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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 will be 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

Update Warning! Material below this mark has not been revised yet for the 2007 Fall term and may be out of date.

  (This schedule is for orientation only, changes may be made at any time as the subject matter and the progress of the lecture requires.)

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

Sequences

2. The Sequence Abstraction (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)

Structures

7. Protein Structure Databases (Boris, Monday, Oct. 1)
8. Structural Domains (Boris, Thursday, Oct. 4)
9. Interpreting Protein Structure (Boris, Monday, Oct. 8)
10. Homology Modeling (Boris, Thursday, Oct. 11)
11. Protein Structure Prediction (Boris, Monday, Oct. 15)
12. Multiple Sequence Alignment (Boris, Thursday, Oct. 18)

Genomes

13. Genome Sequencing (John, Monday, Oct. 22)
14. Genomes (John, Thursday, Oct. 25)
15. Functional Annotation (Shoshana, Monday, Oct. 29)
16. Fast Sequence Database searches (Boris, Thursday, Nov. 1)

Evolution

17. Phylogenetic Analysis (Boris, Monday, Nov. 5)
18. Clinical Genomics (Boris, Thursday, Nov. 8)
19. Comparative Genomics (John, Monday, Nov. 12)

Systems

20. Proteomics (Boris, Thursday, Nov. 15)
21. Microarray Expression Analysis (Boris, Monday, Nov. 19)
22. Gene regulation I (Shoshana, Thursday, Nov. 22)
23. Gene regulation II (Shoshana, Monday, Nov. 26)
24. Interaction Databases (Shoshana, Thursday, Nov. 29)
25. Pathways and Networks (Gary Bader, Monday, Dec. 3)
26. Computational Systems Biology (John, Thursday, Dec. 7)

Assignments

• First Assignment - Databases and Molecular Models
• Second Assignment - Search, Retrieve and Annotate
• Third Assignment - Multiple Sequence Alignment
• Fourth Assignment - Phylogenetic Analysis
• Fifth Assignment - Homology Modeling
• Sixth Assignment - Systems

 

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.