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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>
 
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</div>
 
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&nbsp;
 
  
 +
<div id="BIO">
 +
<div class="b1" style="padding-left:7%;">
  
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<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>
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&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>
  
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== The Course ==
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[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Applying Bioinformatics Concepts</span>]]
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−
 
 
−
Follow the link to read feedback from those who have taken this course before you..
 
−
 
 
−
* '''[[Feedback_2007|Fall 2007 feedback]]'''
 
−
 
 
−
 
 
−
<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
 
−
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>
 
−
 
 
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== Organization ==
 
−
 
 
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'''Slowly gearing up for the 2008 Fall term ...'''
 
−
 
 
−
;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.
 
−
 
 
−
 
 
−
== Lecture Schedule ==
 
−
<small>This is the current schedule for 2008, but changes may be still be made if required.</small>
 
−
 
 
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<table cellpadding="5">
 
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<tr class="s0">
 
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<td>'''#'''</td>
 
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<td>'''Date'''</td>
 
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<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
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<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">
 
−
<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="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
+
<div style="font-size:50%;font-weight:bold;">
−
<ol  start="9">
+
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Boris Steipe&nbsp;&nbsp;(2006 – 2020)</span>]]
−
<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>
 
</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>
 
</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_2007 Course Google Group].
 
−
*[[Netiquette]] for the Group mailing list
 
−
*Previous [[Exam_questions]]
 
−
&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]
 
−
&nbsp;<br>
 
−
 
−
 
−
 
−
<!--
 
−
;Course Wiki
 
−
*[[Help:Introduction|Introduction:]] Concept and contents of the Course Wiki
 
−
*[[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.
 
−
*[[Help:Editing| Editing:]] Editing principles and Wiki markup syntax for the Course Wiki pages
 
−
*[[Sandbox]]: A page for your editing experiments. Content added to this page will not stay permanently.
 
−
*[[Feedback]]: Share your views on the course, suggest improvements.
 
−
-->
 
−
 
−
 
−
 
−
&nbsp;<br>
 
−
 
−
 
−
 
−
<!--- Color schemes
 
−
<div style="padding: 3px; background: #457DB5;  border:solid 1px #AAAAAA;">Level 1</div>
 
−
&nbsp;
 
−
<div style="padding: 3px; background: #6F9BD0;  border:solid 1px #AAAAAA;">Level 2</div>
 
−
&nbsp;
 
−
<div style="padding: 3px; background: #9CC86F;  border:solid 1px #AAAAAA;">Level 3</div>
 
−
&nbsp;
 
−
<div style="padding: 3px; background: #F0F07A;  border:solid 1px #AAAAAA;">Alert</div>
 
−
&nbsp;
 
−
<div style="padding: 3px; background: #FF4560;  border:solid 1px #AAAAAA;">Warning!</div>
 
−
&nbsp;
 
−
--->
 

Latest revision as of 08:17, 8 September 2020

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