Difference between revisions of "Bioinformatics Main Page"

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<!-- small>The lecture recordings linked below are copyrighted material, for the personal use of participants of the course only. It is not permissible to repost them elsewhere. If in doubt, ask me.</small -->
 
<!-- small>The lecture recordings linked below are copyrighted material, for the personal use of participants of the course only. It is not permissible to repost them elsewhere. If in doubt, ask me.</small -->
  
−
===I n t r o d u c t i o n===
+
===PREPARATION===
  
 
&nbsp;
 
&nbsp;
 +
  
 
<table width="90%" align="center">
 
<table width="90%" align="center">
 
<tr class="sh">
 
<tr class="sh">
 
<td class="sc" width="5%">'''Week'''</td>
 
<td class="sc" width="5%">'''Week'''</td>
−
<td class="sc" width="10%">'''Date'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Sept. 15'''</td>
−
<td class="sc" width="65%">'''Topics'''</td>
+
<td class="sc" width="30%">'''Readings'''</td>
−
<td class="sc" width="15%">'''Activities'''</td>
+
<td class="sc" width="20%">'''Assignment'''</td>
−
<td class="sc" width="15%">'''Assignment'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Sept. 22'''</td>
 
</tr>
 
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">1</td>
 +
<td class="sc">Organization</td>
 +
<td class="sc">R Tutorial</td>
 +
<td class="sc">Assignment 1</td>
 +
<td class="sc">Quiz 1
  
−
<!-- ===================  I N T R O  ===================  -->
+
----
  
 +
In Depth ...
 +
</td>
 +
</tr>
 +
</table>
  
  
−
<tr class="s1">
+
&nbsp;
−
<td class="sc">Intro</td>
+
 
−
<td class="sc">Sept.&nbsp;14&nbsp;-&nbsp;20</td>
+
===BIOINFORMATICS ON THE WEB===
−
<td class="sc">
 
−
<div class="table-intro-text">Bioinformatics focusses on the data and methods, and Computational Biology defines the objectives, to bring our understanding of  Biology to a rigorous, principled, quantitative and predictive level. Over the last two decades, ever since bioinformatics began to take centre stage in the life sciences, the rate of change in the discipline has continuously accelerated. In part, driven by the growth of the Internet, in part through novel algorithms, but to the largest part driven through a very large increase in the volume and quality of data, opportunities for computational analysis in the life science lab have grown in leaps and bounds. One of the associated challenges is to keep abreast of  the rapidly changing methods and tools that are available. This course focuses on the basic principles and concepts of the field and emphasis techniques and skills that are easily accessible and freely available to every life science researcher.</div>
 
  
 +
&nbsp;
  
  
−
* Course Organisation
+
<table width="90%" align="center">
−
* [[BIO_Introduction|Current bioinformatics]]
+
<tr class="sh">
−
* [[BIO_databases|Databases]]
+
<td class="sc" width="5%">'''Week'''</td>
−
* [[BIO_services|Services]]
+
<td class="sc" width="35%">'''In class: Tuesday, Sept. 22'''</td>
−
* [[BIO_tools|Tools]]
+
<td class="sc" width="30%">'''Readings'''</td>
 +
<td class="sc" width="20%">'''Assignment'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Sept. 29'''</td>
 +
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">2</td>
 +
<td class="sc">Introduction..</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 2</td>
 +
<td class="sc">Quiz 2
  
 
----
 
----
−
<!-- use template {{PDFlink... , then  {{PDFlinkOld...  after semester closes down -->
 
−
 
−
{{PDFlinkOld|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/01-Introduction_2014.pdf Lecture notes 2014: 01 - Introduction <small>(PDF 5.9 MB)</small>]}}<br />
 
  
 +
In Depth ...
 
</td>
 
</td>
−
<td class="sc">&mdash;</td>
 
−
<td class="sc">[[BIO_Assignment_Week_1|Assignment&nbsp;1]]</td>
 
 
</tr>
 
</tr>
 
</table>
 
</table>
 +
  
 
&nbsp;
 
&nbsp;
  
−
=== D a t a &nbsp;a n d &nbsp;D a t a &nbsp;A n a l y s i s ===
+
===SEQUENCE ANALYSIS===
  
 
&nbsp;
 
&nbsp;
 +
  
 
<table width="90%" align="center">
 
<table width="90%" align="center">
 
<tr class="sh">
 
<tr class="sh">
 
<td class="sc" width="5%">'''Week'''</td>
 
<td class="sc" width="5%">'''Week'''</td>
−
<td class="sc" width="10%">'''Date'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Sept. 29'''</td>
−
<td class="sc" width="65%">'''Topics'''</td>
+
<td class="sc" width="30%">'''Readings'''</td>
−
<td class="sc" width="15%">'''Activities'''</td>
+
<td class="sc" width="20%">'''Assignment'''</td>
−
<td class="sc" width="15%">'''Assignment'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Oct. 6'''</td>
 
</tr>
 
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">3</td>
 +
<td class="sc">Introduction..</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 2</td>
 +
<td class="sc">Quiz 2
  
−
<!-- ===================  C L A S S  1    ===================  -->
+
----
 +
 
 +
In Depth ...
 +
</td>
 +
</tr>
 +
</table>
  
  
 +
&nbsp;
  
−
<tr class="s1">
+
 
−
<td class="sc">1</td>
+
===SEQUENCE ALIGNMENT===
−
<td class="sc">Sept.&nbsp;21&nbsp;-&nbsp;27</td>
+
 
−
<td class="sc">
+
&nbsp;
−
<div class="table-intro-text">In principle, most of the data of interest to us is freely available on the Web, in public repositories. However, the number of databases and associated Web services is large and in constant flux and integrating the data has its own issues. The most important issue is to be clear about the abstractions we use and how they relate back to the biology they describe.</div>
 
−
* [[BIO_Sequence]]
 
−
* [[BIO_Structure]]
 
  
  
−
----
+
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Sept. 29'''</td>
 +
<td class="sc" width="30%">'''Readings'''</td>
 +
<td class="sc" width="20%">'''Assignment'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Oct. 6'''</td>
 +
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">4</td>
 +
<td class="sc">Introduction..</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 3</td>
 +
<td class="sc">Quiz 3
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/02-SequenceData_2014.pdf Lecture notes 2014: 02 - Sequence Data <small>(PDF 4.5 MB)</small>]}}<br />
+
----
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/03-StructureData_2014.pdf Lecture notes 2014: 03 - Structure Data <small>(PDF 14.1 MB)</small>]}}<br />
 
−
<!--
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/02-Sequences-2013.mp4 Lecture recordings 2013: 02 - Sequences <small>(mp4, 23.0 MB)</small>]<br />
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/03-Structures-2013.mp4 Lecture recordings 2013: 03 - Structure data <small>(mp4, 18.1 MB)</small>] -->
 
  
 +
In Depth ...
 
</td>
 
</td>
−
<td class="sc">Quiz 1</td>
 
−
<td class="sc">[[BIO_Assignment_Week_2|Assignment&nbsp;2]]</td>
 
 
</tr>
 
</tr>
 +
</table>
  
  
−
<!-- ===================  C L A S S  2  ===================  -->
+
&nbsp;
  
 +
===STRUCTURE ANALYSIS===
  
−
<tr class="s2">
+
&nbsp;
−
<td class="sc">2</td>
 
−
<td class="sc">Sept.&nbsp;28&nbsp;-&nbsp;Oct.&nbsp;4</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text">...</div>
 
−
* [[Sequence_analysis]]
 
−
* [[BIO Machine learning]]
 
  
−
----
 
  
 +
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Oct. 6'''</td>
 +
<td class="sc" width="30%">'''Readings'''</td>
 +
<td class="sc" width="20%">'''Assignment'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Oct. 13'''</td>
 +
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">5</td>
 +
<td class="sc">Introduction ...</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 4</td>
 +
<td class="sc">Quiz 4
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/04-SequenceAnalysis_I_2014.pdf Lecture notes 2014: 04 - Sequence Analysis I <small>(PDF 12.5 MB)</small>]}}<br />
+
----
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/05-SequenceAnalysis_II_2014.pdf Lecture notes 2014: 05 - Sequence Analysis II <small>(PDF 8.9 MB)</small>]}}<br />
 
  
−
<!-- [http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/04-SequenceAnalysis_I-2013.mp4 Lecture recordings 2013: 04 - Sequence Analysis I <small>(mp4, 12.8 MB)</small>]<br />
+
In Depth ...
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/05-SequenceAnalysis_II-2013.mp4 Lecture recordings 2013: 05 - Sequence Analysis II <small>(mp4, 20.7 MB)</small>]<br /> -->
 
 
</td>
 
</td>
−
<td class="sc">Quiz 2</td>
 
−
<td class="sc">[[BIO_Assignment_Week_3|Assignment&nbsp;3]]</td>
 
 
</tr>
 
</tr>
 +
</table>
  
  
−
<!-- ===================  C L A S S  3  ===================  -->
+
&nbsp;
  
 +
===FUNCTION===
  
−
<tr class="s1">
+
&nbsp;
−
<td class="sc">3</td>
 
−
<td class="sc">Oct.&nbsp;5&nbsp;-&nbsp;11</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* [[Protein domains]]
 
−
* [[Protein structure interpretation]]
 
  
  
−
----
+
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Oct. 13'''</td>
 +
<td class="sc" width="30%">'''Readings'''</td>
 +
<td class="sc" width="20%">'''Assignment'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Oct. 20'''</td>
 +
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">6</td>
 +
<td class="sc">Introduction ...</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 5</td>
 +
<td class="sc">Quiz 5
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/06-StructuralDomains_2014.pdf Lecture notes 2014: 06 - Structural Domains <small>(PDF 12.5 MB)</small>]}}<br />
+
----
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/07-InterpretingProteinStructure_2014.pdf Lecture notes 2014: 07 - Interpreting Protein Structure<small>(PDF 16.5 MB)</small>]}}<br />
 
−
 
 
−
<!-- [http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/06-StructureInterpretation-2013.mp4 Lecture recordings 2013: 06 - Interpreting Protein Structure <small>(mp4, 34.9 MB)</small>]<br />
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/07-Domains-2013.mp4 Lecture recordings 2013: 07 - Protein Domains <small>(mp4, 9.7 MB)</small>] -->
 
  
 +
In Depth ...
 
</td>
 
</td>
−
<td class="sc">Quiz 3, first phase of project due</td>
 
−
<td class="sc">[[BIO_Assignment_Week_4|Assignment&nbsp;4]]</td>
 
 
</tr>
 
</tr>
 
</table>
 
</table>
 +
  
 
&nbsp;
 
&nbsp;
  
−
=== H o m o l o g y ===
+
===PREDICTIONS===
  
 
&nbsp;
 
&nbsp;
 +
  
 
<table width="90%" align="center">
 
<table width="90%" align="center">
 
<tr class="sh">
 
<tr class="sh">
 
<td class="sc" width="5%">'''Week'''</td>
 
<td class="sc" width="5%">'''Week'''</td>
−
<td class="sc" width="10%">'''Date'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Oct. 20'''</td>
−
<td class="sc" width="65%">'''Topics'''</td>
+
<td class="sc" width="30%">'''Readings'''</td>
−
<td class="sc" width="15%">'''Activities'''</td>
+
<td class="sc" width="20%">'''Assignment'''</td>
−
<td class="sc" width="15%">'''Assignment'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Oct. 27'''</td>
 
</tr>
 
</tr>
−
 
−
 
−
<!-- ===================  C L A S S  4  ===================  -->
 
−
 
  
 
<tr class="s1">
 
<tr class="s1">
−
<td class="sc">4</td>
+
<td class="sc">7</td>
−
<td class="sc">Oct.&nbsp;12&nbsp;-&nbsp;18</td>
+
<td class="sc">Introduction ...</td>
−
<td class="sc">
+
<td class="sc">Readings</td>
−
<div class="table-intro-text"> ... </div>
+
<td class="sc">Assignment 6</td>
−
* [[Homology principles|Homology I: Principles]]
+
<td class="sc">Quiz 6
−
* [[Sequence alignment|Homology II: Sequence Alignment]]
 
−
 
 
  
 
----
 
----
  
−
 
+
In Depth ...
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/08-Homology_I_Principles_2014.pdf Lecture notes 2014: 08 - Homology I: Principles <small>(PDF 9.3 MB)</small>]}}<br />
 
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/09-Homology_II_Alignment_2014.pdf Lecture notes 2014: 09 - Homology II: Alignment <small>(PDF 8.4 MB)</small>]}}<br />
 
−
 
 
−
<!-- [http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/08-Homology_I-2013.mp4            Lecture recordings 2013: 08 - Homology: Principles          <small>(mp4, 24.7 MB)</small>]<br />
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/09-Homology_II-2013.mp4            Lecture recordings 2013: 09 - Homology: Alignment          <small>(mp4, 13.9 MB)</small>]<br /> -->
 
−
 
 
 
</td>
 
</td>
−
<td class="sc">Quiz 4</td>
 
−
<td class="sc">[[BIO_Assignment_Week_5|Assignment&nbsp;5]]</td>
 
 
</tr>
 
</tr>
 +
</table>
  
  
−
<!-- ===================  C L A S S  5  ===================  -->
+
&nbsp;
  
  
 +
===PHYLOGENETIC ANALYSIS===
  
−
<tr class="s2">
+
&nbsp;
−
<td class="sc">5</td>
 
−
<td class="sc">Oct.&nbsp;19&nbsp;-&nbsp;25</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* [[BLAST|Homology III: BLAST]]
 
−
* [[Multiple sequence alignment|Homology IV: Multiple sequence alignment]]
 
  
  
−
----
+
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Oct. 27'''</td>
 +
<td class="sc" width="30%">'''Readings'''</td>
 +
<td class="sc" width="20%">'''Assignment'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Nov. 3'''</td>
 +
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">8</td>
 +
<td class="sc">Introduction ...</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 7</td>
 +
<td class="sc">Quiz 7
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/10-Homology_III_BLAST_2014.pdf Lecture notes 2014: 10 - Homology III: BLAST <small>(PDF 7.4 MB)</small>]}}<br />
+
----
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/11-Homology_IV_MSA_2014.pdf Lecture notes 2014: 11 - Homology IV: MSA  <small>(PDF 9.4 MB)</small>]}}<br />
 
  
−
<!-- [http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/10-Homology_III-2013.mp4          Lecture recordings 2013: 10 - Homology: BLAST              <small>(mp4, 21.8 MB)</small>]<br />
+
In Depth ...
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/11-Homology_IV-2013.mp4            Lecture recordings 2013: 11 - Homology: MSA                <small>(mp4, 19.3 MB)</small>]
 
−
<br /> -->
 
 
</td>
 
</td>
−
<td class="sc">Quiz 5</td>
 
−
<td class="sc">[[BIO_Assignment_Week_6|Assignment&nbsp;6]]</td>
 
 
</tr>
 
</tr>
 +
</table>
  
  
−
<!-- ===================  C L A S S  6  ===================  -->
+
&nbsp;
  
  
−
<tr class="s1">
+
===GENOME ANALYSIS===
−
<td class="sc">6</td>
+
 
−
<td class="sc">Oct.&nbsp;26&nbsp;- Nov.&nbsp;1</td>
+
&nbsp;
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* [[Statistics]] and [[EDA|Exploratory Data Analysis]]
 
−
* [[Information theory]]
 
  
  
−
----
+
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Nov. 3'''</td>
 +
<td class="sc" width="30%">'''Readings'''</td>
 +
<td class="sc" width="20%">'''Assignment'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Nov. 17'''</td>
 +
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">9</td>
 +
<td class="sc">Introduction ...</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 8</td>
 +
<td class="sc">Quiz 8
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/12-Statistics_2014.pdf Lecture notes 2014: 12 - Statistics and Exploratory Data Analysis <small>(PDF 21.5 MB)</small>]}}<br />
+
----
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/13-Information_Theory_2014.pdf Lecture notes 2014: 13 - Information Theory  <small>(PDF 3.9 MB)</small>]}}<br />
 
  
−
<!-- [http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/12-StatisticsAndEDA-2013.mp4      Lecture recordings 2013: 12 - Statistics and EDA            <small>(mp4, 16.1 MB)</small>]<br />
+
In Depth ...
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/13-InformationTheory-2013.mp4      Lecture recordings 2013: 13 - Information Theory            <small>(mp4, 21.6 MB)</small>]<br /> -->
 
 
</td>
 
</td>
−
<td class="sc">Quiz 6</td>
 
−
<td class="sc">[[BIO_Assignment_Week_7|Assignment&nbsp;7]]</td>
 
 
</tr>
 
</tr>
 +
</table>
  
  
−
<!-- ===================  C L A S S  7  ===================  -->
+
&nbsp;
  
 +
===EXPRESSION ANALYSIS===
  
−
<tr class="s2">
+
&nbsp;
−
<td class="sc">7</td>
 
−
<td class="sc">Nov.&nbsp;2&nbsp;-&nbsp;8</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* [[Homology modelling]]
 
−
* [[Molecular dynamics]]
 
−
* [[De novo structure prediction|''De novo'' Structure Prediction and Design]]
 
  
  
−
----
+
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Nov. 17'''</td>
 +
<td class="sc" width="30%">'''Readings'''</td>
 +
<td class="sc" width="20%">'''Assignment'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Nov. 24'''</td>
 +
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">10</td>
 +
<td class="sc">Introduction ...</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 9</td>
 +
<td class="sc">Quiz 9
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/14-PredictingProteinStructure_I_2014.pdf Lecture notes 2014: 14 - Predicting Protein Structure: I <small>(PDF 11.5 MB)</small>]}}<br />
+
----
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/15-PredictingProteinStructure_II_2014.pdf Lecture notes 2014: 15 - Predicting Protein Structure: II <small>(PDF 14.0 MB)</small>]}}<br />
 
−
 
 
−
<!-- [http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/14-ProteinStructurePrediction-2013 Lecture recordings 2013: 14 - Protein Structure Prediction  <small>(mp4, 31.2 MB)</small>]<br /> -->
 
  
 +
In Depth ...
 
</td>
 
</td>
−
<td class="sc">Quiz 7</td>
 
−
<td class="sc">[[BIO_Assignment_Week_8|Assignment&nbsp;8]]</td>
 
 
</tr>
 
</tr>
 
</table>
 
</table>
 +
  
 
&nbsp;
 
&nbsp;
  
−
===G e n o m e s===
+
===PROTEIN-PROTEIN INTERACTIONS===
  
 
&nbsp;
 
&nbsp;
 +
  
 
<table width="90%" align="center">
 
<table width="90%" align="center">
−
 
 
<tr class="sh">
 
<tr class="sh">
 
<td class="sc" width="5%">'''Week'''</td>
 
<td class="sc" width="5%">'''Week'''</td>
−
<td class="sc" width="10%">'''Date'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Nov. 17'''</td>
−
<td class="sc" width="65%">'''Topics'''</td>
+
<td class="sc" width="30%">'''Readings'''</td>
−
<td class="sc" width="15%">'''Activities'''</td>
+
<td class="sc" width="20%">'''Assignment'''</td>
−
<td class="sc" width="15%">'''Assignment'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Nov. 24'''</td>
 
</tr>
 
</tr>
−
<!-- ===================    /THEME  ===================  -->
 
  
 +
<tr class="s1">
 +
<td class="sc">11</td>
 +
<td class="sc">Introduction ...</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 10</td>
 +
<td class="sc">Quiz 10
  
−
<!-- ===================  C L A S S  8  ===================  -->
+
----
  
 +
In Depth ...
 +
</td>
 +
</tr>
 +
</table>
  
−
<tr class="s1">
 
−
<td class="sc">8</td>
 
−
<td class="sc">Nov.&nbsp;9&nbsp;-&nbsp;15</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* '''Fall break - no class on Tuesday, Nov. 10'''
 
−
* [[Genome sequencing]]
 
−
* [[Genome annotation]]
 
  
−
----
+
&nbsp;
  
 +
===SYSTEMS===
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/16-NextGenerationSequencing_2014.pdf Lecture notes 2014: 16 - Next Generation Sequencing<small>(PDF 6.6 MB)</small>]}}<br />
+
&nbsp;
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/17-GenomeAnnotation_2014.pdf Lecture notes 2014: 17 - Genome Annotation <small>(PDF 8.0 MB)</small>]}}<br />
 
  
−
<!--
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/17-HumanGenomics-2013.mp4            Lecture recordings 2013: 15 - Human Genomics                <small>(mp4, 21.3 MB)</small>]<br />
 
−
-->
 
  
−
</td>
+
<table width="90%" align="center">
−
<td class="sc">Quiz 8</td>
+
<tr class="sh">
−
<td class="sc">[[BIO_Assignment_Week_9|Assignment&nbsp;9]]</td>
+
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Nov. 24'''</td>
 +
<td class="sc" width="30%">'''Readings'''</td>
 +
<td class="sc" width="20%">'''Assignment'''</td>
 +
<td class="sc" width="35%">'''In class: Tuesday, Dec. 1'''</td>
 
</tr>
 
</tr>
  
 +
<tr class="s1">
 +
<td class="sc">12</td>
 +
<td class="sc">Introduction ...</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 11</td>
 +
<td class="sc">Quiz 11
  
−
<!-- ===================  C L A S S  9  ===================  -->
 
−
 
−
 
−
<tr class="s2">
 
−
<td class="sc">9</td>
 
−
<td class="sc">Nov.&nbsp;16&nbsp;-&nbsp;22</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* [[SNPs]] and [[Human genomics]]
 
 
----
 
----
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/18-HumanGenomics_2014.pdf Lecture notes 2014: 18 - Human Genomics <small>(PDF 7.9 MB)</small>]}}<br />
+
In Depth ...
−
 
 
−
<!--
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/17-HumanGenomics-2013.mp4            Lecture recordings 2013: 15 - Human Genomics                <small>(mp4, 21.3 MB)</small>]<br />
 
−
-->
 
−
 
 
 
</td>
 
</td>
−
<td class="sc">Quiz 9, project submission due</td>
 
−
<td class="sc">[[BIO_Assignment_Week_10|Assignment&nbsp;10]]</td>
 
 
</tr>
 
</tr>
 +
</table>
  
−
</table>
 
  
 
&nbsp;
 
&nbsp;
  
−
===P h y l o g e n i e s===
+
 
 +
 
 +
===COMPUTATIONAL DISCOVERIS===
  
 
&nbsp;
 
&nbsp;
 +
  
 
<table width="90%" align="center">
 
<table width="90%" align="center">
 
<tr class="sh">
 
<tr class="sh">
 
<td class="sc" width="5%">'''Week'''</td>
 
<td class="sc" width="5%">'''Week'''</td>
−
<td class="sc" width="10%">'''Date'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Dec. 1'''</td>
−
<td class="sc" width="65%">'''Topics'''</td>
+
<td class="sc" width="30%">'''Readings'''</td>
−
<td class="sc" width="15%">'''Activities'''</td>
+
<td class="sc" width="20%">'''Assignment'''</td>
−
<td class="sc" width="15%">'''Assignment'''</td>
+
<td class="sc" width="35%">'''In class: Tuesday, Dec. 8'''</td>
 
</tr>
 
</tr>
−
<!-- ===================    /THEME  ===================  -->
 
  
 +
<tr class="s1">
 +
<td class="sc">13</td>
 +
<td class="sc">Introduction ...</td>
 +
<td class="sc">Readings</td>
 +
<td class="sc">Assignment 12</td>
 +
<td class="sc">Quiz 12
 +
 +
----
 +
 +
In Depth ...
 +
</td>
 +
</tr>
 +
</table>
  
−
<!-- ===================  C L A S S  1 0  ===================  -->
 
  
 +
&nbsp;
  
−
<tr class="s1">
 
−
<td class="sc">10</td>
 
−
<td class="sc">Nov.&nbsp;13&nbsp;-&nbsp;29</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* '''Fall break - no class on Tuesday, Nov. 18'''
 
−
* [[Phylogenetic analysis principles]]
 
−
* [[Phylogenetic tree interpretation]]
 
  
  
  
−
----
 
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/19-PhylogeneticAnalysis_I_2014.pdf Lecture notes 2014: 19 - Phylogenetic Analysis I: <small>Principles (PDF 11.5 MB)</small>]}}<br />
 
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/20-PhylogeneticAnalysis_II_2014.pdf Lecture notes 2014: 20 - Phylogenetic Analysis II: <small>Interpreting trees (PDF 5.4 MB)</small>]}}<br />
 
  
−
<!--
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/19-PhylogeneticAnalysis_1-2013.mp4 Lecture recordings 2013: 19 - Phylogeny: Principles        <small>(mp4, 17.2 MB)</small>]<br />
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/20-PhylogeneticAnalysis_2-2013.mp4 Lecture recordings 2013: 20 - Phylogeny: Tree construction  <small>(mp4, 18.3 MB)</small>]<br /> -->
 
  
−
</td>
 
−
<td class="sc">Quiz 10</td>
 
−
<td class="sc">[[BIO_Assignment_Week_11|Assignment&nbsp;11]]</td>
 
−
</tr>
 
  
  
−
<!-- ===================  C L A S S  1 1  ===================  -->
 
  
  
−
<tr class="s2">
 
−
<td class="sc">11</td>
 
−
<td class="sc">Nov.&nbsp;30&nbsp;- Dec.&nbsp;6</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* [[Phylogenetic inference|Inference From Phylogenies]]
 
−
* [[Function prediction|Function Annotation and Function Prediction]]
 
  
  
−
----
 
  
−
{{PDFlink|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/21-FunctionAnnotation_2014.pdf Lecture notes 2014: 21 - Function Annotation <small>(PDF 10.1 MB)</small>]}}<br />
 
  
−
<!-- {[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/21-PhylogeneticAnalysis_3-2013.mp4 Lecture recordings 2013: 21 - Phylogeny: Interpreting trees <small>(mp4, 17.3 MB)</small>]<br />
 
−
[http://local.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/22-FunctionAnnotation-2013.mp4  Lecture recordings 2013: 22 - Function Annotation          <small>(mp4, 16.5 MB)</small>]<br /> -->
 
  
−
</td>
 
−
<td class="sc">Quiz 11, project reviews due</td>
 
−
<td class="sc">[[BIO_Assignment_Week_12|Assignment&nbsp;12]]</td>
 
−
</tr>
 
  
  
−
<!-- ===================  C L A S S  1 2  ===================  -->
 
  
  
−
<tr class="s1">
 
−
<td class="sc">12</td>
 
−
<td class="sc">Dec.&nbsp;8</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text"> ... </div>
 
−
* Exam review
 
−
<hr />
 
−
Previous '''[[BCH441 Final Exam|Exam questions]]'''
 
−
</td>
 
−
<td class="sc">Quiz 12</td>
 
−
<td class="sc">&nbsp;</td>
 
−
</tr>
 
  
−
</table>
 
  
−
&nbsp;
 
  
  
−
<!--
 
−
=== Add this material ===
 
−
* Quantitative evolution: signals of recent change and selective pressure
 
−
-->
 
  
 
&nbsp;
 
&nbsp;

Revision as of 04:44, 15 September 2015

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.



This course will be taught again in September 2015. First class is on September 15. No tutorial on that day, i.e. we will meet at 18:00.

DO NOT MISS THE FIRST CLASS.

Attendance at the first lecture is mandatory and you will receive 2 points for attending.

There will be extensive changes to integrate systems biology material into the syllabus. This will affect lecture topics, assignments and the marking scheme. Proceed with caution until this note has been removed. Contact the course coordinator with any questions you may have.

</div-->



The Course

This course is an introduction to bioinformatics, for life science undergraduates and graduates and the specialists in the BCB Program. The course focusses on foundational techniques, the use of web sites for analysis, judicious interpretation of results and above all, proper, evidence based reasoning about biology. It also introduces programming with the statistical workbench and programming languageR. The course introduces the analysis of single biomolecule sequence and structure, omics-scale datasets, and the integration of biological data towards systems biology. We will explore the foundations of the field, and some more advanced topics with a special emphasis on defining the function of biomolecules. The course is complemented by BCB420 (offered in the Winter Term) which consolidates aspects of cutting-edge computational systems biology in a project context.

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


Organization

General
We will make an attempt to teach BCH441H following an inverted teaching model. Concepts will be introduced through background reading and extensive, hands-on assignments. We will use the classroom time
  • to assess contents-milestones in a weekly quiz;
  • to discuss fine points, perspectives, and to resolve uncertainties; and
  • to introduce concepts for the upcoming week.


Dates
BCH441/BCH1441 is a Fall Term course.
Tutorial sessions: Tuesday, 17:00 to 18:00 for open discussion of lecture material, in-class quizzes, quiz debriefings, exam preparation and other activities. Class begins at 10 minutes past the hour.
Lectures: right after the tutorials: Tuesday, 18:00 to 20:00.


Location
MS 4279 (Medical Sciences Building)


The Student Wiki.
Many of your activities will take place on a Wiki site (the "Student Wiki").


The Mailing List.
All course announcements and all course discussion (outside of class) will take place on a mailing list. We use Google Groups for this purpose. You will be subscribed to the list in the first class. You will not be able to participate fully in the course if you are not subscribed. Make sure you are subscribed with the email address you use most frequently and set your preferences to immediate delivery - "Digest" or "Web only" delivery won't allow you to participate actively in discussions and your participation mark will suffer.


Coordinator
Boris Steipe


Office hours
I do not hold regular office hours. I prefer communication via e-mail since it leaves you with a document trail of what was discussed, and we can share points of general interest more easily with the class. If you feel you must have a face-to-face meeting, coordinate with me.


Prerequisites
Introductory courses to biochemistry and molecular biology provide the contents background to the course. Such might be obtained through the listed prerequistes: BCH210H1/BCH242Y1; BCH311H1/MGY311Y1/PSL350H1[1]; special permission of the course coordinator can be granted.
It is assumed that students have access to the Internet via their own computer.


Exclusions & Enrolment controls
none


Printed material
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. Printing of course material is expressly discouraged since the material is updated frequently.


Recommended textbooks

Depending on your background, various levels of textbooks may be suitable. I will bring my evaluation copies to class so you can have a look.
Understanding Bioinformatics (Zvelebil & Baum) is a decent general introduction to many aspects of bioinformatics. It was published in 2007, an updated version is urgently needed. Still, some of the basics (like the algorithm for optimal sequence alignment) don't change. (Amazon) (Indigo) (ABE books)
Practical Bioinformatics (Agostino) covers some of the material of the BCH441 exercises. Expect a no-nonsense introduction to the very most basic stuff. I have my pet peeves about this book (as I have for many others, eg. why in the world do they still teach CLUSTAL when all available studies demonstrate it to be the least accurate MSA algorithm by a margin???), but if you haven't taken BCH441, this may serve you well. And if you did take BCH441, it may consolidate some ideas that I wasn't clear about. (Amazon) (Indigo) (ABE books)
If you are aware of more recent good textbooks, or have your own opinions about these or other books, let me know.


 

Grading and Activities

Syllabus and assignments may still undergo changes throughout the term.


 

Activity Weight
BCH441 - (Undergraduates)		 Weight
BCH1441 - (Graduates)
12 In-class quizzes 42 marks (12 x 3.5) 24 marks (12 x 2)
Bioinformatics project 28 marks (5 + 14 + 9) 28 marks
"Classroom" participation 10 marks 10 marks
Thesis Project   18 marks
Final exam 20 marks 20 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.

 

Timetable and syllabus

 

PREPARATION

 


Week In class: Tuesday, Sept. 15 Readings Assignment In class: Tuesday, Sept. 22
1 Organization R Tutorial Assignment 1 Quiz 1

In Depth ...


 

BIOINFORMATICS ON THE WEB

 


Week In class: Tuesday, Sept. 22 Readings Assignment In class: Tuesday, Sept. 29
2 Introduction.. Readings Assignment 2 Quiz 2

In Depth ...


 

SEQUENCE ANALYSIS

 


Week In class: Tuesday, Sept. 29 Readings Assignment In class: Tuesday, Oct. 6
3 Introduction.. Readings Assignment 2 Quiz 2

In Depth ...


 


SEQUENCE ALIGNMENT

 


Week In class: Tuesday, Sept. 29 Readings Assignment In class: Tuesday, Oct. 6
4 Introduction.. Readings Assignment 3 Quiz 3

In Depth ...


 

STRUCTURE ANALYSIS

 


Week In class: Tuesday, Oct. 6 Readings Assignment In class: Tuesday, Oct. 13
5 Introduction ... Readings Assignment 4 Quiz 4

In Depth ...


 

FUNCTION

 


Week In class: Tuesday, Oct. 13 Readings Assignment In class: Tuesday, Oct. 20
6 Introduction ... Readings Assignment 5 Quiz 5

In Depth ...


 

PREDICTIONS

 


Week In class: Tuesday, Oct. 20 Readings Assignment In class: Tuesday, Oct. 27
7 Introduction ... Readings Assignment 6 Quiz 6

In Depth ...


 


PHYLOGENETIC ANALYSIS

 


Week In class: Tuesday, Oct. 27 Readings Assignment In class: Tuesday, Nov. 3
8 Introduction ... Readings Assignment 7 Quiz 7

In Depth ...


 


GENOME ANALYSIS

 


Week In class: Tuesday, Nov. 3 Readings Assignment In class: Tuesday, Nov. 17
9 Introduction ... Readings Assignment 8 Quiz 8

In Depth ...


 

EXPRESSION ANALYSIS

 


Week In class: Tuesday, Nov. 17 Readings Assignment In class: Tuesday, Nov. 24
10 Introduction ... Readings Assignment 9 Quiz 9

In Depth ...


 

PROTEIN-PROTEIN INTERACTIONS

 


Week In class: Tuesday, Nov. 17 Readings Assignment In class: Tuesday, Nov. 24
11 Introduction ... Readings Assignment 10 Quiz 10

In Depth ...


 

SYSTEMS

 


Week In class: Tuesday, Nov. 24 Readings Assignment In class: Tuesday, Dec. 1
12 Introduction ... Readings Assignment 11 Quiz 11

In Depth ...


 


COMPUTATIONAL DISCOVERIS

 


Week In class: Tuesday, Dec. 1 Readings Assignment In class: Tuesday, Dec. 8
13 Introduction ... Readings Assignment 12 Quiz 12

In Depth ...


 













 

Resources

Course related


 

Contents related

 

Notes

  1. ↑ Please check the official Calendar for the academic year to confirm.



 

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