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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
Here are two tasks I would like you to complete before Thursday's class.
- 1. Please subscribe yourself to the Course Mailing List
- 2. Please download and install VMD
(follow the links above for more information).
Organization
- 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.
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 any target average for the class. 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 | - | - |
| The objects of bioinformatics | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 1 | Thu. Sept 11 | Steipe | Sequence abstraction and sequence databases | - | Ch 3 |
| 2 | Mon. Sept 15 | Steipe | Protein Structure Databases | - | - |
| 3 | Thu. Sept 18 | Steipe | Bioinformatics methods | - | - |
| Analysis based on properties | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 4 | Mon. Sept 22 | Steipe | Sequence properties | - | Ch 4.9, 11, 12 |
| 5 | Thu. Sept 25 | Steipe | Sequence Analysis | - | - |
| 6 | Mon. Sept 29 | Steipe | Interpreting protein structure | - | Ch. 14 |
| 7 | Thu. Oct 2 | Parkinson | Genome sequencing, genome browsers | - | Ch. 9, 10 |
| 8 | Mon. Oct 6 | Parkinson | Genomes and genome structure | - | - |
| Analysis based on homology | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 9 | Thu. Oct 9. | Steipe | Homology I: the principles | - | - |
| 10 | Thu. Oct 16 | Steipe | Homology II: Sequence alignment | - | Ch. 4 |
| 11 | Mo. Oct 20 | Steipe | Homology III: Multiple sequence alignment | - | Ch. 5 |
| 12 | Mon. Oct 20 | Steipe | Homology IV: fast sequence database searches | - | Ch 6 |
| 13 | Thu. Oct 23 | Steipe | Structural domains | - | - |
| 14 | Mon. Oct 27 | Steipe | Homology modeling and structure prediction | - | Ch. 13 |
| Analysis based on conservation | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 15 | Thu. Oct 30 | Steipe | Essential concepts of probability and information theory | - | Appendix A |
| 16 | Mon. Nov 3 | Parkinson | Comparative genomics | - | Ch. 9.8, 10.8 |
| 17 | Thu. Nov 6 | NN | Human population genomics | - | - |
| 18 | Mon. Nov 10 | Steipe | Phylogenetic analysis I | - | Ch. 7, 8 |
| 19 | Thu. Nov 13 | Steipe | Phylogenetic analysis II | - | - |
| 20 | Mon. Nov 17 | Steipe | Protein structure motifs | - | - |
| Analysis based on context | |||||
| # | Date | Lecturer | Topic | Handout | Book |
| 21 | Thu. Nov 20 | Wodak | Gene regulation I | - | Ch. 15 |
| 22 | Mon. Nov 24 | Wodak | Gene regulation II | - | - |
| 23 | Thu. Nov 27 | Wodak | Functional annotation | - | Appendix A |
| 24 | Mon. Dec 1 | Wodak | Metabolic networks | - | Ch. 17.1 |
| 25 | Thu. Dec 4 | Parkinson | Computational systems biology | - | 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
- Contents related
- A Stereo Vision tutorial
- MetaDatabase
- NAR January-2008 Database issue
- NAR July-2008 Web server issue
