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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.
Contents
The Course
We'll be back in September 2009.
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 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 | Introduction | Ch 1, 2 |
| The objects of bioinformatics | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 1 | Thu. Sept 11 | Steipe | Sequence abstraction and sequence databases | Sequence data | Ch 3 |
| Assignment 1 handed out | |||||
| 2 | Mon. Sept 15 | Steipe | Protein Structure Data | Structure data | - |
| 3 | Thu. Sept 18 | Steipe | Sequence properties | Raw lecture PDF | Ch 4.9, 11, 12 |
| Analysis based on properties | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 4 | Mon. Sept 22 | Steipe | Sequence Analysis | Raw lecture PDF | - |
| 5 | Thu. Sept 25. | Assignment 1 due | |||
| First quiz in class | |||||
| Steipe | Lecture: Interpreting protein structure |
Raw lecture PDF | - | ||
| Assignment 2 handed out | |||||
| 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) | - |
| Analysis based on homology | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 9 | Thu. Oct 9. | Assignment 2 due | |||
| Steipe | Lecture: Homology II: Sequence alignment |
Raw lecture PDF | - | ||
| Assignment 3 handed out | |||||
| 10 | Thu. Oct 16 | Steipe | Lecture: Homology III: Fast sequence database searches | BLAST | Ch. 4 |
| 11 | Mo. Oct 20 | Steipe | Homology IV: Multiple sequence alignment | Multiple Sequence Alignment | Ch. 5 |
| Second quiz in class (13:00 tutorial time slot) | |||||
| Steipe | - | Ch 6 | |||
| 12 | Thu. Oct 23. | Assignment 3 due | |||
| Steipe | Lecture: Structural domains |
Raw lecture PDF | - | ||
| Analysis based on conservation | |||||
| # | Date | Lecture | |||
| 13 | Mon. Oct 27 | (Steipe) Phylogenetic analysis I (Book: Ch. 7,8) Raw lecture PDF Third quiz in class, 13:00 in tutorial time-slot |
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| 14 | Thu. Oct 30 | (Steipe) Phylogenetic analysis II (Book: Ch. 7,8) |
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| 15 | Mon. Nov 3 | (Parkinson) Comparative genomics (Book: Ch. Ch. 9.8, 10.8) |
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| 16 | Thu. Nov 6 | (Steipe) Quiz pickup, Human population genomics (Part 1) |
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| 17 | Mon. Nov 10 | (Steipe) Human population genomics (Part 2) Raw lecture PDF Assignment 4 to be posted. |
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| 18 | Thu. Nov 13 | (Steipe) Homology modeling and structure prediction (Part 1) Raw lecture PDF |
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| 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. |
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| Analysis based on context | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 20 | Thu. Nov 20 | Wodak | Gene regulation I | Lecture slide PDFs (2.1 MB) | Ch. 15 |
| 21 | Mon. Nov 24 | Wodak | Gene regulation II | - | - |
| 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...
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
