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| − | <div style="padding: 5px; background: #457DB5; border:solid 1px #AAAAAA; font-size:300%;font-weight:bold; color:#FFFFFF">
| + | #REDIRECT [[Bioinformatics_Main_Page]] |
| − | BCH441 - Bioinformatics
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| − | <div style="font-size:50%;font-weight:normal;">
| + | {{Vspace}} |
| − | Welcome to the BCH441 Course Wiki.
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| − | </div>
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| − | </div>
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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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| | + | <div id="BIO"> |
| | + | <div class="b1" style="padding-left:7%;"> |
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| − | == The Course ==
| + | <br/> |
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| − | We have begun to collect feedback specifically for future students, from those who have taken this course before you. Follow the link to read.
| + | <div style="font-size:150%;font-weight:bold;"> |
| − | | + | [[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">A B C</span>]] |
| − | * '''[[Feedback_2007|Fall 2007 feedback]]'''
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| − | 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.
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| − | <div style="padding: 5px; background: #A6AFD0; border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;"> | |
| − | The first session for the 2008 term will be Monday, September 8., 13:00.
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| − | 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.
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| | </div> | | </div> |
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| | + | [[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Applying Bioinformatics Concepts</span>]] |
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| − | | + | <div style="font-size:50%;font-weight:bold;"> |
| − | == Organization ==
| + | [[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Boris Steipe (2006 – 2020)</span>]] |
| − | | |
| − | '''Slowly gearing up for the 2008 Fall term ...'''
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| − | | |
| − | ;Dates
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| − | :Monday and Thursday, 12:00 to 13:00
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| − | :<small>Optional tutorial sessions will be offered as the need arises, most likely on Mondays, probably from 13:00 to 14:00.</small>
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| − | :First class: Monday, September 8. 2008
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| − | | |
| − | ;Location
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| − | :MSB 2173 (Medical Sciences Building)
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| − | See the [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/ Course Web page] for general information.
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| − | | |
| − | | |
| − | == Lecture Schedule ==
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| − | <small>(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.)</small>
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| − | | |
| − | <ol start="1">
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| − | <li>[[Lecture_01|'''Organisation and Orientation''']] (Boris, Monday, Sept. 10)
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| − | </ol>
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| − | | |
| − | ;Sequences | |
| − | <ol start="2">
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| − | <li>[[Lecture_02|'''Sequence Abstraction + Sequence Databases''']] (Boris, Thursday, Sept. 13)
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| − | <li>[[Lecture_03|'''Sequence Properties''']] (Boris, Monday, Sept. 17)
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| − | <li>[[Lecture_04|'''Sequence Analysis''']] (Boris, Thursday, Sept. 20)
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| − | <li>[[Lecture_05|'''Homology I: the principles''']] (Boris, Monday, Sept. 24)
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| − | <li>[[Lecture_06|'''Homology II: Sequence Alignment''']] (Boris, Thursday, Sept. 27)
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| − | <li>[[Lecture_07|'''Homology III: Multiple Sequence Alignment''']] (Boris, Monday, Oct. 1)
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| − | <li>[[Lecture_08|'''Homology IV: Fast Sequence Database searches''']] (Boris, Thursday, Oct. 4)
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| − | </ol>
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| − | | |
| − | | |
| − | ;Structures | |
| − | <ol start="9">
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| − | <li>[[Lecture_09|'''Protein Structure Databases''']] (Boris, Thursday, Oct. 11)
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| − | <li>[[Lecture_10|'''Interpreting Protein Structure''']] (Boris, Monday, Oct. 15'''*''') | |
| − | <div style="color: #AAAAAA;">
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| − | <li>[[Lecture_11|Structural Domains]] (Boris, Monday, Oct. 15'''*''')
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| − | <li>[[Lecture_12|Homology Modeling + Protein Structure Prediction]] (Boris, Thursday, Oct. 18) | |
| | </div> | | </div> |
| − | </ol>
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| − | <p> | + | <br/> |
| − | <small>('''*''') Double lecture (12:00 - 14:00) to make up for Thanksgiving, Oct 8.</small>
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| | | | |
| − | ;Genomes
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| − | <ol start="13">
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| − | <li>[[Lecture_13|'''Genome Sequencing''']] (John, Monday, Oct. 22)
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| − | <li>[[Lecture_14|'''Genomes''']] (John, Thursday, Oct. 25)
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| − | <li>[[Lecture_15|'''Comparative Genomics''']] (John, Monday, Oct. 29)
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| − | <div style="color: #AAAAAA;">
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| − | <li>[[Lecture_16|Phylogenetic Analysis]] (Boris, Thursday, Nov. 1)
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| | </div> | | </div> |
| − | </ol>
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| − |
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| − | ;Systems
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| − | <ol start="17">
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| − | <li>[[Lecture_17|'''Functional Annotation''']] (Shoshana, Monday, Nov. 5)
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| − | <div style="color: #AAAAAA;">
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| − | <li>[[Lecture_18|Human Population Genomics]] (Boris, Nov. 8)
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| − | <li>[[Lecture_19|Proteomics]] (Boris, Monday, Nov. 12)
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| | </div> | | </div> |
| − | <li>[[Lecture_20|'''Gene regulation I''']] (Shoshana, Thursday, Nov. 15)
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| − | <li>[[Lecture_21|'''Gene regulation II''']] (Shoshana, Monday, Nov. 19)
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| − | <div style="color: #AAAAAA;">
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| − | <li>[[Lecture_22|Microarray Expression Analysis]] ([http://hugheslab.ccbr.utoronto.ca/ Tim Hughes], Thursday, Nov. 22)
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| − | </div>
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| − | <li>[[Lecture_23|'''Pathways and Networks''']] ([http://baderlab.org/ Gary Bader], Monday, Nov. 26)
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| − | <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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| − | == Assignments ==
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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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| − |
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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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| − |
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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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| − |
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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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| − |
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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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| − |
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| − |
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| − | ==In depth...==
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| − |
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| − | * [[Glossary]]
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| − | * [[Mutation Data Matrices]]
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| − | <!-- * [[Database Identifiers]] -->
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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_2007 Course Google Group].
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| − | *[[Netiquette]] for the Group mailing list
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| − | *Previous [[Exam_questions]]
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| − | <br>
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| − | ;Contents related
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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/vol35/suppl_1/index.dtl NAR January-2007 '''Database''' issue]
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| − | *[http://nar.oxfordjournals.org/content/vol35/suppl_2/index.dtl NAR July-2007 '''Web server''' issue]
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| − | <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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| − | <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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| − | <div style="padding: 3px; background: #FF4560; border:solid 1px #AAAAAA;">Warning!</div>
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| − |
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| − | --->
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