Bioinformatics Main Page

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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 2 has been posted.
Quiz on the assignment: Next Wednesday, September 26 in the tutorial session.
Please remember to propose your "Open Project" topics in time!



The Course

BCH441H1F is the undergraduate course code.
BCH1441H1F is the cross-listed course code for graduate students.


Organization

Dates
BCH441 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.

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
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

 

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.
  • Course Organisation
  • Current bioinformatics
  • Databases
  • Services
  • Tools

--

Lecture slides 2012: 01 - Introduction
Lecture recordings 2012: 01 - Introduction (mp4, 14.3 MB)

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.
  • Sequences
  • Structures
Quiz 1 Assignment 2
3 Sept. 24 - 30
...
  • Sequence analysis
  • Machine learning
Quiz 2, project concept due Assignment 3
4 Oct. 1 - 7
...
  • Protein structure interpretation
  • Protein structure domains
Quiz 3 Assignment 4

 

H o m o l o g y

 

Week Date Topics Activities Assignment
5 Oct. 8 - 14
...
  • Homology principles
  • BIO Statistics
Quiz 4, project outline due Assignment 5
6 Oct. 15 - 21
...
  • Sequence alignment
  • BLAST
Quiz 5 Assignment 6
7 Oct. 22 - 28
...
  • Multiple sequence alignment
  • Information theory
Quiz 6 Assignment 7
8 Oct. 29 - Nov. 4
...
  • Homology modelling
  • Molecular dynamics
  • Ab initio structure prediction
Quiz 7 Assignment 8

 

G e n o m e s

 

Week Date Topics Activities Assignment
9 Nov. 5 - 11
...
  • Genome sequencing and annotation
Quiz 8 Assignment 9
10 Nov. 12 - 18
...
  • Fall break - no class on Tuesday, Nov. 13
  • SNPs
  • Human genomics
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
...
  • Phylogenetic analysis principles
  • Phylogenetic tree building
Quiz 10 Assignment 11
12 Nov. 26 - Dec. 2
...
  • Phylogenetic data interpretation
  • Functional annotation and Function prediction
Quiz 11 Assignment 12
- Dec. 4
...
  • Exam review
Quiz 12  

 

Lecture slides 2012

None yet.