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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.

Organization

The first lecture of the 2007 Fall term was held Monday, Sept. 10, 12:00.

Dates

Monday and Thursday, 12:00 to 13:00

A tutorial session for Bioinformatics and Computational Biology Specialists will be offered Mondays, from 13:00 to 14:00.

Location

MSB 2173

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 current draft for 2007 and has not been confirmed by all lecturers.)

1. Organisation and Orientation (Boris, Monday, Sept. 10)

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. Structural Domains (Boris, Monday, Oct. 15*)
11. Interpreting Protein Structure (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 (TBD, Nov. 8)
19. Proteomics (TBD, Monday, Nov. 12)
20. Gene regulation I (Shoshana, Thursday, Nov. 15)
21. Gene regulation II (Shoshana, Monday, Nov. 19)
22. Microarray Expression Analysis (TBD, Thursday, Nov. 22)
23. Pathways and Networks (TBD, Monday, Nov. 26)
24. Interaction Databases (TBD, Thursday, Nov. 29)
25. Metabolic Networks (TBD, Monday, Dec. 3)
26. Computational Systems Biology (John, Thursday, Dec. 7)

Assignments

   

First Assignment	Databases and Molecular Models	to be posted Sept. 13, due Oct. 1.
Second Assignment	Search, Retrieve and Annotate	to be posted Sept. 24, due Oct. 8.
Third Assignment	Multiple Sequence Alignment	to be posted Oct. 8, due Oct. 22.
Fourth Assignment	Phylogenetic Analysis	to be posted Oct. 22, due Nov. 5.
Fifth Assignment	Homology Modeling	to be posted Nov. 5, due Nov. 19.
Sixth Assignment	Systems	to be posted Nov. 19, due Dec. 3.

 

In depth...

• Glossary
• Mutation Data Matrices

Resources

 

Course Wiki

• Introduction: Concept and contents of the Course Wiki
• Soapbox: A page to commmunicate. Do you want to leave a message? Alert the course members? Voice an opinion? Praise or flame? Use this page.
• Editing: Editing principles and Wiki markup syntax for the Course Wiki pages
• Sandbox: A page for your editing experiments. Content added to this page will not stay permanently.
• Feedback: Share your views on the course, suggest improvements.

 

• MetaDatabase

 

Exam_questions

 
 

Course Web

• The Course Web site.