Difference between revisions of "Main Page"

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<tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
 
<tr class="st">
 
<tr class="st">
 
<td colspan="7">'''A b s t r a c t i o n s'''</td>
 
<td colspan="7">'''A b s t r a c t i o n s'''</td>
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<td>3</td>
 
<td>3</td>
 
<td>Mon. Sept 15</td>
 
<td>Mon. Sept 15</td>
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</tr>
 
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<tr class="s2">
+
<!--  ===================    TOPIC    ===================  -->
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<td>3</td>
+
<tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
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<td>Thu. Sept 18</td>
+
<tr class="st">
−
<td>Steipe</td>
+
<td colspan="7">'''A n a l y s i s'''</td>
−
<td>Sequence properties</td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/SequenceProperties.pdf Raw lecture PDF]</small></td>
 
−
<td>Ch 4.9, 11, 12</td>
 
−
<td>-</td>
 
 
</tr>
 
</tr>
  
−
</table>
+
<tr class="sh">
−
 
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on properties'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
 
<td>'''#'''</td>
 
<td>'''#'''</td>
 
<td>'''Date'''</td>
 
<td>'''Date'''</td>
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<td>'''Handout'''</td>
 
<td>'''Handout'''</td>
 
<td>'''Book'''</td>
 
<td>'''Book'''</td>
 +
<td>'''Note'''</td>
 
</tr>
 
</tr>
  
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
+
<tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
  
−
<tr class="s0">
+
<tr class="s1">
 +
<td>3</td>
 +
<td>Thu. Sept 18</td>
 +
<td>Steipe</td>
 +
<td>Sequence properties</td>
 +
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/SequenceProperties.pdf Raw lecture PDF]</small></td>
 +
<td>Ch 4.9, 11, 12</td>
 +
<td>-</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 
<td>4</td>
 
<td>4</td>
 
<td>Mon. Sept 22</td>
 
<td>Mon. Sept 22</td>
 
<td>Steipe</td>
 
<td>Steipe</td>
−
<td> Sequence Analysis </td>
+
<td> Sequence Analysis and Bioinformatics methods</td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/SequenceAnalysis.pdf Raw lecture PDF]</small></td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/SequenceAnalysis.pdf Raw lecture PDF]</small></td>
 
<td>-</td>
 
<td>-</td>
−
 
+
<td>-</td>
 +
</tr>
  
 
<tr class="s1">
 
<tr class="s1">
−
<td rowspan="4">5</td>
+
<td>5</td>
−
<td rowspan="4">Thu. Sept 25.</td>
+
<td>Thu. Sept 25.</td>
−
<td colspan="4">[[Assignment 1]] due</td>
+
<td>Steipe</td>
−
</tr>
+
<td>Interpreting protein structure</td>
−
<tr class="s1">
+
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/InterpretingProteinStructure.pdf Raw lecture PDF]</td>
−
<td colspan="4">'''First quiz''' in class</td>
+
<td>-</td>
 +
<td>[[Assignment 1]] due<br>
 +
<hr>
 +
'''First quiz''' in class<br>
 +
<hr>
 +
[[Assignment 2]] to be posted
 +
</td>
 
</tr>
 
</tr>
 +
 
<tr class="s1">
 
<tr class="s1">
 +
<td>12</td>
 +
<td>Thu. Oct 23.</td>
 
<td>Steipe</td>
 
<td>Steipe</td>
−
<td>Lecture: Interpreting protein structure<br></td>
+
<td>Structural domains</td>
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/InterpretingProteinStructure.pdf Raw lecture PDF]</small></td>
+
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/StructuralDomains.pdf Raw lecture PDF]</small></td>
 
<td>-</td>
 
<td>-</td>
 +
<td>[[Assignment 3]] due</td>
 
</tr>
 
</tr>
 +
 
<tr class="s1">
 
<tr class="s1">
−
<td colspan="4">[[Assignment 2]] handed out
 
−
</td>
 
−
</tr>
 
−
 
−
<tr class="s0">
 
 
<td>6</td>
 
<td>6</td>
 
<td>Mon. Sept 29</td>
 
<td>Mon. Sept 29</td>
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<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Homology_I_Principles.pdf Raw lecture PDF]</small></td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Homology_I_Principles.pdf Raw lecture PDF]</small></td>
 
<td>Ch. 14</td>
 
<td>Ch. 14</td>
 +
<td>-</td>
 +
</tr>
  
 
<tr class="s1">
 
<tr class="s1">
Line 234: Line 240:
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genome_sequencing.pdf Lecture slide PDFs (1.8 MB)]</small></td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genome_sequencing.pdf Lecture slide PDFs (1.8 MB)]</small></td>
 
<td>Ch. 9, 10</td>
 
<td>Ch. 9, 10</td>
 +
<td>-</td>
 
</tr>
 
</tr>
  
−
<tr class="s0">
+
<tr class="s2">
 
<td>8</td>
 
<td>8</td>
 
<td>Mon. Oct 6</td>
 
<td>Mon. Oct 6</td>
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<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genomes.pdf Lecture slide PDFs (2.4 MB)]</td>
 
<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genomes.pdf Lecture slide PDFs (2.4 MB)]</td>
 
<td>-</td>
 
<td>-</td>
 +
<td>-</td>
 +
</tr>
  
−
</table>
+
<!--  ===================    TOPIC    ===================  -->
−
 
+
<tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
−
 
+
<tr class="st">
−
 
+
<td colspan="7">'''H o m o l o g y'''</td>
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on homology'''</td>
 
 
</tr>
 
</tr>
  
−
<tr class="s1">
+
<tr class="sh">
 
<td>'''#'''</td>
 
<td>'''#'''</td>
 
<td>'''Date'''</td>
 
<td>'''Date'''</td>
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<td>'''Handout'''</td>
 
<td>'''Handout'''</td>
 
<td>'''Book'''</td>
 
<td>'''Book'''</td>
 +
<td>'''Note'''</td>
 
</tr>
 
</tr>
  
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
+
<tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
  
−
<tr class="s0">
+
<tr class="s1">
−
<td rowspan="3">9</td>
+
<td>9</td>
−
<td rowspan="3">Thu. Oct 9.</td>
+
<td>Thu. Oct 9.</td>
−
<td colspan="4">[[Assignment 2]] due</td>
 
−
</tr>
 
−
<tr class="s0">
 
 
<td>Steipe</td>
 
<td>Steipe</td>
−
<td>Lecture: Homology II: Sequence alignment<br></td>
+
<td>Lecture: Homology II: Sequence alignment</td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Homology_II_Alignment.pdf Raw lecture PDF]</small></td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Homology_II_Alignment.pdf Raw lecture PDF]</small></td>
−
<td>-</td>
+
<td></td>
−
</tr>
+
<td>[[Assignment 2]] due<br>
−
<tr class="s0">
+
<hr>
−
<td colspan="4">[[Assignment 3]] handed out
+
[[Assignment 3]] to be posted
 +
<hr>
 
</td>
 
</td>
 
</tr>
 
</tr>
  
−
<tr class="s1">
+
 
 +
<tr class="s2">
 
<td>10</td>
 
<td>10</td>
 
<td>'''Thu. Oct 16'''</td>
 
<td>'''Thu. Oct 16'''</td>
Line 287: Line 292:
 
<td>Lecture: Homology III: Fast sequence database searches</td>
 
<td>Lecture: Homology III: Fast sequence database searches</td>
 
<td>[[BLAST]]</td>
 
<td>[[BLAST]]</td>
−
<td>Ch. 4</td>
+
<td>Ch. 5</td>
 +
<td>-</td>
 +
</tr>
  
−
<tr class="s0">
+
<tr class="s1">
−
<td rowspan="3">11</td>
+
<td>11</td>
−
<td rowspan="3">Mo. Oct 20</td>
+
<td>Mo. Oct 20</td>
 
<td>Steipe</td>
 
<td>Steipe</td>
 
<td>Homology IV: Multiple sequence alignment</td>
 
<td>Homology IV: Multiple sequence alignment</td>
 
<td>[[Multiple Sequence Alignment]]</td>
 
<td>[[Multiple Sequence Alignment]]</td>
−
<td>Ch. 5</td>
+
<td>Ch. 6</td>
 +
<td>'''Second quiz''' in class (13:00 tutorial time slot)</td>
 
</tr>
 
</tr>
−
<tr class="s0">
+
 
−
<td colspan="4">'''Second quiz''' in class (13:00 tutorial time slot)</td>
+
<tr class="s2">
−
</tr>
+
<td>18</td>
−
<tr class="s0">
+
<td>Thu. Nov 13</td>
 
<td>Steipe</td>
 
<td>Steipe</td>
−
<td><!-- Lecture: Bioinformatics methods --></td>
+
<td>Homology modeling and structure prediction (Part 1)</td>
 +
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PredictingProteinStructure_I.pdf Raw lecture PDF]</small></td>
 
<td>-</td>
 
<td>-</td>
−
<td>Ch 6</td>
+
<td>-</td>
−
 
+
</tr>
  
 
<tr class="s1">
 
<tr class="s1">
−
<td rowspan="3">12</td>
+
<td>19</td>
−
<td rowspan="3">Thu. Oct 23.</td>
+
<td>Mon. Nov 17</td>
−
<td colspan="4">[[Assignment 3]] due</td>
 
−
</tr>
 
−
<tr class="s1">
 
 
<td>Steipe</td>
 
<td>Steipe</td>
−
<td>Lecture: Structural domains<br></td>
+
<td>Homology modeling and structure prediction (Part 2)</td>
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/StructuralDomains.pdf Raw lecture PDF]</small></td>
+
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PredictingProteinStructure_II.pdf Raw lecture PDF]</small></td>
 
<td>-</td>
 
<td>-</td>
 +
<td>[[Assignment 4]] due.
 +
<hr>
 +
'''Fourth quiz''' in class: 13:00 in tutorial time slot.
 +
<hr>
 +
[[Assignment 5]] to be posted.</td>
 
</tr>
 
</tr>
  
−
</table>
 
  
  
−
 
+
<!--  ===================    TOPIC    ===================  -->
−
 
+
<tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
−
 
+
<tr class="st">
−
<table cellpadding="5">
+
<td colspan="7">'''P h y l o g e n y'''</td>
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on conservation'''</td>
 
 
</tr>
 
</tr>
  
−
<tr class="s1">
+
<tr class="sh">
 
<td>'''#'''</td>
 
<td>'''#'''</td>
 
<td>'''Date'''</td>
 
<td>'''Date'''</td>
−
<td>'''Lecture'''</td>
+
<td>'''Lecturer'''</td>
 +
<td>'''Topic'''</td>
 +
<td>'''Handout'''</td>
 +
<td>'''Book'''</td>
 +
<td>'''Note'''</td>
 
</tr>
 
</tr>
  
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
+
<tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
  
−
<tr class="s0">
+
<tr class="s1">
 
<td>13</td>
 
<td>13</td>
 
<td>Mon. Oct 27</td>
 
<td>Mon. Oct 27</td>
−
<td>(Steipe) Phylogenetic analysis I (Book: Ch. 7,8)<br><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PhylogeneticAnalysis_I.pdf Raw lecture PDF]</small>
+
<td>Steipe</td>
−
<hr>
+
<td>Phylogenetic analysis I</td>
−
'''Third quiz''' in class, 13:00 in tutorial time-slot
+
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PhylogeneticAnalysis_I.pdf Raw lecture PDF]</small></td>
−
</td>
+
<td>Ch. 7,8</td>
 +
<td>'''Third quiz''' in class, 13:00 in tutorial time-slot</td>
 
</tr>
 
</tr>
  
−
<tr class="s1">
+
<tr class="s2">
 
<td>14</td>
 
<td>14</td>
 
<td>Thu. Oct 30</td>
 
<td>Thu. Oct 30</td>
−
<td>(Steipe) Phylogenetic analysis II (Book: Ch. 7,8)<br>
+
<td>Steipe</td>
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PhylogeneticAnalysis_II.pdf Raw lecture PDF]</small>
+
<td>Phylogenetic analysis II</td>
−
</td>
+
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PhylogeneticAnalysis_II.pdf Raw lecture PDF]</small></td>
 +
<td>Ch. 7,8</td>
 +
<td>-</td>
 
</tr>
 
</tr>
  
−
<tr class="s0">
+
<tr class="s1">
 
<td>15</td>
 
<td>15</td>
 
<td>Mon. Nov 3</td>
 
<td>Mon. Nov 3</td>
−
<td>(Parkinson) Comparative genomics (Book: Ch. Ch. 9.8, 10.8)<br>
+
<td>Parkinson</td>
−
[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/ComparativeGenomics.pdf Lecture slide PDFs (1.6 MB)]
+
<td>Comparative genomics</td>
−
</td>
+
<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/ComparativeGenomics.pdf Lecture slide PDFs (1.6 MB)]</td>
 +
<td>Ch. 9.8, 10.8</td>
 +
<td>-</td>
 
</tr>
 
</tr>
  
−
<tr class="s1">
+
<tr class="s2">
−
<td>16</td>
 
−
<td>Thu. Nov 6</td>
 
−
<td>(Steipe) Quiz pickup, Human population genomics (Part 1)<br>
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
 
<td>17</td>
 
<td>17</td>
 
<td>Mon. Nov 10</td>
 
<td>Mon. Nov 10</td>
−
<td>(Steipe) Human population genomics (Part 2)<br>
+
<td>Steipe</td>
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/HumanPopulationGenomics.pdf Raw lecture PDF]</small><hr>
+
<td>Human population genomics</td>
−
[[Assignment 4]] to be posted.
+
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/HumanPopulationGenomics.pdf Raw lecture PDF]</small></td>
−
</td>
+
<td>-</td>
 +
<td>[[Assignment 4]] to be posted</td>
 
</tr>
 
</tr>
  
−
 
+
<!--  ===================    TOPIC    ===================  -->
−
<tr class="s1">
+
<tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
−
<td>18</td>
+
<tr class="st">
−
<td>Thu. Nov 13</td>
+
<td colspan="7">'''I n t e r a c t i o n s'''</td>
−
<td>(Steipe) Homology modeling and structure prediction (Part 1)<br>
 
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PredictingProteinStructure_I.pdf Raw lecture PDF]</small></td>
 
 
</tr>
 
</tr>
  
−
<tr class="s0">
+
<tr class="sh">
−
<td>19</td>
 
−
<td>Mon. Nov 17</td>
 
−
<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>
 
−
[[Assignment 4]] due.
 
−
<hr>
 
−
'''Fourth quiz''' in class: 13:00 in tutorial time slot.
 
−
<hr>
 
−
[[Assignment 5]] to be posted.
 
−
</td>
 
−
</tr>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on context'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
 
<td>'''#'''</td>
 
<td>'''#'''</td>
 
<td>'''Date'''</td>
 
<td>'''Date'''</td>
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<td>'''Handout'''</td>
 
<td>'''Handout'''</td>
 
<td>'''Book'''</td>
 
<td>'''Book'''</td>
 +
<td>'''Note'''</td>
 
</tr>
 
</tr>
  
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
+
<tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
  
−
<tr class="s0">
+
<tr class="s1">
 
<td>20</td>
 
<td>20</td>
 
<td>Thu. Nov 20</td>
 
<td>Thu. Nov 20</td>
 
<td> Wodak </td>
 
<td> Wodak </td>
−
<td>Gene regulation I</td>
+
<td>Gene regulation (Part 1)</td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/GeneRegulation.pdf Lecture slide PDFs (2.1 MB)]</small></td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/GeneRegulation.pdf Lecture slide PDFs (2.1 MB)]</small></td>
 
<td>Ch. 15</td>
 
<td>Ch. 15</td>
 +
<td>-</td>
 
</tr>
 
</tr>
  
−
<tr class="s1">
+
<tr class="s2">
 
<td>21</td>
 
<td>21</td>
 
<td>Mon. Nov 24</td>
 
<td>Mon. Nov 24</td>
 
<td>Wodak</td>
 
<td>Wodak</td>
−
<td>Gene regulation II</td>
+
<td>Gene regulation (Part 2)</td>
 +
<td>-</td>
 
<td>-</td>
 
<td>-</td>
 
<td>-</td>
 
<td>-</td>
 
</tr>
 
</tr>
  
−
<tr class="s0">
+
<tr class="s1">
 
<td>22</td>
 
<td>22</td>
 
<td>Thu. Nov 27</td>
 
<td>Thu. Nov 27</td>
Line 446: Line 435:
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/FunctionalAnnotations.pdf Lecture slide PDFs ('''10.6 MB''')]</small></td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/FunctionalAnnotations.pdf Lecture slide PDFs ('''10.6 MB''')]</small></td>
 
<td>Appendix A</td>
 
<td>Appendix A</td>
 +
<td>-</td>
 
</tr>
 
</tr>
  
  
−
<tr class="s1">
+
<tr class="s2">
−
<td rowspan="2">23</td>
+
<td>23</td>
−
<td rowspan="2">Mon. Dec 1</td>
+
<td>Mon. Dec 1</td>
 
<td>Wodak</td>
 
<td>Wodak</td>
 
<td>Metabolic networks</td>
 
<td>Metabolic networks</td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PathwaysAndNetworks.pdf Lecture slide PDFs (3.1 MB)]</small></td>
 
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PathwaysAndNetworks.pdf Lecture slide PDFs (3.1 MB)]</small></td>
 
<td>Ch. 17.1</td>
 
<td>Ch. 17.1</td>
−
</tr>
+
<td>[[Assignment 5]] due<br>
−
<tr class="s1">
 
−
<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>
 
</tr>
 
</tr>
  
−
<tr class="s0">
+
<tr class="s1">
 
<td>24</td>
 
<td>24</td>
 
<td>Thu. Dec 4</td>
 
<td>Thu. Dec 4</td>
Line 470: Line 459:
 
<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/ComputationalSystemsBiology.pdf Lecture slide PDFs (3.4 MB)]</td>
 
<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/ComputationalSystemsBiology.pdf Lecture slide PDFs (3.4 MB)]</td>
 
<td>Ch. 17</td>
 
<td>Ch. 17</td>
 +
<td>-</td>
 
</tr>
 
</tr>
  

Revision as of 17:18, 23 July 2009

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

We'll be back soon:

First class: Thursday, September 10. 2009

Organization

Dates
Lectures: Monday and Thursday, 12:00 to 13:00
Tutorial sessions: Mondays, 13:00 to 14:00   for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.
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 section is currently under construction.


I n t r o d u c t i o n
# Date Lecturer Topic Handout Book Note
1 Mon. Sept 8 Steipe Organisation and Orientation Introduction Ch 1, 2 -
A b s t r a c t i o n s
# Date Lecturer Topic Handout Book Note
2 Thu. Sept 11 Steipe Sequence abstraction and sequence databases Sequence data Ch 3 Assignment 1 to be handed out
3 Mon. Sept 15 Steipe Protein Structure Data Structure data - -
A n a l y s i s
# Date Lecturer Topic Handout Book Note
3 Thu. Sept 18 Steipe Sequence properties Raw lecture PDF Ch 4.9, 11, 12 -
4 Mon. Sept 22 Steipe Sequence Analysis and Bioinformatics methods Raw lecture PDF - -
5 Thu. Sept 25. Steipe Interpreting protein structure Raw lecture PDF - Assignment 1 due

First quiz in class

Assignment 2 to be posted

12 Thu. Oct 23. Steipe Structural domains Raw lecture PDF - Assignment 3 due
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) - -
H o m o l o g y
# Date Lecturer Topic Handout Book Note
9 Thu. Oct 9. Steipe Lecture: Homology II: Sequence alignment Raw lecture PDF Assignment 2 due

Assignment 3 to be posted

10 Thu. Oct 16 Steipe Lecture: Homology III: Fast sequence database searches BLAST Ch. 5 -
11 Mo. Oct 20 Steipe Homology IV: Multiple sequence alignment Multiple Sequence Alignment Ch. 6 Second quiz in class (13:00 tutorial time slot)
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.
P h y l o g e n y
# Date Lecturer Topic Handout Book Note
13 Mon. Oct 27 Steipe Phylogenetic analysis I Raw lecture PDF Ch. 7,8 Third quiz in class, 13:00 in tutorial time-slot
14 Thu. Oct 30 Steipe Phylogenetic analysis II Raw lecture PDF Ch. 7,8 -
15 Mon. Nov 3 Parkinson Comparative genomics Lecture slide PDFs (1.6 MB) Ch. 9.8, 10.8 -
17 Mon. Nov 10 Steipe Human population genomics Raw lecture PDF - Assignment 4 to be posted
I n t e r a c t i o n s
# Date Lecturer Topic Handout Book Note
20 Thu. Nov 20 Wodak Gene regulation (Part 1) Lecture slide PDFs (2.1 MB) Ch. 15 -
21 Mon. Nov 24 Wodak Gene regulation (Part 2) - - -
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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