Difference between revisions of "Bioinformatics Main Page"

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*Classroom change: all classes will take place in MS4171.
 
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*By now you ''must'' all be subscribed to the mailing list and you ''must'' all have an account on the Student Wiki.
  
 
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Revision as of 20:39, 16 September 2013

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.


Tasks and concepts are topics for the first quiz, next Wednesday, September 18.


  • Classroom change: all classes will take place in MS4171.
  • By now you must all be subscribed to the mailing list and you must all have an account on the Student Wiki.



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

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 in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.


Location
MSB 4171 (Medical Sciences Building)


General
BCH441H is a bioinformatics survey course, cross-listed 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. Special emphasis will be on a self-directed "Open Project" in the field.


Coordinator

Boris Steipe


Prerequisites
BCH210H/242Y, MGB311Y/JLM349H/BIO349H
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 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

This section is under revision for the 2013 term...


  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. 9 - 15
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. 16 - 22
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. 23 - 29
...


 Quiz 2, project concept due Assignment 3
4 Sept. 30 - Oct. 6
...



Quiz 3 Assignment 4

 

H o m o l o g y

 

Week Date Topics Activities Assignment
5 Oct. 7 - 13
...



Quiz 4, project outline due Assignment 5
6 Oct. 14 - 20
...



Quiz 5 Assignment 6
7 Oct. 21 - 27
...



Quiz 6 Assignment 7
8 Oct. 28 - Nov. 3
...



Quiz 7 Assignment 8

 

G e n o m e s

 

Week Date Topics Activities Assignment
9 Nov. 4 - 10
...



Quiz 8 Assignment 9
10 Nov. 11 - 17
...


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. 18 - 24
...



Quiz 10 Assignment 11
12 Nov. 25 - Dec. 1
...



Quiz 11 Assignment 12
- Dec. 3
...
  • Exam review

Previous Exam questions

Quiz 12  

 


 

Resources

Course related


 

Contents related

 



 

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