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<div style="padding: 5px; background: #457DB5;  border:solid 1px #AAAAAA; font-size:300%;font-weight:bold; color:#FFFFFF">
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#REDIRECT [[Bioinformatics_Main_Page]]
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BCH441 - Bioinformatics
 
  
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<div style="font-size:50%;font-weight:normal;">
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{{Vspace}}
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Welcome to the BCH441 Course Wiki.
 
−
</div>
 
−
</div>
 
−
 
 
−
<small>'''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 [http://en.wikipedia.org/wiki/Bioinformatics Wikipedia article on bioinformatics], or visit [http://www.openwetware.org/wiki/Wikiomics Wikiomics]. Contact boris.steipe(at)utoronto.ca with any questions you may have.</small>
 
−
 
 
−
 
 
−
== The Course ==
 
  
−
<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
+
<div id="BIO">
 +
<div class="b1" style="padding-left:7%;">
  
−
I will offer a final tutorial/review on Monday, December 8. starting at 12:00 in the lecture room.
+
&nbsp;<br/>
  
 +
<div style="font-size:150%;font-weight:bold;">
 +
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">A&nbsp;&nbsp;B&nbsp;&nbsp;C</span>]]
 
</div>
 
</div>
  
−
== Organization ==
+
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Applying Bioinformatics Concepts</span>]]
−
 
 
−
;Dates
 
−
: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>
 
−
:First class: Monday, September 8. 2008
 
−
 
 
−
;Location
 
−
:MSB 2173 (Medical Sciences Building)
 
−
 
 
−
See the [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/ Course Web page] for general information.
 
−
 
 
−
We are recommending '''[http://www.garlandscience.com/textbooks/0815340249.asp Understanding Bioinformatics]''', Zvelebil &amp; Baum, Garland 2008 as a background textbook for the course. <small>([http://www.amazon.ca/Understanding-Bioinformatics-Market-Zvelebil/dp/0815340249 amazon], [http://www.uoftbookstore.com/online/merchant.ihtml?pid=1051140&step=4 UofT Bookstore])</small>
 
−
 
 
−
== Grading and Activities ==
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="sh">
 
−
<td>'''Activity'''</td>
 
−
<td>'''Weight'''<br><small>(Undergraduates)</small></td>
 
−
<td>'''Weight'''<br><small>(Graduates)</small></td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>[[Assignments|'''5 Assignments''' (drop 1)]]</td>
 
−
<td>16 marks <small>(4 x 4)</small></td>
 
−
<td>12 marks <small>(4 x 3)</small></td>
 
−
</tr>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td>[[Quizzes|'''5 In-class quizzes''' (drop 1)]]</td>
 
−
<td>32 marks <small>(4 x 8)</small></td>
 
−
<td>20 marks <small>(4 x 5)</small></td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>'''[[Group project]]'''</td>
 
−
<td>10 marks</td>
 
−
<td>6 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''[[Participation]]'''</td>
 
−
<td>2 marks</td>
 
−
<td>2 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>'''[[Graduate project]]'''</td>
 
−
<td>&nbsp;</td>
 
−
<td>20 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>[[Exam questions|'''Final exam''']]</td>
 
−
<td>40 marks</td>
 
−
<td>40 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>'''Total'''</td>
 
−
<td>100 marks</td>
 
−
<td>100 marks</td>
 
−
</tr>
 
−
 
 
−
</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.
 
−
 
 
−
== Lecture Schedule ==
 
−
<small>This is the current schedule for 2008, but changes may be still be made if required.</small>
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>0</td>
 
−
<td>Mon. Sept 8</td>
 
−
<td>Steipe</td>
 
−
<td>Organisation and Orientation</td>
 
−
<td>[[Introduction]]</td>
 
−
<td>Ch 1, 2</td>
 
−
</tr>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''The objects of bioinformatics'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td rowspan="2">1</td>
 
−
<td rowspan="2">Thu. Sept 11</td>
 
−
<td>Steipe</td>
 
−
<td>Sequence abstraction and sequence databases</td>
 
−
<td>[[Sequence data]]</td>
 
−
<td>Ch 3</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td colspan="4">[[Assignment 1|Assignment 1 handed out]]</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>2</td>
 
−
<td>Mon. Sept 15</td>
 
−
<td>Steipe</td>
 
−
<td>Protein Structure Data</td>
 
−
<td>[[Structure data]]</td>
 
−
<td>-</td>
 
−
 
 
−
<tr class="s0">
 
−
<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>
 
−
</tr>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on properties'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>4</td>
 
−
<td>Mon. Sept 22</td>
 
−
<td>Steipe</td>
 
−
<td> Sequence Analysis </td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/SequenceAnalysis.pdf Raw lecture PDF]</small></td>
 
−
<td>-</td>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td rowspan="4">5</td>
 
−
<td rowspan="4">Thu. Sept 25.</td>
 
−
<td colspan="4">[[Assignment 1]] due</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td colspan="4">'''First quiz''' in class</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td>Steipe</td>
 
−
<td>Lecture: Interpreting protein structure<br></td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/InterpretingProteinStructure.pdf Raw lecture PDF]</small></td>
 
−
<td>-</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td colspan="4">[[Assignment 2]] handed out
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>6</td>
 
−
<td>Mon. Sept 29</td>
 
−
<td>Steipe</td>
 
−
<td>Homology I: the principles</td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Homology_I_Principles.pdf Raw lecture PDF]</small></td>
 
−
<td>Ch. 14</td>
 
−
 
 
−
<tr class="s1">
 
−
<td>7</td>
 
−
<td>Thu. Oct 2</td>
 
−
<td>Parkinson</td>
 
−
<td>Genome sequencing, genome browsers</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>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>8</td>
 
−
<td>Mon. Oct 6</td>
 
−
<td>Parkinson</td>
 
−
<td>Genomes and genome structure</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on homology'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td rowspan="3">9</td>
 
−
<td rowspan="3">Thu. Oct 9.</td>
 
−
<td colspan="4">[[Assignment 2]] due</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td>Steipe</td>
 
−
<td>Lecture: Homology II: Sequence alignment<br></td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Homology_II_Alignment.pdf Raw lecture PDF]</small></td>
 
−
<td>-</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td colspan="4">[[Assignment 3]] handed out
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>10</td>
 
−
<td>'''Thu. Oct 16'''</td>
 
−
<td>Steipe</td>
 
−
<td>Lecture: Homology III: Fast sequence database searches</td>
 
−
<td>[[BLAST]]</td>
 
−
<td>Ch. 4</td>
 
−
 
 
−
<tr class="s0">
 
−
<td rowspan="3">11</td>
 
−
<td rowspan="3">Mo. Oct 20</td>
 
−
<td>Steipe</td>
 
−
<td>Homology IV: Multiple sequence alignment</td>
 
−
<td>[[Multiple Sequence Alignment]]</td>
 
−
<td>Ch. 5</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td colspan="4">'''Second quiz''' in class (13:00 tutorial time slot)</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td>Steipe</td>
 
−
<td><!-- Lecture: Bioinformatics methods --></td>
 
−
<td>-</td>
 
−
<td>Ch 6</td>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td rowspan="3">12</td>
 
−
<td rowspan="3">Thu. Oct 23.</td>
 
−
<td colspan="4">[[Assignment 3]] due</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td>Steipe</td>
 
−
<td>Lecture: Structural domains<br></td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/StructuralDomains.pdf Raw lecture PDF]</small></td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
 
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on conservation'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecture'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>13</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>
 
−
<hr>
 
−
'''Third quiz''' in class, 13:00 in tutorial time-slot
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>14</td>
 
−
<td>Thu. Oct 30</td>
 
−
<td>(Steipe) Phylogenetic analysis II (Book: Ch. 7,8)<br>
 
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PhylogeneticAnalysis_II.pdf Raw lecture PDF]</small>
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>15</td>
 
−
<td>Mon. Nov 3</td>
 
−
<td>(Parkinson) Comparative genomics (Book: Ch. Ch. 9.8, 10.8)<br>
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<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>Mon. Nov 10</td>
 
−
<td>(Steipe) Human population genomics (Part 2)<br>
 
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/HumanPopulationGenomics.pdf Raw lecture PDF]</small><hr>
 
−
Assignment 4 to be posted.
 
−
</td>
 
−
</tr>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td>18</td>
 
−
<td>Thu. Nov 13</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 class="s0">
 
−
<td>18</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>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>20</td>
 
−
<td>Thu. Nov 20</td>
 
−
<td> Wodak </td>
 
−
<td>Gene regulation I</td>
 
−
<td>-</td>
 
−
<td>Ch. 15</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>21</td>
 
−
<td>Mon. Nov 24</td>
 
−
<td>Wodak</td>
 
−
<td>Gene regulation II</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>22</td>
 
−
<td>Thu. Nov 27</td>
 
−
<td>Wodak</td>
 
−
<td>Functional annotation</td>
 
−
<td>-</td>
 
−
<td>Appendix A</td>
 
−
</tr>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td rowspan="2">23</td>
 
−
<td rowspan="2">Mon. Dec 1</td>
 
−
<td>Wodak</td>
 
−
<td>Metabolic networks</td>
 
−
<td>-</td>
 
−
<td>Ch. 17.1</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td colspan="4">Assignment 5 due<br>
 
−
<hr>
 
−
'''Fifth quiz''' in class: 13:00 in tutorial time slot</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>24</td>
 
−
<td>Thu. Dec 4</td>
 
−
<td>Parkinson</td>
 
−
<td>Computational systems biology</td>
 
−
<td>-</td>
 
−
<td>Ch. 17</td>
 
−
</tr>
 
−
 
 
  
−
</table>
+
<div style="font-size:50%;font-weight:bold;">
−
<!--
+
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Boris Steipe&nbsp;&nbsp;(2006 – 2020)</span>]]
−
 
 
−
;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>
 
</div>
−
</ol>
 
−
 
−
<p>
 
−
<small>('''*''') Double lecture (12:00 - 14:00) to make up for Thanksgiving, Oct 8.</small>
 
  
−
;Genomes
+
&nbsp;<br/>
−
<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>
 
</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)
 
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<li>[[Lecture_25|'''Metabolic Networks''']] (Shoshana,  Monday, Dec. 3)
 
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<li>[[Lecture_26|'''Computational Systems Biology''']] (John,  Thursday, Dec. 7)
 
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</ol>
 
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-->
 
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<div style="padding: 5px; background: #FFDD33;  border:solid 3px #000000; font-size:150%;font-weight:bold;">
 
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Ongoing construction <br>
 
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<small>Don't trust information below.</small>
 
 
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== Assignments ==
 
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&nbsp;
 
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&nbsp;
 
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<table border="0" cellpadding="5">
 
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<tr>
 
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<td>[[Assignment_1|'''First Assignment''']]</td>
 
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<td>Databases and Molecular Models</td>
 
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<td>''posted Sept. 13, due Oct. 1.''</td>
 
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</tr>
 
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<tr>
 
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<td>[[Assignment_2|'''Second Assignment''']]</td>
 
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<td>Search, Retrieve and Annotate</td>
 
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<td>''posted Sept. 24, due Oct. 9.''</td>
 
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</tr>
 
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<tr>
 
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<td>[[Assignment_3|'''Third Assignment''']]</td>
 
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<td>Multiple Sequence Alignment</td>
 
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<td>posted Oct. 10, due Oct. 22.</td>
 
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</tr>
 
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<tr>
 
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<td>[[Assignment_4|'''Fourth Assignment''']]</td>
 
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<td>Homology Modeling</td>
 
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<td>posted Nov. 1, due Nov. 12.</td>
 
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</tr>
 
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<tr>
 
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<td>[[Assignment_5|'''Fifth Assignment''']]</td>
 
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<td>Phylogenetic Analysis</td>
 
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<td>posted Nov. 28, due Dec. 7.''</td>
 
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</tr>
 
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<tr>
 
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<td>[[Assignment_6|'''Sixth Assignment''']]</td>
 
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<td>Systems</td>
 
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<td>posted Dec. 4, due Dec. 7 (last day of class)</td>
 
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</tr>
 
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</table>
 
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&nbsp;
 
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-->
 
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==In depth...==
 
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* [[Glossary]]
 
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* [[Mutation Data Matrices]]
 
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* [http://en.wikipedia.org/wiki/List_of_standard_amino_acids Amino acids]
 
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<!-- * [[Database Identifiers]] -->
 
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&nbsp;
 
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== Resources ==
 
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;Course related
 
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*The [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/ Course Web site].
 
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*The [http://groups.google.com/group/bch441_2008 Course Google Group].
 
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*[[Netiquette]] for the Group mailing list
 
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*Previous [[Exam_questions]]
 
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*[[Feedback_2007|2007 course feedback]]
 
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&nbsp;<br>
 
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;Contents related
 
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*The '''[[VMD]]''' tutorial
 
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*A '''[[Stereo Vision]]''' tutorial
 
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*[http://biodatabase.org/index.php/Main_Page MetaDatabase]
 
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*[http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl NAR January-2008 '''Database''' issue]
 
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*[http://nar.oxfordjournals.org/content/vol36/suppl_2/index.dtl NAR July-2008 '''Web server''' issue]
 
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&nbsp;<br>
 
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<!--
 
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;Course Wiki
 
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*[[Help:Introduction|Introduction:]] Concept and contents of the Course Wiki
 
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*[[Soapbox]]: A page to commmunicate. Do you want to leave a message? Alert the course members? Voice an opinion? Praise or flame? Use this page.
 
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*[[Help:Editing| Editing:]] Editing principles and Wiki markup syntax for the Course Wiki pages
 
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*[[Sandbox]]: A page for your editing experiments. Content added to this page will not stay permanently.
 
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*[[Feedback]]: Share your views on the course, suggest improvements.
 
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-->
 
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&nbsp;<br>
 
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<!--- Color schemes
 
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<div style="padding: 3px; background: #457DB5;  border:solid 1px #AAAAAA;">Level 1</div>
 
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<div style="padding: 3px; background: #6F9BD0;  border:solid 1px #AAAAAA;">Level 2</div>
 
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<div style="padding: 3px; background: #9CC86F;  border:solid 1px #AAAAAA;">Level 3</div>
 
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<div style="padding: 3px; background: #F0F07A;  border:solid 1px #AAAAAA;">Alert</div>
 
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&nbsp;
 
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<div style="padding: 3px; background: #FF4560;  border:solid 1px #AAAAAA;">Warning!</div>
 
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&nbsp;
 
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--->
 

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