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BCH441 - Bioinformatics

Welcome to the BCH441 Course Wiki.

 


This is our main tool to coordinate information, activities and projects in University of Toronto's bioinformatics course BCH441. If you are not one of our 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

Follow the link to read feedback from those who have taken this course before you..

I anticipate changes to the grading scheme, the schedule and the assignments. All changes will be posted here as they get decided on. Check back here in August.


The first session for the 2008 term will be held Monday, September 8., 12:00.
It is crucial that you make every effort to attend: we will be discussing access to the course Wiki, the mailing list and how groupwork will be organized.

Organization

Slowly gearing up for the 2008 Fall term ...

Dates
Monday and Thursday, 12:00 to 13:00
Optional tutorial sessions will be offered as the need arises, most likely on Mondays, probably from 13:00 to 14:00.
First class: Monday, September 8. 2008
Location
MSB 2173 (Medical Sciences Building)

See the Course Web page for general information.


Lecture Schedule

This is the current schedule for 2008, but changes may be still be made if required.


# Date Lecturer Topic Handout Book
0 Mon. Sept 8 Steipe Organisation and Orientation - -


The objects of bioinformatics
# Date Lecturer Topic Handout Book
1 Thu. Sept 11 Steipe Sequence abstraction and sequence databases - Ch 3
2 Mon. Sept 15 Steipe Protein Structure Databases - -
3 Thu. Sept 18 Steipe Bioinformatics methods - -


Analysis based on properties
# Date Lecturer Topic Handout Book
4 Mon. Sept 22 Steipe Sequence properties - Ch 4.9, 11, 12
5 Thu. Sept 25 Steipe Sequence Analysis - -
6 Mon. Sept 29 Steipe Interpreting protein structure - Ch. 14
7 Thu. Oct 2 Parkinson Genome sequencing, genome browsers - Ch. 9, 10
8 Mon. Oct 6 Parkinson Genomes and genome structure - -


Analysis based on homology
# Date Lecturer Topic Handout Book
9 Thu. Oct 9. Steipe Homology I: the principles - -
10 Thu. Oct 16 Steipe Homology II: Sequence alignment - Ch. 4
11 Mo. Oct 20 Steipe Homology III: Multiple sequence alignment - Ch. 5
12 Mon. Oct 20 Steipe Homology IV: fast sequence database searches - Ch 6
13 Thu. Oct 23 Steipe Structural domains - -
14 Mon. Oct 27 Steipe Homology modeling and structure prediction - Ch. 13


Analysis based on conservation
# Date Lecturer Topic Handout Book
15 Thu. Oct 30 Steipe Essential concepts of probability and information theory - Appendix A
16 Mon. Nov 3 Parkinson Comparative genomics - Ch. 9.8, 10.8
17 Thu. Nov 6 NN Human population genomics - -
18 Mon. Nov 10 Steipe Phylogenetic analysis I - Ch. 7, 8
19 Thu. Nov 13 Steipe Phylogenetic analysis II - -
20 Mon. Nov 17 Steipe Protein structure motifs - -


Analysis based on context
# Date Lecturer Topic Handout Book
21 Thu. Nov 20 Wodak Gene regulation I - Ch. 15
22 Mon. Nov 24 Wodak Gene regulation II - -
23 Thu. Nov 27 Wodak Functional annotation - Appendix A
24 Mon. Dec 1 Wodak Metabolic networks - Ch. 17.1
25 Thu. Dec 4 Parkinson Computational systems biology - Ch. 17


Ongoing construction
Don't trust information below.

Assignments

   

First Assignment Databases and Molecular Models posted Sept. 13, due Oct. 1.
Second Assignment Search, Retrieve and Annotate posted Sept. 24, due Oct. 9.
Third Assignment Multiple Sequence Alignment posted Oct. 10, due Oct. 22.
Fourth Assignment Homology Modeling posted Nov. 1, due Nov. 12.
Fifth Assignment Phylogenetic Analysis posted Nov. 28, due Dec. 7.
Sixth Assignment Systems posted Dec. 4, due Dec. 7 (last day of class)

 

In depth...

 

Resources

Course related

 

Contents related

 




 



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