Bioinformatics Main Page

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.

This course will resume on Tuesday, September 9. 2014 at 17:10 in MS 4171.

Do not miss the first class! The first assignment will be handed out, you will sign up to the course mailing list and to the course Student Wiki.

If you miss the first class and I have to go through extra effort to accommodate this, you may lose participation marks.

The Course

This course is an introduction to bioinformatics, for life science undergraduates and graduates and the specialists in the BCB Program. The course focusses on foundational techniques, the use of web sites for analysis, judicious interpretation of results and above all, proper, evidence based reasoning about biology. The emphasis in this course is the analysis of single biomolecule sequence and structure, the course is complemented by BCB420 (offered in the Winter Term) with a systems biology focus.

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

Organization

General

BCH441H is a bioinformatics survey course, cross-listed for graduate students as BCH1441H. The course provides an overview of current applications of computational techniques in life-science laboratories. It discusses the most important strategies and resources for annotation of biological sequences on the Internet, their judicious application, and the interpretation of results. Assignments will complement the lectures by practicing techniques of computational molecular data analysis, with an emphasis on Web based tools. Students will be introduced to the programming language and statistical workbench R. Special emphasis in the course will be on a self-directed "Bioinformatics Project" in the field.

Dates

BCH441/BCH1441 is a Fall Term course.

Lectures: Tuesday, 17:00 to 18:00 and Wednesday, 15:00 to 16:00

Tutorial sessions: Wednesday, 14:00 to 15:00 for open discussion of lecture material, in-class quizzes, quiz debriefings, exam preparation and other activities.

Location

MS 4171 (Medical Sciences Building)

The Student Wiki.

Many of your activities will take place on a Wiki site I have installed for this purpose.

Coordinator

Boris Steipe

Office hours

I do not hold regular office hours. I prefer communication via e-mail, since it leaves you with a document trail of what was discussed, and we can share points of general interest more easily with the class. If you feel you must have a verbal meeting, coordinate with me.

Prerequisites

BCH210H/242Y, BCH311/MGB311Y/JLM349H/BIO349H or special permission of the course coordinator.

It is assumed that students have access to the Internet via their own computer.

Exclusions & Enrolment controls

none

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 since the material 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 have a look.

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

Syllabus, marking scheme details and assignments are currently under revision.

 

Activity	Weight BCH441 - (Undergraduates)	Weight BCH1441 - (Graduates)
12 In-class quizzes	42 marks (12 x 3.5)	24 marks (12 x 2)
Bioinformatics 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. 8 - 14	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 notes 2013: 01 - Introduction (PDF 2.1 MB) Lecture recordings 2013: 01 - Introduction (mp4, 11.2 MB). Note: due to a disconnected cable, the second half of the lecture was not recorded. Refer to the notes instead.	—	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. 15 - 21	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. BIO_Sequence BIO_Structure Lecture notes 2013: 02 - Sequence Data (PDF 4.5 MB) Lecture notes 2013: 03 - Structure Data (PDF 18.1 MB)	Quiz 1	Assignment 2
3	Sept. 22 - 28	... Sequence_analysis BIO Machine learning Lecture notes 2013: 04 - Sequence Analysis I (PDF 4.9 MB) Lecture notes 2013: 05 - Sequence Analysis II (PDF 3.3 MB)	Quiz 2, project concept due	Assignment 3
4	Sept. 29 - Oct. 5	... Protein structure interpretation Protein domains Lecture notes 2013: 06 - Interpreting Protein Structure (PDF 8.6 MB) Lecture notes 2013: 07 - Structural Domains (PDF 6.4 MB)	Quiz 3	Assignment 4

 

H o m o l o g y

 

Week	Date	Topics	Activities	Assignment
5	Oct. 6 - 12	... Homology I: Principles Homology II: Sequence Alignment Lecture notes 2013: 08 - Homology I: Principles (PDF 2.9 MB) Lecture notes 2013: 09 - Homology II: Alignment (PDF 2.4 MB)	Quiz 4, project outline due	Assignment 5
6	Oct. 13 - 19	... Homology III: BLAST Homology IV: Multiple sequence alignment Lecture notes 2013: 10 - Homology III: BLAST (PDF 2.6 MB) Lecture notes 2013: 11 - Homology IV: MSA (PDF 2.5 MB)	Quiz 5	Assignment 6
7	Oct. 20 - 26	... Statistics and Exploratory Data Analysis Information theory Lecture notes 2013: 12 - Statistics (PDF 6.1 MB) Lecture notes 2013: 13 - Information Theory (PDF 2.9 MB)	Quiz 6	Assignment 7
8	Oct. 27 - Nov. 2	... Homology modelling Molecular dynamics De novo Structure Prediction and Design Lecture notes 2013: 14 - Predicting Protein Structure: I (Homology Modelling) (PDF 2.3 MB) Lecture notes 2013: 15 - Predicting Protein Structure: II (De novo prediction) (PDF 10.7 MB)	Quiz 7	Assignment 8

 

G e n o m e s

 

Week	Date	Topics	Activities	Assignment
9	Nov. 3 - 9	... Genome sequencing Genome annotation Lecture notes 2013: 16 - Next Generation Sequencing (PDF 4.7 MB) Lecture notes 2013: 17 - Genome Annotation (PDF 3.9 MB)	Quiz 8	Assignment 9
10	Nov. 10 - 16	... SNPs and Human genomics Lecture notes 2013: 18 - Human Genomics (PDF 5.8 MB)	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. 17 - 23	... Fall break - no class on Tuesday, Nov. 18 Phylogenetic analysis principles Phylogenetic tree interpretation Lecture notes 2013: 19 - Phylogenetic Analysis I: Principles (PDF 2.9 MB) Lecture notes 2013: 20 - Phylogenetic Analysis II: Interpreting trees (PDF 4.2 MB)	Quiz 10	Assignment 11
12	Nov. 24 - 30	... Inference From Phylogenies Function Annotation and Function Prediction Lecture notes 2013: 21 - Phylogenetic Analysis III: Inference from Phylogenies (PDF 1.3 MB) Lecture notes 2013: 22 - Function Annotation (PDF 6.7 MB)	Quiz 11	Assignment 12
-	Dec. 2	... Exam review Previous Exam questions	Quiz 12

 

 

Resources

Course related

• The 2013 Course Google Group.
• Netiquette for the Group mailing list
• Previous BCH441_Final_Exam
• BIO course feedback

 

Contents related

• The VMD tutorial
• The Stereo Vision tutorial
• The Aminoacid tutorial
• The Database Identifiers tutorial
• The Introduction to R tutorial
• MetaDatabase
• NAR January-2012 Database issue
• NAR July-2012 Web server issue