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<small>Don't trust information below.</small>
 
<small>Don't trust information below.</small>
 
</div>
 
</div>
 +
 +
 +
 +
<table cellpadding="5">
 +
 +
<tr>
 +
<td  style="border:solid 1px #000000;">'''#'''</td>
 +
<td  style="border:solid 1px #000000;">'''Date'''</td>
 +
<td  style="border:solid 1px #000000;">'''Lecturer'''</td>
 +
<td  style="border:solid 1px #000000;">'''Topic'''</td>
 +
<td  style="border:solid 1px #000000;">'''Handout'''</td>
 +
<td  style="border:solid 1px #000000;">'''Book'''</td>
 +
</tr>
 +
 +
<tr>
 +
<td  style="border:solid 1px #000000;">0</td>
 +
<td  style="border:solid 1px #000000;">Mon. Sept 8</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;">Organisation and Orientation</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
</tr>
 +
 +
</table>
 +
 +
 +
 +
<table cellpadding="5">
 +
 +
<tr>
 +
<td colspan="6"  style="border:solid 1px #000000;">'''The objects of bioinformatics'''</td>
 +
</tr>
 +
 +
<tr>
 +
<td  style="border:solid 1px #000000;">'''#'''</td>
 +
<td  style="border:solid 1px #000000;">'''Date'''</td>
 +
<td  style="border:solid 1px #000000;">'''Lecturer'''</td>
 +
<td  style="border:solid 1px #000000;">'''Topic'''</td>
 +
<td  style="border:solid 1px #000000;">'''Handout'''</td>
 +
<td  style="border:solid 1px #000000;">'''Book'''</td>
 +
</tr>
 +
 +
<tr>
 +
<td  style="border:solid 1px #000000;">1</td>
 +
<td  style="border:solid 1px #000000;">Thu. Sept 11</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;">Sequence abstraction and sequence databases</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">Ch 3</td>
 +
</tr>
 +
 +
<tr>
 +
<td  style="border:solid 1px #000000;">2</td>
 +
<td  style="border:solid 1px #000000;">Mon. Sept 15</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;">Protein Structure Databases</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
 +
<tr>
 +
<td  style="border:solid 1px #000000;">3</td>
 +
<td  style="border:solid 1px #000000;">Thu. Sept 18</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;">Bioinformatics methods</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
</tr>
 +
 +
</table>
 +
 +
  
 
<table cellpadding="5">
 
<table cellpadding="5">
  
 
<tr>
 
<tr>
−
<td class="syllabus">'''#'''</td>
+
<td colspan="6"  style="border:solid 1px #000000;">'''Analysis based on properties'''</td>
−
<td class="syllabus">'''Date'''</td>
+
</tr>
−
<td class="syllabus">'''Lecturer'''</td>
+
 
−
<td class="syllabus">'''Topic'''</td>
+
<tr>
−
<td class="syllabus">'''Handout'''</td>
+
<td  style="border:solid 1px #000000;">'''#'''</td>
−
<td class="syllabus">'''Book'''</td>
+
<td style="border:solid 1px #000000;">'''Date'''</td>
 +
<td style="border:solid 1px #000000;">'''Lecturer'''</td>
 +
<td style="border:solid 1px #000000;">'''Topic'''</td>
 +
<td style="border:solid 1px #000000;">'''Handout'''</td>
 +
<td style="border:solid 1px #000000;">'''Book'''</td>
 +
</tr>
 +
 
 +
<tr>
 +
<td  style="border:solid 1px #000000;">4</td>
 +
<td  style="border:solid 1px #000000;">Mon. Sept 22</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;">Sequence properties</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">Ch 4.9, 11, 12</td>
 +
 
 +
<tr>
 +
<td  style="border:solid 1px #000000;">5</td>
 +
<td  style="border:solid 1px #000000;">Thu. Sept 25</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;"> Sequence Analysis </td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 
</tr>
 
</tr>
  
 
<tr>
 
<tr>
−
<td class="syllabus">0</td>
+
<td style="border:solid 1px #000000;">6</td>
−
<td class="syllabus">Mon. Sept 8</td>
+
<td style="border:solid 1px #000000;">Mon. Sept 29</td>
−
<td class="syllabus">Steipe</td>
+
<td style="border:solid 1px #000000;">Steipe</td>
−
<td class="syllabus">Organisation and Orientation</td>
+
<td style="border:solid 1px #000000;">Interpreting protein structure</td>
−
<td class="syllabus">-</td>
+
<td style="border:solid 1px #000000;">-</td>
−
<td class="syllabus">-</td>
+
<td style="border:solid 1px #000000;">Ch. 14</td>
 +
 
 +
<tr>
 +
<td  style="border:solid 1px #000000;">7</td>
 +
<td  style="border:solid 1px #000000;">Thu. Oct 2</td>
 +
<td  style="border:solid 1px #000000;">Parkinson</td>
 +
<td  style="border:solid 1px #000000;">Genome sequencing, genome browsers</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">Ch. 9, 10</td>
 
</tr>
 
</tr>
 +
 +
<tr>
 +
<td  style="border:solid 1px #000000;">8</td>
 +
<td  style="border:solid 1px #000000;">Mon. Oct 6</td>
 +
<td  style="border:solid 1px #000000;">Parkinson</td>
 +
<td  style="border:solid 1px #000000;">Genomes and genome structure</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">-</td>
  
 
</table>
 
</table>
  
−
<!--
 
  
−
<table border="1" cellpadding="5">
+
 
 +
<table cellpadding="5">
 +
 
 +
<tr>
 +
<td colspan="6"  style="border:solid 1px #000000;">'''Analysis based on homology'''</td>
 +
</tr>
 +
 
 +
<tr>
 +
<td  style="border:solid 1px #000000;">'''#'''</td>
 +
<td  style="border:solid 1px #000000;">'''Date'''</td>
 +
<td  style="border:solid 1px #000000;">'''Lecturer'''</td>
 +
<td  style="border:solid 1px #000000;">'''Topic'''</td>
 +
<td  style="border:solid 1px #000000;">'''Handout'''</td>
 +
<td  style="border:solid 1px #000000;">'''Book'''</td>
 +
</tr>
  
 
<tr>
 
<tr>
−
<td colspan="6" class="syllabus">'''The objects of bioinformatics'''</td>
+
<td style="border:solid 1px #000000;"></td>
 +
<td  style="border:solid 1px #000000;">Thu. Oct 9.</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;">Homology I: the principles</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 
</tr>
 
</tr>
  
 
<tr>
 
<tr>
−
<td class="syllabus">'''#'''</td>
+
<td style="border:solid 1px #000000;"></td>
−
<td class="syllabus">'''Date'''</td>
+
<td  style="border:solid 1px #000000;">'''Thu. Oct 16'''</td>
−
<td class="syllabus">'''Lecturer'''</td>
+
<td style="border:solid 1px #000000;">Steipe</td>
−
<td class="syllabus">'''Topic'''</td>
+
<td  style="border:solid 1px #000000;">Homology II: Sequence alignment</td>
−
<td class="syllabus">'''Handout'''</td>
+
<td  style="border:solid 1px #000000;">-</td>
−
<td class="syllabus">'''Book'''</td>
+
<td  style="border:solid 1px #000000;">Ch. 4</td>
 +
 
 +
<tr>
 +
<td  style="border:solid 1px #000000;"></td>
 +
<td  style="border:solid 1px #000000;">Mo. Oct 20</td>
 +
<td style="border:solid 1px #000000;">Steipe</td>
 +
<td style="border:solid 1px #000000;">Homology III: Multiple sequence alignment</td>
 +
<td style="border:solid 1px #000000;">-</td>
 +
<td style="border:solid 1px #000000;">Ch. 5</td>
 
</tr>
 
</tr>
  
 +
<tr>
 +
<td  style="border:solid 1px #000000;"></td>
 +
<td  style="border:solid 1px #000000;">'''Mon. Oct 20'''</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;">Homology IV: fast sequence database searches</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">Ch 6</td>
  
 
<tr>
 
<tr>
−
<td class="syllabus">1</td>
+
<td style="border:solid 1px #000000;"></td>
−
<td class="syllabus">Thu. Sept 11</td>
+
<td style="border:solid 1px #000000;">Thu. Oct 23</td>
−
<td class="syllabus">Steipe</td>
+
<td style="border:solid 1px #000000;">Steipe</td>
−
<td class="syllabus">Sequence abstraction and sequence databases</td>
+
<td style="border:solid 1px #000000;">Structural domains</td>
−
<td class="syllabus">-</td>
+
<td style="border:solid 1px #000000;">-</td>
−
<td class="syllabus">Ch 3</td>
+
<td style="border:solid 1px #000000;">-</td>
 
</tr>
 
</tr>
 +
 +
<tr>
 +
<td  style="border:solid 1px #000000;"></td>
 +
<td  style="border:solid 1px #000000;">Mon. Oct 27</td>
 +
<td  style="border:solid 1px #000000;">Steipe</td>
 +
<td  style="border:solid 1px #000000;">Homology modeling and structure prediction</td>
 +
<td  style="border:solid 1px #000000;">-</td>
 +
<td  style="border:solid 1px #000000;">Ch. 13</td>
  
 
</table>
 
</table>
  
−
-->
+
 
 +
<!--
  
 
;Sequences
 
;Sequences
Line 155: Line 305:
 
<li>[[Lecture_26|'''Computational Systems Biology''']] (John,  Thursday, Dec. 7)
 
<li>[[Lecture_26|'''Computational Systems Biology''']] (John,  Thursday, Dec. 7)
 
</ol>
 
</ol>
 +
-->
  
 
== Assignments ==
 
== Assignments ==

Revision as of 15:13, 8 September 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

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 schedule is for orientation only, changes may be made at any time as the subject matter and the progress of the lecture requires. This is the old schedule for 2007 with the 2007 dates and will be rearranged and changed for 2008.)


Ongoing construction
Don't trust information below.


# 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
Thu. Oct 9. Steipe Homology I: the principles - -
Thu. Oct 16 Steipe Homology II: Sequence alignment - Ch. 4
Mo. Oct 20 Steipe Homology III: Multiple sequence alignment - Ch. 5
Mon. Oct 20 Steipe Homology IV: fast sequence database searches - Ch 6
Thu. Oct 23 Steipe Structural domains - -
Mon. Oct 27 Steipe Homology modeling and structure prediction - Ch. 13


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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