Difference between revisions of "Bioinformatics Main Page"

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<div class="alert">
 
<div class="alert">
 
Welcome to the 2012 edition of the course.
 
Welcome to the 2012 edition of the course.
 
Classes will meet
 
* Tuesdays from 16:00 to 17:00 (Lecture)
 
* Wednesdays  from 14:00 to 16:00 (Tutorial and lecture)
 
 
The classroom is MS 2173
 
 
We will discuss the coordination of the course on Tuesday, September 11. Don't miss this class!
 
  
 
There will be no tutorial on Wednesday, September 12.
 
There will be no tutorial on Wednesday, September 12.
 
</div>
 
</div>
 +
  
 
__TOC__
 
__TOC__
  
<!--
 
  
 
== The Course ==
 
== The Course ==
Line 37: Line 29:
 
;Dates
 
;Dates
  
The course will be next held in the Fall Term - September to December 2012.
+
:BCH441 is a Fall-term course.
 
+
:Lectures: Tuesday, 16:00 to 17:00 and Wednesday, 15:00 to 16:00  
:Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00  
+
:Tutorial sessions: Wednesday, 14:00 to 15:00 for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.  
:Tutorial sessions: Mondays, 12:00 to 13:00   for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.  
 
  
 
;Location
 
;Location
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<table cellpadding="5">
+
 
 +
<table>
  
 
<tr class="sh">
 
<tr class="sh">
 
<td><b>Activity</b></td>
 
<td><b>Activity</b></td>
<td><b>Weight</b><br><small>(Undergraduates)</small></td>
+
<td><b>Weight</b><br><small>BCH441 - (Undergraduates)</small></td>
<td><b>Weight</b><br><small>(Graduates)</small></td>
+
<td><b>Weight</b><br><small>BCH1441 - (Graduates)</small></td>
 
</tr>
 
</tr>
  
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
+
<tr><td colspan="3" class="sp"></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">
 
<tr class="s2">
<td>[[Quizzes|'''5 In-class quizzes''']]</td>
+
<td>[[BIO_Quizzes|'''12 In-class quizzes''']]</td>
 
+
<td>42 marks <small>(12 x 3.5)</small></td>
<td>35 marks <small>(5 x 7)</small></td>
+
<td>24 marks <small>(12 x 2)</small></td>
<td>25 marks <small>(5 x 5)</small></td>
 
 
</tr>
 
</tr>
  
 
<tr class="s1">
 
<tr class="s1">
<td>[[Open project|'''Open project''']]</td>
+
<td>[[BIO_Open project|'''Open project''']]</td>
<td>7 marks</td>
+
<td>28 marks <small>(7 + 7 + 14)</small></td>
<td>5 marks</td>
+
<td>28 marks</td>
 
</tr>
 
</tr>
  
 
<tr class="s2">
 
<tr class="s2">
<td>[[Participation|'''"Classroom" participation''']]</td>
+
<td>[[CSB_Participation|'''"Classroom" participation''']]</td>
<td>3 marks</td>
+
<td>10 marks</td>
<td>3 marks</td>
+
<td>10 marks</td>
 
</tr>
 
</tr>
  
 
<tr class="s1">
 
<tr class="s1">
<td>[[Graduate project|'''Graduate project''']]</td>
+
<td>[[BIO_Thesis_Project|'''Thesis Project''']]</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>17 marks</td>
+
<td>30 marks</td>
 
</tr>
 
</tr>
  
<tr class="s2">
+
<tr><td colspan="3" class="sp"></td></tr>
<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="s1">
 
<tr class="s1">
 
<td>'''Total'''</td>
 
<td>'''Total'''</td>
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</table>
 
</table>
  
 
<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="s2">
 
<td>[[Quizzes|'''9 In-class quizzes''']]</td>
 
 
<td>55 marks <small>(11 x 5)</small></td>
 
<td>44 marks <small>(11 x 4)</small></td>
 
</tr>
 
 
<tr class="s1">
 
<td>[[Open project|'''Open project''']]</td>
 
<td>18 marks</td>
 
<td>18 marks</td>
 
</tr>
 
 
<tr class="s2">
 
<td>[[Participation|'''"Classroom" participation''']]</td>
 
<td>7 marks</td>
 
<td>7 marks</td>
 
</tr>
 
 
<tr class="s1">
 
<td>[[Graduate project|'''Graduate project''']]</td>
 
<td>&nbsp;</td>
 
<td>11 marks</td>
 
</tr>
 
 
<tr class="s2">
 
<td>[[Exam questions|'''Final exam''']]</td>
 
<td>20 marks</td>
 
<td>20 marks</td>
 
</tr>
 
 
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
<tr class="s1">
 
<td>'''Total'''</td>
 
<td>100 marks</td>
 
<td>100 marks</td>
 
</tr>
 
 
</table>
 
  
  
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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>
 
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 ==
+
[...]
 
 
<div class="alert">
 
[[Assignment 5]] has been posted.
 
<br>
 
<span style="font-size:60%;">Due Monday, Dec. 5.</span>
 
</div>
 
 
 
 
 
== Temporary links for material ==
 
 
 
 
 
===Lecture slides 2012===
 
 
 
''None yet.''
 
 
 
 
 
===Lecture slides 2011===
 
 
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/01-Introduction.pdf 01 - Introduction to the course <small>(pdf, 6.1 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/02-SequenceData.pdf 02 - Sequence Data <small>(pdf, 4.6 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/03-StructureData.pdf  03 - Structure Data <small>(pdf, 13.6 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/04-SequenceAnalysis_I.pdf  04 - Sequence Analysis I <small>(pdf, 8.6 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/05-SequenceAnalysis_II.pdf  05 - Sequence Analysis II <small>(pdf, 3.1 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/06-InterpretingProteinStructure.pdf 06 - Interpreting Protein Structure <small>(pdf, 6.6 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/07-StructuralDomains.pdf 07 - Structural Domains <small>(pdf, 5.8 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/08-Genome_Sequencing_2011.pdf 08 - Genome Sequencing <small>(pdf, 1.4 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/09-GenomeAnnotation_2011.pdf 09 - Genome Annotation <small>(pdf, 4.2 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/10-Homology_I_Principles.pdf 10 - Homology I: Principles <small>(pdf, 2.6 MB)</small>]
 
*[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>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/12-Homology_III_BLAST.pdf 12 - Homology III: BLAST <small>(pdf, 2.6 MB)</small>]
 
*[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>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/15-PhylogeneticAnalysis_I.pdf 15 - Phylogenetic Analysis I <small>(pdf, 3.3 MB)</small>]
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/16-PhylogeneticAnalysis_II.pdf 16 - Phylogenetic Analysis II <small>(pdf, 1.0 MB)</small>]
 
* 17 - ''Comparative Genomics ''
 
* 18 - ''Computational Systems Biology ''
 
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/19-StatisticsAndExploratoryDataAnalysis.pdf 19 - Statistics and Exploratory Data Analysis <small>(pdf, 3.4 MB)</small>]
 
* [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/20-PredictingProteinStructure_II.pdf 20 - Structure Prediction II: ''ab initio'' Prediction  <small>(pdf, 10.0 MB)</small>]
 
* [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/22-Outlook-ComputationalSystemsBiology.pdf 22 - Outlook: Computational Systems Biology <small>(pdf, 2.4 MB)</small>]
 
 
 
 
 
A selection of [[Bioinformatics lecture recordings 2011|Lecture recordings of the 2011 course]] is available.
 
 
 
 
 
=== Add this material ===
 
* Quantitative evolution: signals of recent change and selective pressure
 
 
 
-->
 
 
 
<!-- * [[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]]
 
*[[Feedback_2008|2008 course feedback]]
 
 
 
 
 
&nbsp;<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]
 
&nbsp;<br>
 
 
 
 
 
  
 
-->
 
-->

Revision as of 19:39, 11 September 2012

BCH441 - Bioinformatics

Welcome to the BCH441 Course Wiki.

These wiki pages are provided to coordinate information, activities and projects in the introductory bioinformatics course taught by Boris Steipe at the University of Toronto. If you are not one of my 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 Wikipedia article on bioinformatics, or visit Wikiomics. Contact boris.steipe(at)utoronto.ca with any questions you may have.


Welcome to the 2012 edition of the course.

There will be no tutorial on Wednesday, September 12.



The Course

BCH441H1F is the undergraduate course code.
BCH1441H1F is the cross-listed course code for graduate students.


Organization

Dates
BCH441 is a Fall-term course.
Lectures: Tuesday, 16:00 to 17:00 and Wednesday, 15:00 to 16:00
Tutorial sessions: Wednesday, 14:00 to 15:00 for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.
Location
MSB 2173 (Medical Sciences Building)
General

See the Course Web page for general information.

We are recommending Understanding Bioinformatics, Zvelebil & Baum, Garland 2008 as a background textbook for the course. (buy used at AbeBooks)

This is an electronic submission only course; but if you must print material, you might consider printing double-sided. Learn how, at the Print-Double-Sided Student Initiative.


Grading and Activities

Activity Weight
BCH441 - (Undergraduates)
Weight
BCH1441 - (Graduates)
12 In-class quizzes 42 marks (12 x 3.5) 24 marks (12 x 2)
Open project 28 marks (7 + 7 + 14) 28 marks
"Classroom" participation 10 marks 10 marks
Thesis Project   30 marks
Total 100 marks 100 marks



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. However I may adjust marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.



 

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