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Revision as of 01:37, 11 December 2012
BCH441 - Bioinformatics
Welcome to the BCH441 Course Wiki.
These wiki pages are provided to coordinate information, activities and projects in the introductory bioinformatics course taught by Boris Steipe at the University of Toronto. If you are not one of my 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.
Assignment 12 has been posted.
Super short and easy quiz on the assignment: Tuesday, December 4. in our final class meeting.
Contents
The Course
BCH441H1F is the undergraduate course code.
BCH1441H1F is the cross-listed course code for graduate students.
Organization
- Dates
- BCH441/BCH1441 is a Fall Term course.
- Lectures: Tuesday, 16:00 to 17:00 and Wednesday, 15:00 to 16:00
- Tutorial sessions: Wednesday, 14:00 to 15:00 for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.
- Location
- MSB 2173 (Medical Sciences Building)
- General
See the Course Web page for general information.
- Printed material
This is an electronic submission only course; but if you must print material, you might consider printing double-sided. Learn how, at the Print-Double-Sided Student Initiative. Printing of course material is expressly discouraged. It is updated frequently.
Recommended textbooks
- Depending on your background, various levels of textbooks may be suitable. I will bring my evaluation copies to class so you can decide what may work for you.
- Understanding Bioinformatics (Zvelebil & Baum) is a decent general introduction to many aspects of bioinformatics. It was published in 2007, an updated version is urgently needed. Still, some of the basics (like the algorithm for optimal sequence alignment) don't change. (Amazon) (Indigo) (ABE books)
- Practical Bioinformatics (Agostino) covers some of the material of the BCH441 exercises. Expect a no-nonsense introduction to the very most basic stuff. I have my pet peeves about this book (as I have for many others, eg. why in the world do they still teach CLUSTAL when all available studies demonstrate it to be the least accurate MSA algorithm by a margin???), but if you haven't taken BCH441, this may serve you well. And if you did take BCH441, it may consolidate some ideas that I wasn't clear about. (Amazon) (Indigo) (ABE books)
- If you are aware of recent good textbooks, or have your own opinions about these or other books, let me know.
Grading and Activities
| Activity | Weight BCH441 - (Undergraduates) |
Weight BCH1441 - (Graduates) |
| 12 In-class quizzes | 42 marks (12 x 3.5) | 24 marks (12 x 2) |
| Open project | 28 marks (7 + 7 + 14) | 28 marks |
| "Classroom" participation | 10 marks | 10 marks |
| Thesis Project | 18 marks | |
| Final exam | 20 marks | 20 marks |
| Total | 100 marks | 100 marks |
- A note on marking
It is not my policy to adjust marks towards a target mean and variance (i.e. there will be no "belling" of grades). I feel strongly that such "normalization" detracts from a collaborative and mutually supportive learning environment. If your classmate gets a great mark because you helped him with a difficult concept, this should never have the effect that it brings down your mark through class average adjustments. Collaborate as much as possible, it is a great way to learn. However I may adjust marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.
Timetable and syllabus
The lecture recordings linked below are copyrighted material, for the personal use of participants of the course only. It is not permissible to repost them elsewhere. If in doubt, ask me.
I n t r o d u c t i o n
| Week | Date | Topics | Activities | Assignment |
| 1 | Sept. 10 - 16 |
Bioinformatics focusses on the data and methods, and Computational Biology defines the objectives, to bring our understanding of Biology to a rigorous, principled, quantitative and predictive level. Over the last two decades, ever since bioinformatics began to take centre stage in the life sciences, the rate of change in the discipline has continuously accelerated. In part, driven by the growth of the Internet, in part through novel algorithms, but to the largest part driven through a very large increase in the volume and quality of data, opportunities for computational analysis in the life science lab have grown in leaps and bounds. One of the associated challenges is to keep abreast of the rapidly changing methods and tools that are available. This course focuses on the basic principles and concepts of the field and emphasis techniques and skills that are easily accessible and freely available to every life science researcher.
|
— | Assignment 1 |
D a t a a n d D a t a A n a l y s i s
| Week | Date | Topics | Activities | Assignment |
| 2 | Sept. 17 - 23 |
In principle, most of the data of interest to us is freely available on the Web, in public repositories. However, the number of databases and associated Web services is large and in constant flux and integrating the data has its own issues. The most important issue is to be clear about the abstractions we use and how they relate back to the biology they describe.
|
Quiz 1 | Assignment 2 |
| 3 | Sept. 24 - 30 |
...
|
Quiz 2, project concept due | Assignment 3 |
| 4 | Oct. 1 - 7 |
...
|
Quiz 3 | Assignment 4 |
H o m o l o g y
| Week | Date | Topics | Activities | Assignment |
| 5 | Oct. 8 - 14 |
...
|
Quiz 4, project outline due | Assignment 5 |
| 6 | Oct. 15 - 21 |
...
|
Quiz 5 | Assignment 6 |
| 7 | Oct. 22 - 28 |
...
|
Quiz 6 | Assignment 7 |
| 8 | Oct. 29 - Nov. 4 |
...
|
Quiz 7 | Assignment 8 |
G e n o m e s
| Week | Date | Topics | Activities | Assignment |
| 9 | Nov. 5 - 11 |
...
|
Quiz 8 | Assignment 9 |
| 10 | Nov. 12 - 18 |
...
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Quiz 9, project final submission due | Assignment 10 |
P h y l o g e n i e s
| Week | Date | Topics | Activities | Assignment |
| 11 | Nov. 19 - 25 |
...
|
Quiz 10 | Assignment 11 |
| 12 | Nov. 26 - Dec. 2 |
...
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Quiz 11 | Assignment 12 |
| - | Dec. 4 |
...
Previous Exam questions |
Quiz 12 |
Lecture slides 2012
None yet.
