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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.
 
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</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://wikiomics.org/wiki/Main_Page Wikiomics]. Contact boris.steipe(at)utoronto.ca with any questions you may have.</small>
+
<div id="BIO">
 +
<div class="b1" style="padding-left:7%;">
  
 +
&nbsp;<br/>
  
−
== The Course ==
+
<div style="font-size:150%;font-weight:bold;">
−
 
+
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">A&nbsp;&nbsp;B&nbsp;&nbsp;C</span>]]
−
<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
+
</div>
−
Here are two tasks I would like you to get completed before the next class.<br>
 
−
 
 
−
<small>
 
−
;1. Please subscribe yourself to the '''[[Course Mailing List]]
 
−
 
 
−
;2. Please download and install [[VMD]]
 
−
 
 
−
(follow the links above for more information).
 
−
 
 
−
</small></div>
 
−
 
 
−
== Organization ==
 
−
 
 
−
;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.
 
−
 
 
−
 
 
−
== 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>-</td>
 
−
<td>-</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="s0">
 
−
<td>1</td>
 
−
<td>Thu. Sept 11</td>
 
−
<td>Steipe</td>
 
−
<td>Sequence abstraction and sequence databases</td>
 
−
<td>-</td>
 
−
<td>Ch 3</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>2</td>
 
−
<td>Mon. Sept 15</td>
 
−
<td>Steipe</td>
 
−
<td>Protein Structure Databases</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
 
 
−
<tr class="s0">
 
−
<td>3</td>
 
−
<td>Thu. Sept 18</td>
 
−
<td>Steipe</td>
 
−
<td>Bioinformatics methods</td>
 
−
<td>-</td>
 
−
<td>-</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="s0">
 
−
<td>4</td>
 
−
<td>Mon. Sept 22</td>
 
−
<td>Steipe</td>
 
−
<td>Sequence properties</td>
 
−
<td>-</td>
 
−
<td>Ch 4.9, 11, 12</td>
 
−
 
 
−
<tr class="s1">
 
−
<td>5</td>
 
−
<td>Thu. Sept 25</td>
 
−
<td>Steipe</td>
 
−
<td> Sequence Analysis </td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>6</td>
 
−
<td>Mon. Sept 29</td>
 
−
<td>Steipe</td>
 
−
<td>Interpreting protein structure</td>
 
−
<td>-</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>-</td>
 
−
<td>Ch. 9, 10</td>
 
−
</tr>
 
  
−
<tr class="s0">
+
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Applying Bioinformatics Concepts</span>]]
−
<td>8</td>
 
−
<td>Mon. Oct 6</td>
 
−
<td>Parkinson</td>
 
−
<td>Genomes and genome structure</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
  
−
</table>
+
<div style="font-size:50%;font-weight:bold;">
−
 
+
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Boris Steipe&nbsp;&nbsp;(2006 – 2020)</span>]]
−
 
 
−
 
 
−
<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="s0">
 
−
<td>9</td>
 
−
<td>Thu. Oct 9.</td>
 
−
<td>Steipe</td>
 
−
<td>Homology I: the principles</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>10</td>
 
−
<td>'''Thu. Oct 16'''</td>
 
−
<td>Steipe</td>
 
−
<td>Homology II: Sequence alignment</td>
 
−
<td>-</td>
 
−
<td>Ch. 4</td>
 
−
 
 
−
<tr class="s0">
 
−
<td>11</td>
 
−
<td>Mo. Oct 20</td>
 
−
<td>Steipe</td>
 
−
<td>Homology III: Multiple sequence alignment</td>
 
−
<td>-</td>
 
−
<td>Ch. 5</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>12</td>
 
−
<td>'''Mon. Oct 20'''</td>
 
−
<td>Steipe</td>
 
−
<td>Homology IV: fast sequence database searches</td>
 
−
<td>-</td>
 
−
<td>Ch 6</td>
 
−
 
 
−
<tr class="s0">
 
−
<td>13</td>
 
−
<td>Thu. Oct 23</td>
 
−
<td>Steipe</td>
 
−
<td>Structural domains</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>14</td>
 
−
<td>Mon. Oct 27</td>
 
−
<td>Steipe</td>
 
−
<td>Homology modeling and structure prediction</td>
 
−
<td>-</td>
 
−
<td>Ch. 13</td>
 
−
 
 
−
</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>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>15</td>
 
−
<td>Thu. Oct 30</td>
 
−
<td>Steipe</td>
 
−
<td>Essential concepts of probability and information theory</td>
 
−
<td>-</td>
 
−
<td>Appendix A</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>16</td>
 
−
<td>Mon. Nov 3</td>
 
−
<td>Parkinson</td>
 
−
<td>Comparative genomics</td>
 
−
<td>-</td>
 
−
<td>Ch. 9.8, 10.8</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>17</td>
 
−
<td>Thu. Nov 6</td>
 
−
<td>NN</td>
 
−
<td>Human population genomics</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>18</td>
 
−
<td>Mon. Nov 10</td>
 
−
<td>Steipe</td>
 
−
<td>Phylogenetic analysis I</td>
 
−
<td>-</td>
 
−
<td>Ch. 7, 8</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>19</td>
 
−
<td>Thu. Nov 13</td>
 
−
<td>Steipe</td>
 
−
<td>Phylogenetic analysis II</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>20</td>
 
−
<td>Mon. Nov 17</td>
 
−
<td>Steipe</td>
 
−
<td>Protein structure motifs</td>
 
−
<td>-</td>
 
−
<td>-</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="s0">
 
−
<td>21</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>22</td>
 
−
<td>Mon. Nov 24</td>
 
−
<td>Wodak</td>
 
−
<td>Gene regulation II</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>23</td>
 
−
<td>Thu. Nov 27</td>
 
−
<td>Wodak</td>
 
−
<td>Functional annotation</td>
 
−
<td>-</td>
 
−
<td>Appendix A</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>24</td>
 
−
<td>Mon. Dec 1</td>
 
−
<td>Wodak</td>
 
−
<td>Metabolic networks</td>
 
−
<td>-</td>
 
−
<td>Ch. 17.1</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>25</td>
 
−
<td>Thu. Dec 4</td>
 
−
<td>Parkinson</td>
 
−
<td>Computational systems biology</td>
 
−
<td>-</td>
 
−
<td>Ch. 17</td>
 
−
</tr>
 
−
 
 
−
 
 
−
</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>
 
</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)
 
−
<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>
 
</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...==
 
−
 
−
* [[Glossary]]
 
−
* [[Mutation Data Matrices]]
 
−
<!-- * [[Database Identifiers]] -->
 
−
 
−
&nbsp;
 
−
 
−
== Resources ==
 
−
;Course related
 
−
*The [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/ Course Web site].
 
−
*The [http://groups.google.com/group/bch441_2008 Course Google Group].
 
−
*[[Netiquette]] for the Group mailing list
 
−
*Previous [[Exam_questions]]
 
−
*[[Feedback_2007|2007 course feedback]]
 
−
 
−
 
−
&nbsp;<br>
 
−
;Contents related
 
−
*A '''[[Stereo Vision]]''' tutorial
 
−
*[http://biodatabase.org/index.php/Main_Page MetaDatabase]
 
−
*[http://nar.oxfordjournals.org/content/vol35/suppl_1/index.dtl NAR January-2007 '''Database''' issue]
 
−
*[http://nar.oxfordjournals.org/content/vol35/suppl_2/index.dtl NAR July-2007 '''Web server''' issue]
 
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