Applied Bioinformatics Main Page

Applied Bioinformatics

Welcome to the Applied Bioinformatics Course Wiki.

These wiki pages are provided to coordinate information, activities and projects in the applied bioinformatics courses 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.

The Course

BCB410H1F is the undergraduate course code and JTB2020H1S is the course code for graduate students. However the delivery and scope of the courses is very different:

• BCB410 is intended for students in the Bioinformatics and Computational Biology Specialist Program. Therefore I assume that all students are very familiar with a wide variety of computer science related topics and their practical application.
• JTB2020 is designed for students in the Collaborative PhD Program in Bioinformatics and Genome Biology. These students have a wide variety of backgrounds and prior experience. They participate in the Computational Systems Biology Course and go through a number of targeted exercises in applied bioinformatics to add as much material to their knowledge- and skill set as can reasonably be acquired in a single term.

Organization

Dates

Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00

Tutorial sessions: Mondays, 12:00 to 13:00 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.

We are recommending Understanding Bioinformatics, Zvelebil & Baum, Garland 2008 as a background textbook for the course. (buy used at AbeBooks)

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.

Grading and Activities

Activity	Weight (Undergraduates)	Weight (Graduates)
5 Assignments	15 marks (5 x 3)	10 marks (5 x 2)
5 In-class quizzes	35 marks (5 x 7)	25 marks (5 x 5)
Open project	7 marks	5 marks
"Classroom" participation	3 marks	3 marks
Graduate project		17 marks
Final exam	40 marks	40 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.

Assignments

Assignment 5 has been posted.
Due Monday, Dec. 5.

Add this material

• GPU and Cloud computing

In depth...

• Glossary
• Mutation Data Matrices
• Amino acids
• Database Identifiers

 

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

 

 

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