17. Functional Annotation (Shoshana, Monday, Nov. 5)
18. Human Population Genomics (Boris, Nov. 8)
19. Proteomics (Boris, Monday, Nov. 12)
20. Gene regulation I (Shoshana, Thursday, Nov. 15)
21. Gene regulation II (Shoshana, Monday, Nov. 19)
22. Microarray Expression Analysis (Tim Hughes, Thursday, Nov. 22)
23. Pathways and Networks (Gary Bader, Monday, Nov. 26)
24. Interaction Databases (Francis Ouelette, OICR, Thursday, Nov. 29)
25. Metabolic Networks (Shoshana, Monday, Dec. 3)
26. Computational Systems Biology (John, Thursday, Dec. 7)

Assignments

   

First Assignment	Databases and Molecular Models	posted Sept. 13, due Oct. 1.
Second Assignment	Search, Retrieve and Annotate	posted Sept. 24, due Oct. 9.
Third Assignment	Multiple Sequence Alignment	posted Oct. 10, due Oct. 22.
Fourth Assignment	Homology Modeling	posted Nov. 1, due Nov. 12.
Fifth Assignment	Phylogenetic Analysis	posted Nov. 28, due Dec. 7.
Sixth Assignment	Systems	posted Dec. 4, due Dec. 7 (last day of class)

 

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

 

Contents related

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