Difference between revisions of "Main Page"

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<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
 
<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
  
−
I will offer a final tutorial/review on Monday, December 8. starting at 12:00 in the lecture room.
+
Good luck with the final exam!
 +
 
 +
<small>Thursday, 11. Dec. 2:00-5:00 p.m.  EX300 ([http://maps.google.ca/maps?f=q&hl=en&geocode=&q=255+McCaul+Street,toronto&sll=49.891235,-97.15369&sspn=51.047948,77.958984&ie=UTF8&ll=43.660312,-79.394567&spn=0.006947,0.009516&z=17&g=255+McCaul+Street,toronto&iwloc=addr 255 McCaul Street])
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Please remember: No aids. Leave your cell-phones and other electronics at home (or off and stowed.)<small>
  
 
</div>
 
</div>
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:Monday and Thursday, 12:00 to 13:00
 
:Monday and Thursday, 12:00 to 13:00
 
:<small>Optional tutorial sessions will be offered as the need arises, most likely on Mondays, probably from 13:00 to 14:00.</small>
 
:<small>Optional tutorial sessions will be offered as the need arises, most likely on Mondays, probably from 13:00 to 14:00.</small>
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:First class: Monday, September 8. 2008
+
<!-- :First class: Monday, September 8. 2008 -->
  
 
;Location
 
;Location
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</table>
 
</table>
  
−
I will not adjust marks towards any target average for the class. If your classmate gets a great mark because you helped him with a difficult concept, this will have no bearing whatsoever on your own mark. Collaborate as much as possible, it is a great way to learn. The only times I will consider adjusting marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.
+
I will not adjust marks towards a target average for the class ("Belling"). If your classmate gets a great mark because you helped him with a difficult concept, this will have no bearing whatsoever on your own mark. Collaborate as much as possible, it is a great way to learn. The only times I will consider adjusting marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.
  
 
== Lecture Schedule ==
 
== Lecture Schedule ==
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<td>Parkinson</td>
 
<td>Parkinson</td>
 
<td>Genomes and genome structure</td>
 
<td>Genomes and genome structure</td>
−
<td>-</td>
+
<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genomes.pdf Lecture slide PDFs (2.4 MB)]</td>
 
<td>-</td>
 
<td>-</td>
  
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<td>Mon. Nov 3</td>
 
<td>Mon. Nov 3</td>
 
<td>(Parkinson) Comparative genomics (Book: Ch. Ch. 9.8, 10.8)<br>
 
<td>(Parkinson) Comparative genomics (Book: Ch. Ch. 9.8, 10.8)<br>
 +
[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/ComparativeGenomics.pdf Lecture slide PDFs (1.6 MB)]
 
</td>
 
</td>
 
</tr>
 
</tr>
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<td>(Steipe) Human population genomics (Part 2)<br>
 
<td>(Steipe) Human population genomics (Part 2)<br>
 
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/HumanPopulationGenomics.pdf Raw lecture PDF]</small><hr>
 
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/HumanPopulationGenomics.pdf Raw lecture PDF]</small><hr>
−
Assignment 4 to be posted.
+
[[Assignment 4]] to be posted.
 
</td>
 
</td>
 
</tr>
 
</tr>
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<tr class="s0">
 
<tr class="s0">
−
<td>18</td>
+
<td>19</td>
 
<td>Mon. Nov 17</td>
 
<td>Mon. Nov 17</td>
 
<td>(Steipe) Homology modeling and structure prediction (Part 2)<br>
 
<td>(Steipe) Homology modeling and structure prediction (Part 2)<br>
 
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PredictingProteinStructure_II.pdf Raw lecture PDF]</small><hr>
 
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PredictingProteinStructure_II.pdf Raw lecture PDF]</small><hr>
−
Assignment 4 due.
+
[[Assignment 4]] due.
 
<hr>
 
<hr>
 
'''Fourth quiz''' in class: 13:00 in tutorial time slot.
 
'''Fourth quiz''' in class: 13:00 in tutorial time slot.
 
<hr>
 
<hr>
−
Assignment 5 to be posted.
+
[[Assignment 5]] to be posted.
 
</td>
 
</td>
 
</tr>
 
</tr>
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</tr>
 
</tr>
 
<tr class="s1">
 
<tr class="s1">
−
<td colspan="4">Assignment 5 due<br>
+
<td colspan="4">[[Assignment 5]] due<br>
 
<hr>
 
<hr>
 
'''Fifth quiz''' in class: 13:00 in tutorial time slot</td>
 
'''Fifth quiz''' in class: 13:00 in tutorial time slot</td>
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<td>Parkinson</td>
 
<td>Parkinson</td>
 
<td>Computational systems biology</td>
 
<td>Computational systems biology</td>
−
<td>-</td>
+
<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genome_sequencing.pdf Lecture slide PDFs (3.4 MB)]</td>
 
<td>Ch. 17</td>
 
<td>Ch. 17</td>
 
</tr>
 
</tr>
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</table>
 
</table>
−
<!--
 
−
 
−
;Sequences
 
−
<ol  start="2">
 
−
<li>[[Lecture_02|'''Sequence Abstraction + Sequence Databases''']] (Boris,  Thursday, Sept. 13)
 
−
<li>[[Lecture_03|'''Sequence Properties''']] (Boris,  Monday, Sept. 17)
 
−
<li>[[Lecture_04|'''Sequence Analysis''']] (Boris,  Thursday, Sept. 20)
 
−
<li>[[Lecture_05|'''Homology I: the principles''']] (Boris,  Monday, Sept. 24)
 
−
<li>[[Lecture_06|'''Homology II: Sequence Alignment''']] (Boris,  Thursday, Sept. 27)
 
−
<li>[[Lecture_07|'''Homology III: Multiple Sequence Alignment''']] (Boris,  Monday, Oct. 1)
 
−
<li>[[Lecture_08|'''Homology IV: Fast Sequence Database searches''']] (Boris,  Thursday, Oct. 4)
 
−
</ol>
 
−
 
−
 
−
;Structures
 
−
<ol  start="9">
 
−
<li>[[Lecture_09|'''Protein Structure Databases''']] (Boris,  Thursday, Oct. 11)
 
−
<li>[[Lecture_10|'''Interpreting Protein Structure''']] (Boris,  Monday, Oct. 15'''*''')
 
−
<div style="color: #AAAAAA;">
 
−
<li>[[Lecture_11|Structural Domains]] (Boris,  Monday, Oct. 15'''*''')
 
−
<li>[[Lecture_12|Homology Modeling + Protein Structure Prediction]]  (Boris,  Thursday, Oct. 18)
 
−
</div>
 
−
</ol>
 
−
 
−
<p>
 
−
<small>('''*''') Double lecture (12:00 - 14:00) to make up for Thanksgiving, Oct 8.</small>
 
−
 
−
;Genomes
 
−
<ol  start="13">
 
−
<li>[[Lecture_13|'''Genome Sequencing''']] (John,  Monday, Oct. 22)
 
−
<li>[[Lecture_14|'''Genomes''']] (John,  Thursday, Oct. 25)
 
−
<li>[[Lecture_15|'''Comparative Genomics''']] (John,  Monday, Oct. 29)
 
−
<div style="color: #AAAAAA;">
 
−
<li>[[Lecture_16|Phylogenetic Analysis]] (Boris,  Thursday, Nov. 1)
 
−
</div>
 
−
</ol>
 
−
 
−
;Systems
 
−
<ol  start="17">
 
−
<li>[[Lecture_17|'''Functional Annotation''']] (Shoshana,  Monday, Nov. 5)
 
−
<div style="color: #AAAAAA;">
 
−
<li>[[Lecture_18|Human Population Genomics]] (Boris, Nov. 8)
 
−
<li>[[Lecture_19|Proteomics]] (Boris,  Monday, Nov. 12)
 
−
</div>
 
−
<li>[[Lecture_20|'''Gene regulation I''']] (Shoshana,  Thursday, Nov. 15)
 
−
<li>[[Lecture_21|'''Gene regulation II''']] (Shoshana,  Monday, Nov. 19)
 
−
<div style="color: #AAAAAA;">
 
−
<li>[[Lecture_22|Microarray Expression Analysis]] ([http://hugheslab.ccbr.utoronto.ca/ Tim Hughes],  Thursday, Nov. 22)
 
−
</div>
 
−
<li>[[Lecture_23|'''Pathways and Networks''']] ([http://baderlab.org/ Gary Bader], Monday, Nov. 26)
 
−
<li>[[Lecture_24|'''Interaction Databases''']] (Francis Ouelette, OICR, Thursday, Nov. 29)
 
−
<li>[[Lecture_25|'''Metabolic Networks''']] (Shoshana,  Monday, Dec. 3)
 
−
<li>[[Lecture_26|'''Computational Systems Biology''']] (John,  Thursday, Dec. 7)
 
−
</ol>
 
−
-->
 
−
 
−
 
−
 
−
<!--
 
−
<div style="padding: 5px; background: #FFDD33;  border:solid 3px #000000; font-size:150%;font-weight:bold;">
 
−
Ongoing construction <br>
 
−
<small>Don't trust information below.</small>
 
−
</div>
 
−
 
−
== Assignments ==
 
−
&nbsp;
 
−
&nbsp;
 
−
 
−
<table border="0" cellpadding="5">
 
−
<tr>
 
−
<td>[[Assignment_1|'''First Assignment''']]</td>
 
−
<td>Databases and Molecular Models</td>
 
−
<td>''posted Sept. 13, due Oct. 1.''</td>
 
−
</tr>
 
  
−
<tr>
 
−
<td>[[Assignment_2|'''Second Assignment''']]</td>
 
−
<td>Search, Retrieve and Annotate</td>
 
−
<td>''posted Sept. 24, due Oct. 9.''</td>
 
−
</tr>
 
  
−
<tr>
 
−
<td>[[Assignment_3|'''Third Assignment''']]</td>
 
−
<td>Multiple Sequence Alignment</td>
 
−
<td>posted Oct. 10, due Oct. 22.</td>
 
−
</tr>
 
  
−
<tr>
 
−
<td>[[Assignment_4|'''Fourth Assignment''']]</td>
 
−
<td>Homology Modeling</td>
 
−
<td>posted Nov. 1, due Nov. 12.</td>
 
−
</tr>
 
  
−
<tr>
 
−
<td>[[Assignment_5|'''Fifth Assignment''']]</td>
 
−
<td>Phylogenetic Analysis</td>
 
−
<td>posted Nov. 28, due Dec. 7.''</td>
 
−
</tr>
 
  
−
<tr>
 
−
<td>[[Assignment_6|'''Sixth Assignment''']]</td>
 
−
<td>Systems</td>
 
−
<td>posted Dec. 4, due Dec. 7 (last day of class)</td>
 
−
</tr>
 
−
</table>
 
−
&nbsp;
 
−
-->
 
  
 
==In depth...==
 
==In depth...==

Revision as of 18:54, 10 December 2008

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

Good luck with the final exam!

Thursday, 11. Dec. 2:00-5:00 p.m. EX300 (255 McCaul Street)

Please remember: No aids. Leave your cell-phones and other electronics at home (or off and stowed.)

Organization

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.
Location
MSB 2173 (Medical Sciences Building)

See the Course Web page for general information.

We are recommending Understanding Bioinformatics, Zvelebil & Baum, Garland 2008 as a background textbook for the course. (amazon, UofT Bookstore)

Grading and Activities

Activity Weight
(Undergraduates)		 Weight
(Graduates)
5 Assignments (drop 1) 16 marks (4 x 4) 12 marks (4 x 3)
5 In-class quizzes (drop 1) 32 marks (4 x 8) 20 marks (4 x 5)
Group project 10 marks 6 marks
Participation 2 marks 2 marks
Graduate project   20 marks
Final exam 40 marks 40 marks
Total 100 marks 100 marks

I will not adjust marks towards a target average for the class ("Belling"). If your classmate gets a great mark because you helped him with a difficult concept, this will have no bearing whatsoever on your own mark. Collaborate as much as possible, it is a great way to learn. The only times I will consider adjusting marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.

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 Introduction Ch 1, 2


The objects of bioinformatics
# Date Lecturer Topic Handout Book
1 Thu. Sept 11 Steipe Sequence abstraction and sequence databases Sequence data Ch 3
Assignment 1 handed out
2 Mon. Sept 15 Steipe Protein Structure Data Structure data -
3 Thu. Sept 18 Steipe Sequence properties Raw lecture PDF Ch 4.9, 11, 12



Analysis based on properties
# Date Lecturer Topic Handout Book
4 Mon. Sept 22 Steipe Sequence Analysis Raw lecture PDF -
5 Thu. Sept 25. Assignment 1 due
First quiz in class
Steipe Lecture: Interpreting protein structure
 Raw lecture PDF -
Assignment 2 handed out
6 Mon. Sept 29 Steipe Homology I: the principles Raw lecture PDF Ch. 14
7 Thu. Oct 2 Parkinson Genome sequencing, genome browsers Lecture slide PDFs (1.8 MB) Ch. 9, 10
8 Mon. Oct 6 Parkinson Genomes and genome structure Lecture slide PDFs (2.4 MB) -



Analysis based on homology
# Date Lecturer Topic Handout Book
9 Thu. Oct 9. Assignment 2 due
Steipe Lecture: Homology II: Sequence alignment
 Raw lecture PDF -
Assignment 3 handed out
10 Thu. Oct 16 Steipe Lecture: Homology III: Fast sequence database searches BLAST Ch. 4
11 Mo. Oct 20 Steipe Homology IV: Multiple sequence alignment Multiple Sequence Alignment Ch. 5
Second quiz in class (13:00 tutorial time slot)
Steipe - Ch 6
12 Thu. Oct 23. Assignment 3 due
Steipe Lecture: Structural domains
 Raw lecture PDF -



Analysis based on conservation
# Date Lecture
13 Mon. Oct 27 (Steipe) Phylogenetic analysis I (Book: Ch. 7,8)
Raw lecture PDF

Third quiz in class, 13:00 in tutorial time-slot

14 Thu. Oct 30 (Steipe) Phylogenetic analysis II (Book: Ch. 7,8)

Raw lecture PDF

15 Mon. Nov 3 (Parkinson) Comparative genomics (Book: Ch. Ch. 9.8, 10.8)

Lecture slide PDFs (1.6 MB)

16 Thu. Nov 6 (Steipe) Quiz pickup, Human population genomics (Part 1)
17 Mon. Nov 10 (Steipe) Human population genomics (Part 2)
Raw lecture PDF

Assignment 4 to be posted.

18 Thu. Nov 13 (Steipe) Homology modeling and structure prediction (Part 1)
Raw lecture PDF
19 Mon. Nov 17 (Steipe) Homology modeling and structure prediction (Part 2)
Raw lecture PDF

Assignment 4 due.

Fourth quiz in class: 13:00 in tutorial time slot.

Assignment 5 to be posted.


Analysis based on context
# Date Lecturer Topic Handout Book
20 Thu. Nov 20 Wodak Gene regulation I Lecture slide PDFs (2.1 MB) Ch. 15
21 Mon. Nov 24 Wodak Gene regulation II - -
22 Thu. Nov 27 Wodak Functional annotation Lecture slide PDFs (10.6 MB) Appendix A
23 Mon. Dec 1 Wodak Metabolic networks Lecture slide PDFs (3.1 MB) Ch. 17.1
Assignment 5 due
Fifth quiz in class: 13:00 in tutorial time slot
24 Thu. Dec 4 Parkinson Computational systems biology Lecture slide PDFs (3.4 MB) Ch. 17




In depth...


 

Resources

Course related


 

Contents related

 




 
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