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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
| |
| | | | |
| − | <div style="font-size:50%;font-weight:normal;">
| + | {{Vspace}} |
| − | 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> | + | <div id="BIO"> |
| | + | <div class="b1" style="padding-left:7%;"> |
| | | | |
| − | == The Course ==
| + | <br/> |
| | | | |
| − | <div style="padding: 5px; background: #FFDD99; border:solid 1px #AAAAAA;"> | + | <div style="font-size:150%;font-weight:bold;"> |
| − | I am in the process of repairing the original course Wiki and many of the pages are still arbitrarily outdated. Please don't use pages other than those that are linked directly from here.
| + | [[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">A B C</span>]] |
| − | <br>
| |
| − | <span style="font-size:80%;">Contact Boris Steipe for all matters of urgency. November 11. 2011</span> | |
| | </div> | | </div> |
| | | | |
| − | ===Organization=== | + | [[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Applying Bioinformatics Concepts</span>]] |
| − | ;Dates | |
| | | | |
| − | :Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00 | + | <div style="font-size:50%;font-weight:bold;"> |
| − | :Tutorial sessions: Mondays, 12:00 to 13:00 for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.
| + | [[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Boris Steipe (2006 – 2020)</span>]] |
| | + | </div> |
| | | | |
| − | ;Location | + | <br/> |
| − | :MSB 2173 (Medical Sciences Building)
| |
| | | | |
| − | ;General
| |
| − | See the [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/index.html Course Web page] for general information.
| |
| − |
| |
| − | We are recommending [http://www.garlandscience.com/textbooks/0815340249.asp '''Understanding Bioinformatics'''], Zvelebil & Baum, Garland 2008 as a background textbook for the course. (<small>buy used at [http://www.abebooks.com/servlet/SearchResults?isbn=9780815340249 AbeBooks]</small>)
| |
| − |
| |
| − | This is an '''electronic submission only''' course; but if you must print material, you might consider printing double-sided. Learn how, at the [http://printdoublesided.sa.utoronto.ca/ Print-Double-Sided Student Initiative].
| |
| − |
| |
| − |
| |
| − | ===Grading and Activities===
| |
| − |
| |
| − |
| |
| − | <table cellpadding="5">
| |
| − |
| |
| − | <tr class="sh">
| |
| − | <td><b>Activity</b></td>
| |
| − | <td><b>Weight</b><br><small>(Undergraduates)</small></td>
| |
| − | <td><b>Weight</b><br><small>(Graduates)</small></td>
| |
| − | </tr>
| |
| − |
| |
| − | <tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
| |
| − |
| |
| − | <tr class="s1">
| |
| − | <td>[[Assignments|'''5 Assignments''']]</td>
| |
| − | <td>15 marks <small>(5 x 3)</small></td>
| |
| − | <td>10 marks <small>(5 x 2)</small></td>
| |
| − | </tr>
| |
| − |
| |
| − | <tr class="s2">
| |
| − | <td>[[Quizzes|'''5 In-class quizzes''']]</td>
| |
| − |
| |
| − | <td>35 marks <small>(5 x 7)</small></td>
| |
| − | <td>25 marks <small>(5 x 5)</small></td>
| |
| − | </tr>
| |
| − |
| |
| − | <tr class="s1">
| |
| − | <td>[[Open project|'''Open project''']]</td>
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| − | <td>7 marks</td>
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| − | <td>5 marks</td>
| |
| − | </tr>
| |
| − |
| |
| − | <tr class="s2">
| |
| − | <td>[[Participation|'''"Classroom" participation''']]</td>
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| − | <td>3 marks</td>
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| − | <td>3 marks</td>
| |
| − | </tr>
| |
| − |
| |
| − | <tr class="s1">
| |
| − | <td>[[Graduate project|'''Graduate project''']]</td>
| |
| − | <td> </td>
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| − | <td>17 marks</td>
| |
| − | </tr>
| |
| − |
| |
| − | <tr class="s2">
| |
| − | <td>[[Exam questions|'''Final exam''']]</td>
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| − | <td>40 marks</td>
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| − | <td>40 marks</td>
| |
| − | </tr>
| |
| − |
| |
| − | <tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
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| − | <tr class="s1">
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| − | <td>'''Total'''</td>
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| − | <td>100 marks</td>
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| − | <td>100 marks</td>
| |
| − | </tr>
| |
| − |
| |
| − | </table>
| |
| − |
| |
| − |
| |
| − | ;A note on marking
| |
| − | It is not my policy to adjust marks towards a target mean and variance (i.e. there will be no "belling" of grades). I feel strongly that such "normalization" detracts from a collaborative and mutually supportive learning environment. If your classmate gets a great mark because you helped him with a difficult concept, this should never have the effect that it brings down your mark through class average adjustments. Collaborate as much as possible, it is a great way to learn. <small>However I may adjust marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.</small>
| |
| − |
| |
| − | == Assignments ==
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| − |
| |
| − | <div style="padding: 5px; background: #A6AFD0; border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
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| − | [[Assignment 4]] has been posted.
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| − | <br>
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| − | <span style="font-size:60%;">Due Monday, Nov. 28.</span>
| |
| | </div> | | </div> |
| − | | + | </div> |
| − | == Temporary links for material ==
| |
| − | | |
| − | ===Lecture slides===
| |
| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/01-Introduction.pdf 01 - Introduction to the course <small>(pdf, 6.1 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/02-SequenceData.pdf 02 - Sequence Data <small>(pdf, 4.6 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/03-StructureData.pdf 03 - Structure Data <small>(pdf, 13.6 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/04-SequenceAnalysis_I.pdf 04 - Sequence Analysis I <small>(pdf, 8.6 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/05-SequenceAnalysis_II.pdf 05 - Sequence Analysis II <small>(pdf, 3.1 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/06-InterpretingProteinStructure.pdf 06 - Interpreting Protein Structure <small>(pdf, 6.6 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/07-StructuralDomains.pdf 07 - Structural Domains <small>(pdf, 5.8 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/08-Genome_Sequencing_2011.pdf 08 - Genome Sequencing <small>(pdf, 1.4 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/09-GenomeAnnotation_2011.pdf 09 - Genome Annotation <small>(pdf, 4.2 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/10-Homology_I_Principles.pdf 10 - Homology I: Principles <small>(pdf, 2.6 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/11-Homology_II_Alignment.pdf 11 - Homology II: Optimal Sequence Alignment <small>(pdf, 2.6 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/12-Homology_III_BLAST.pdf 12 - Homology III: BLAST <small>(pdf, 2.6 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/13-Homology_IV_MSA.pdf 13 - Homology IV: Multiple Sequence Alignment <small>(pdf, 4.3 MB)</small>]
| |
| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/14-PredictingProteinStructure_I.pdf 14 - Predicting Protein Structure I: Homology Modeling <small>(pdf, 2.3 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/15-PhylogeneticAnalysis_I.pdf 15 - Phylogenetic Analysis I <small>(pdf, 3.3 MB)</small>]
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/16-PhylogeneticAnalysis_II.pdf 16 - Phylogenetic Analysis II <small>(pdf, 1.0 MB)</small>]
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| − | * 17 - ''Comparative Genomics ''
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| − | * 18 - ''Computational Systems Biology ''
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| − | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/19-StatisticsAndExploratoryDataAnalysis.pdf 19 - Statistics and Exploratory Data Analysis <small>(pdf, 3.4 MB)</small>]
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| − | * 20 - ''Structure Prediction II: ''ab initio'' Prediction''
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| − | * 21 - ''Gene regulation''
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| − | * 22 - ''Metabolic Pathways''
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| − | | |
| − | ===Lecture recordings===
| |
| − | *Thursday, 15. September 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/02-SequenceData_2011.mp4 Lecture 02 (Sequence data) <small>(mp4, 16.4 MB)</small>]
| |
| − | *Monday, 19. September 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/03-Structure-Data_2011.mp4 Lecture 03 (Sequence data ''cont.''; Structure Data) <small>(mp4, 17.2 MB)</small>]
| |
| − | *Thursday, 22. September 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/04-StructureData-SequenceAnalysis_I_2011.mp4 Lecture 04 (Structure data ''cont.''; Sequence Analysis I) <small>(mp4, 16.9 MB)</small>]
| |
| − | *Monday, 26. September 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/05-SequenceAnalysis_I-II_2011.mp4 Lecture 05 Sequence Analysis I ''cont.'' & II <small>(mp4, 15.3 MB)</small>]
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| − | *Thursday, 29. September 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/06-SequenceAnalysis_II-StructureAnalysis_2011.mp4 Lecture 06 Sequence Analysis II ''cont.'' & Analysis of structure <small>(mp4, 15.6 MB)</small>]
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| − | *Monday, 3. October 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-10-03_Topic-06b.mp4 Analysis of Structure (cont.) <small>(mp4, 18.3 MB)</small>]
| |
| − | *Thursday, 6. October 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-10-06_Topic-07.mp4 Lecture 07 Protein Structural Domains <small>(mp4, 16.3 MB)</small>]
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| − | *Thursday, 13. October 2011: (Parkinson)
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| − | *Monday, 17. October 2011: (Parkinson)
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| − | *Thursday, 20. October 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-10-20_Topic-10.mp4 Lecture 10 Homology I: Principles <small>(mp4, 19.4 MB)</small>]
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| − | | |
| − | *Monday, 24. October 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-10-24_Topic-11.mp4 Lecture 11 Homology II: Optimal Sequence Alignment <small>(mp4, 12.4 MB)</small>]
| |
| − | *Thursday, 27. October 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-10-27_Topic-12.mp4 Lecture 12 Homology III: BLAST <small>(mp4, 16.8 MB)</small>]
| |
| − | *Monday, 31. October 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-10-31_Topic-13.mp4 Lecture 13 Homology IV: Multiple Sequence Alignment <small>(mp4, 22.7 MB)</small>]
| |
| − | *Thursday, 3. November 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-11-04_Topic-14.mp4 Lecture 14 Predicting Protein Structure I: Homology Modeling <small>(mp4, 18.7 MB)</small>]
| |
| − | *Thursday, 10. November 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-11-10_Topic-15.mp4 Lecture 15 Phylogenetic Analysis I: Principles <small>(mp4, 16.7 MB)</small>]
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| − | | |
| − | | |
| − | *''Monday, 14. November 2011: Lecture 16 Phylogenetic Analysis II'' '''(Quiz 3)'''
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| − | *''Thursday, 17. November 2011: Lecture 17 Comparative Genomics (Parkinson) ''
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| − | *''Monday, 21. November 2011: Lecture 18 Computational Systems Biology (Parkinson) '' '''(Quiz 4)'''
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| − | *''Thursday, 24. November 2011: Lecture 19 Exploratory Data Analysis''
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| − | *''Monday, 28. November 2011: Lecture 20 Protein structure prediction II: ab initio''
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| − | *''Thursday, 1. December 2011: Lecture 21 Gene Regulation''
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| − | *''Monday, 6. December 2011: Lecture 22 Metabolic Pathways'' '''(Quiz 5)'''
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| − | *''Virtual Monday, 7. December 2011: Exam review''
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| − | | |
| − | | |
| − | | |
| − | | |
| − | | |
| − | <!--
| |
| − | == Organization ==
| |
| − | | |
| − | ;Dates
| |
| − | :''Lectures'': Monday and Thursday, 12:00 to 13:00
| |
| − | :''Tutorial sessions'': Mondays, 13:00 to 14:00 <small> for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.</small>
| |
| − | | |
| − | ;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 & 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>
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| − | <td>10 marks</td>
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| − | <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> </td>
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| − | <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 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 ==
| |
| − | <small>This section is currently under construction.</small>
| |
| − | | |
| − | | |
| − | <table cellpadding="5">
| |
| − | | |
| − | <tr class="st">
| |
| − | <td colspan="7">'''I n t r o d u c t i o n'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sh">
| |
| − | <td>'''#'''</td>
| |
| − | <td>'''Date'''</td>
| |
| − | <td>'''Lecturer'''</td>
| |
| − | <td>'''Topic'''</td>
| |
| − | <td>'''Handout'''</td>
| |
| − | <td>'''Book'''</td>
| |
| − | <td>'''Note'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>1</td>
| |
| − | <td>Mon. Sept 8</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Organisation and Orientation</td>
| |
| − | <td>[[Introduction]]</td>
| |
| − | <td>Ch 1, 2</td>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | | |
| − | | |
| − | | |
| − | --><!-- =================== TOPIC =================== --><!--
| |
| − | <tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
| |
| − | <tr class="st">
| |
| − | <td colspan="7">'''A b s t r a c t i o n s'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sh">
| |
| − | <td>'''#'''</td>
| |
| − | <td>'''Date'''</td>
| |
| − | <td>'''Lecturer'''</td>
| |
| − | <td>'''Topic'''</td>
| |
| − | <td>'''Handout'''</td>
| |
| − | <td>'''Book'''</td>
| |
| − | <td>'''Note'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>2</td>
| |
| − | <td>Thu. Sept 11</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Sequence abstraction and sequence databases</td>
| |
| − | <td>[[Sequence data]]</td>
| |
| − | <td>Ch 3</td>
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| − | <td>[[Assignment 1|Assignment 1 to be handed out]]</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s2">
| |
| − | <td>3</td>
| |
| − | <td>Mon. Sept 15</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Protein Structure Data</td>
| |
| − | <td>[[Structure data]]</td>
| |
| − | <td>-</td>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | --><!-- =================== TOPIC =================== --><!--
| |
| − | <tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
| |
| − | <tr class="st">
| |
| − | <td colspan="7">'''A n a l y s i s'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sh">
| |
| − | <td>'''#'''</td>
| |
| − | <td>'''Date'''</td>
| |
| − | <td>'''Lecturer'''</td>
| |
| − | <td>'''Topic'''</td>
| |
| − | <td>'''Handout'''</td>
| |
| − | <td>'''Book'''</td>
| |
| − | <td>'''Note'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
| |
| − | | |
| − | <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>Mon. Sept 22</td>
| |
| − | <td>Steipe</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>-</td>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>5</td>
| |
| − | <td>Thu. Sept 25.</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Interpreting protein structure</td>
| |
| − | <td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/InterpretingProteinStructure.pdf Raw lecture PDF]</td>
| |
| − | <td>-</td>
| |
| − | <td>[[Assignment 1]] due<br>
| |
| − | <hr>
| |
| − | '''First quiz''' in class<br>
| |
| − | <hr>
| |
| − | [[Assignment 2]] to be posted
| |
| − | </td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>12</td>
| |
| − | <td>Thu. Oct 23.</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Structural domains</td>
| |
| − | <td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/StructuralDomains.pdf Raw lecture PDF]</small></td>
| |
| − | <td>-</td>
| |
| − | <td>[[Assignment 3]] due</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <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>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | <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>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s2">
| |
| − | <td>8</td>
| |
| − | <td>Mon. Oct 6</td>
| |
| − | <td>Parkinson</td>
| |
| − | <td>Genomes and genome structure</td>
| |
| − | <td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genomes.pdf Lecture slide PDFs (2.4 MB)]</td>
| |
| − | <td>-</td>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | --><!-- =================== 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>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sh">
| |
| − | <td>'''#'''</td>
| |
| − | <td>'''Date'''</td>
| |
| − | <td>'''Lecturer'''</td>
| |
| − | <td>'''Topic'''</td>
| |
| − | <td>'''Handout'''</td>
| |
| − | <td>'''Book'''</td>
| |
| − | <td>'''Note'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>9</td>
| |
| − | <td>Thu. Oct 9.</td>
| |
| − | <td>Steipe</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></td>
| |
| − | <td>[[Assignment 2]] due<br>
| |
| − | <hr>
| |
| − | [[Assignment 3]] to be posted
| |
| − | <hr>
| |
| − | </td>
| |
| − | </tr>
| |
| − | | |
| − | | |
| − | <tr class="s2">
| |
| − | <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. 5</td>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>11</td>
| |
| − | <td>Mo. Oct 20</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Homology IV: Multiple sequence alignment</td>
| |
| − | <td>[[Multiple Sequence Alignment]]</td>
| |
| − | <td>Ch. 6</td>
| |
| − | <td>'''Second quiz''' in class (13:00 tutorial time slot)</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s2">
| |
| − | <td>18</td>
| |
| − | <td>Thu. Nov 13</td>
| |
| − | <td>Steipe</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>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>19</td>
| |
| − | <td>Mon. Nov 17</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Homology modeling and structure prediction (Part 2)</td>
| |
| − | <td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PredictingProteinStructure_II.pdf Raw lecture PDF]</small></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>
| |
| − | | |
| − | | |
| − | | |
| − | --><!-- =================== TOPIC =================== --><!--
| |
| − | <tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
| |
| − | <tr class="st">
| |
| − | <td colspan="7">'''P h y l o g e n y'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sh">
| |
| − | <td>'''#'''</td>
| |
| − | <td>'''Date'''</td>
| |
| − | <td>'''Lecturer'''</td>
| |
| − | <td>'''Topic'''</td>
| |
| − | <td>'''Handout'''</td>
| |
| − | <td>'''Book'''</td>
| |
| − | <td>'''Note'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>13</td>
| |
| − | <td>Mon. Oct 27</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Phylogenetic analysis I</td>
| |
| − | <td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PhylogeneticAnalysis_I.pdf Raw lecture PDF]</small></td>
| |
| − | <td>Ch. 7,8</td>
| |
| − | <td>'''Third quiz''' in class, 13:00 in tutorial time-slot</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s2">
| |
| − | <td>14</td>
| |
| − | <td>Thu. Oct 30</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Phylogenetic analysis II</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 class="s1">
| |
| − | <td>15</td>
| |
| − | <td>Mon. Nov 3</td>
| |
| − | <td>Parkinson</td>
| |
| − | <td>Comparative genomics</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 class="s2">
| |
| − | <td>17</td>
| |
| − | <td>Mon. Nov 10</td>
| |
| − | <td>Steipe</td>
| |
| − | <td>Human population genomics</td>
| |
| − | <td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/HumanPopulationGenomics.pdf Raw lecture PDF]</small></td>
| |
| − | <td>-</td>
| |
| − | <td>[[Assignment 4]] to be posted</td>
| |
| − | </tr>
| |
| − | | |
| − | --><!-- =================== TOPIC =================== --><!--
| |
| − | <tr class="sp"><td colspan="7" style="height: 10px;"></td></tr>
| |
| − | <tr class="st">
| |
| − | <td colspan="7">'''I n t e r a c t i o n s'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sh">
| |
| − | <td>'''#'''</td>
| |
| − | <td>'''Date'''</td>
| |
| − | <td>'''Lecturer'''</td>
| |
| − | <td>'''Topic'''</td>
| |
| − | <td>'''Handout'''</td>
| |
| − | <td>'''Book'''</td>
| |
| − | <td>'''Note'''</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>20</td>
| |
| − | <td>Thu. Nov 20</td>
| |
| − | <td> Wodak </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>Ch. 15</td>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s2">
| |
| − | <td>21</td>
| |
| − | <td>Mon. Nov 24</td>
| |
| − | <td>Wodak</td>
| |
| − | <td>Gene regulation (Part 2)</td>
| |
| − | <td>-</td>
| |
| − | <td>-</td>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>22</td>
| |
| − | <td>Thu. Nov 27</td>
| |
| − | <td>Wodak</td>
| |
| − | <td>Functional annotation</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>-</td>
| |
| − | </tr>
| |
| − | | |
| − | | |
| − | <tr class="s2">
| |
| − | <td>23</td>
| |
| − | <td>Mon. Dec 1</td>
| |
| − | <td>Wodak</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>Ch. 17.1</td>
| |
| − | <td>[[Assignment 5]] due<br>
| |
| − | <hr>
| |
| − | '''Fifth quiz''' in class: 13:00 in tutorial time slot
| |
| − | </td>
| |
| − | </tr>
| |
| − | | |
| − | <tr class="s1">
| |
| − | <td>24</td>
| |
| − | <td>Thu. Dec 4</td>
| |
| − | <td>Parkinson</td>
| |
| − | <td>Computational systems biology</td>
| |
| − | <td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/ComputationalSystemsBiology.pdf Lecture slide PDFs (3.4 MB)]</td>
| |
| − | <td>Ch. 17</td>
| |
| − | <td>-</td>
| |
| − | </tr>
| |
| − | | |
| − | | |
| − | </table>
| |
| − | | |
| − | ==In depth...==
| |
| − | | |
| − | * [[Glossary]]
| |
| − | * [[Mutation Data Matrices]]
| |
| − | * [http://en.wikipedia.org/wiki/List_of_standard_amino_acids Amino acids]
| |
| − | | |
| − | --><!-- * [[Database Identifiers]] --><!--
| |
| − | | |
| − |
| |
| − | | |
| − | == 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]]
| |
| − | *[[Feedback_2008|2008 course feedback]]
| |
| − | | |
| − | | |
| − | <br>
| |
| − | ;Contents related
| |
| − | *The '''[[VMD]]''' tutorial
| |
| − | *A '''[[Stereo Vision]]''' tutorial
| |
| − | *[http://biodatabase.org/index.php/Main_Page MetaDatabase]
| |
| − | *[http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl NAR January-2008 '''Database''' issue]
| |
| − | *[http://nar.oxfordjournals.org/content/vol36/suppl_2/index.dtl NAR July-2008 '''Web server''' issue]
| |
| − | <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.
| |
| − | -->
| |
| − | | |
| − | | |
| − | | |
| − | <br>
| |
| − | | |
| − | | |
| − | | |
| − | <!--- Color schemes
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| − | <div style="padding: 3px; background: #457DB5; border:solid 1px #AAAAAA;">Level 1</div>
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| − |
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| − | <div style="padding: 3px; background: #6F9BD0; border:solid 1px #AAAAAA;">Level 2</div>
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| − |
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| − | <div style="padding: 3px; background: #9CC86F; border:solid 1px #AAAAAA;">Level 3</div>
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| − |
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| − | <div style="padding: 3px; background: #F0F07A; border:solid 1px #AAAAAA;">Alert</div>
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| − |
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| − | <div style="padding: 3px; background: #FF4560; border:solid 1px #AAAAAA;">Warning!</div>
| |
| − |
| |
| − | --->
| |
