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.
+
[[BIO_Assignment_Week_1|Assignment&nbsp;1]] has been posted.<br />
−
 
+
Quiz on the assignment: Next Wednesday, September 19 in the tutorial session.
−
There will be no tutorial on Wednesday, September 12.
 
 
</div>
 
</div>
  
Line 29: Line 28:
 
;Dates
 
;Dates
  
−
:BCH441 is a Fall-term course.
+
:BCH441 is a Fall Term course.
 
:Lectures: Tuesday, 16:00 to 17:00 and Wednesday, 15:00 to 16:00  
 
: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.  
 
:Tutorial sessions: Wednesday, 14:00 to 15:00  for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.  
Line 42: Line 41:
  
 
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].
 
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===
 
===Grading and Activities===
Line 71: Line 69:
  
 
<tr class="s2">
 
<tr class="s2">
−
<td>[[CSB_Participation|'''"Classroom" participation''']]</td>
+
<td>[[BIO_Participation|'''"Classroom" participation''']]</td>
 
<td>10 marks</td>
 
<td>10 marks</td>
 
<td>10 marks</td>
 
<td>10 marks</td>
Line 79: Line 77:
 
<td>[[BIO_Thesis_Project|'''Thesis Project''']]</td>
 
<td>[[BIO_Thesis_Project|'''Thesis Project''']]</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
−
<td>18 marks</td>
+
<td>30 marks</td>
 
</tr>
 
</tr>
  
Line 100: Line 98:
  
  
 +
;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>
 +
 +
&nbsp;
 +
 +
== Timetable and syllabus ==
 +
 +
&nbsp;
 +
 +
===I n t r o d u c t i o n===
 +
 +
&nbsp;
 +
 +
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="10%">'''Date'''</td>
 +
<td class="sc" width="65%">'''Topics'''</td>
 +
<td class="sc" width="15%">'''Activities'''</td>
 +
<td class="sc" width="15%">'''Assignment'''</td>
 +
</tr>
 +
 +
<tr class="s1">
 +
<td class="sc">1</td>
 +
<td class="sc">Sept. 10 - 16</td>
 +
<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>
 +
 +
* Course Organisation
 +
* Current bioinformatics
 +
* Databases
 +
* Services
 +
* Tools
 +
 +
</td>
 +
<td class="sc">&mdash;</td>
 +
<td class="sc">[[BIO_Assignment_Week_1|Assignment&nbsp;1]]</td>
 +
</tr>
 +
</table>
 +
 +
&nbsp;
 +
 +
=== D a t a &nbsp;a n d &nbsp;D a t a &nbsp;A n a l y s i s ===
 +
 +
&nbsp;
 +
 +
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="10%">'''Date'''</td>
 +
<td class="sc" width="65%">'''Topics'''</td>
 +
<td class="sc" width="15%">'''Activities'''</td>
 +
<td class="sc" width="15%">'''Assignment'''</td>
 +
</tr>
 +
 +
<tr class="s1">
 +
<td class="sc">2</td>
 +
<td class="sc">Sept. 17 - 23</td>
 +
<td class="sc">
 +
<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>
 +
* Sequences
 +
* Structures
 +
 +
</td>
 +
<td class="sc">Quiz 1</td>
 +
<td class="sc">Assignment&nbsp;2</td>
 +
</tr>
 +
 +
<tr class="s2">
 +
<td class="sc">3</td>
 +
<td class="sc">Sept. 24 - 30</td>
 +
<td class="sc">
 +
<div class="table-intro-text">...</div>
 +
* Sequence_analysis
 +
* Machine learning
 +
</td>
 +
<td class="sc">Quiz 2, project concept due</td>
 +
<td class="sc">Assignment&nbsp;3</td>
 +
</tr>
 +
 +
<tr class="s1">
 +
<td class="sc">4</td>
 +
<td class="sc">Oct. 1 - 7</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Protein structure interpretation
 +
* Protein structure domains
 +
</td>
 +
<td class="sc">Quiz 3</td>
 +
<td class="sc">Assignment&nbsp;4</td>
 +
</tr>
 +
</table>
 +
 +
&nbsp;
 +
 +
=== H o m o l o g y ===
 +
 +
&nbsp;
 +
 +
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="10%">'''Date'''</td>
 +
<td class="sc" width="65%">'''Topics'''</td>
 +
<td class="sc" width="15%">'''Activities'''</td>
 +
<td class="sc" width="15%">'''Assignment'''</td>
 +
</tr>
 +
 +
<tr class="s1">
 +
<td class="sc">5</td>
 +
<td class="sc">Oct. 8 - 14</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Homology principles
 +
* BIO Statistics
 +
</td>
 +
<td class="sc">Quiz 4, project outline due</td>
 +
<td class="sc">Assignment&nbsp;5</td>
 +
</tr>
  
 +
<tr class="s2">
 +
<td class="sc">6</td>
 +
<td class="sc">Oct. 15 - 21</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Sequence alignment
 +
* BLAST
 +
</td>
 +
<td class="sc">Quiz 5</td>
 +
<td class="sc">Assignment&nbsp;6</td>
 +
</tr>
  
−
;A note on marking
+
<tr class="s1">
−
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>
+
<td class="sc">7</td>
 +
<td class="sc">Oct. 22 - 28</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Multiple sequence alignment
 +
* Information theory
 +
</td>
 +
<td class="sc">Quiz 6</td>
 +
<td class="sc">Assignment&nbsp;7</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td class="sc">8</td>
 +
<td class="sc">Oct. 29 - Nov. 4</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Homology modelling
 +
* Molecular dynamics
 +
* ''Ab initio'' structure prediction
 +
</td>
 +
<td class="sc">Quiz 7</td>
 +
<td class="sc">Assignment&nbsp;8</td>
 +
</tr>
 +
</table>
 +
 
 +
&nbsp;
 +
 
 +
===G e n o m e s===
 +
 
 +
&nbsp;
 +
 
 +
<table width="90%" align="center">
 +
 
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="10%">'''Date'''</td>
 +
<td class="sc" width="65%">'''Topics'''</td>
 +
<td class="sc" width="15%">'''Activities'''</td>
 +
<td class="sc" width="15%">'''Assignment'''</td>
 +
</tr>
 +
<!-- ===================    /THEME  ===================  -->
 +
 
 +
<tr class="s1">
 +
<td class="sc">9</td>
 +
<td class="sc">Nov. 5 - 11</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Genome sequencing and annotation
 +
</td>
 +
<td class="sc">Quiz 8</td>
 +
<td class="sc">Assignment&nbsp;9</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td class="sc">10</td>
 +
<td class="sc">Nov. 12 - 18</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* '''Fall break - no class on Tuesday, Nov. 13'''
 +
* SNPs
 +
* Human genomics
 +
</td>
 +
<td class="sc">Quiz 9, project final submission due</td>
 +
<td class="sc">Assignment&nbsp;10</td>
 +
</tr>
 +
 
 +
</table>
 +
 
 +
&nbsp;
 +
 
 +
===P h y l o g e n i e s===
 +
 
 +
&nbsp;
 +
 
 +
<table width="90%" align="center">
 +
<tr class="sh">
 +
<td class="sc" width="5%">'''Week'''</td>
 +
<td class="sc" width="10%">'''Date'''</td>
 +
<td class="sc" width="65%">'''Topics'''</td>
 +
<td class="sc" width="15%">'''Activities'''</td>
 +
<td class="sc" width="15%">'''Assignment'''</td>
 +
</tr>
 +
<!-- ===================    /THEME  ===================  -->
 +
 
 +
<tr class="s1">
 +
<td class="sc">11</td>
 +
<td class="sc">Nov. 19 - 25</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Phylogenetic analysis principles
 +
* Phylogenetic tree building
 +
</td>
 +
<td class="sc">Quiz 10</td>
 +
<td class="sc">Assignment&nbsp;11</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td class="sc">12</td>
 +
<td class="sc">Nov. 26 - Dec. 2</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Phylogenetic data interpretation
 +
* Functional annotation and Function prediction
 +
</td>
 +
<td class="sc">Quiz 11</td>
 +
<td class="sc">Assignment&nbsp;12</td>
 +
</tr>
 +
 
 +
<tr class="s1">
 +
<td class="sc">-</td>
 +
<td class="sc">Dec. 4</td>
 +
<td class="sc">
 +
<div class="table-intro-text"> ... </div>
 +
* Exam review
 +
</td>
 +
<td class="sc">Quiz 12</td>
 +
<td class="sc">&nbsp;</td>
 +
</tr>
 +
 
 +
</table>
 +
 
 +
&nbsp;
 +
 
 +
==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_2012 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 23:54, 13 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.


Assignment 1 has been posted.
Quiz on the assignment: Next Wednesday, September 19 in the tutorial session.



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
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

 

I n t r o d u c t i o n

 

Week Date Topics Activities Assignment
1 Sept. 10 - 16
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.
  • Course Organisation
  • Current bioinformatics
  • Databases
  • Services
  • Tools
 — Assignment 1

 

D a t a  a n d  D a t a  A n a l y s i s

 

Week Date Topics Activities Assignment
2 Sept. 17 - 23
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.
  • Sequences
  • Structures
 Quiz 1 Assignment 2
3 Sept. 24 - 30
...
  • Sequence_analysis
  • Machine learning
 Quiz 2, project concept due Assignment 3
4 Oct. 1 - 7
...
  • Protein structure interpretation
  • Protein structure domains
 Quiz 3 Assignment 4

 

H o m o l o g y

 

Week Date Topics Activities Assignment
5 Oct. 8 - 14
...
  • Homology principles
  • BIO Statistics
 Quiz 4, project outline due Assignment 5
6 Oct. 15 - 21
...
  • Sequence alignment
  • BLAST
 Quiz 5 Assignment 6
7 Oct. 22 - 28
...
  • Multiple sequence alignment
  • Information theory
 Quiz 6 Assignment 7
8 Oct. 29 - Nov. 4
...
  • Homology modelling
  • Molecular dynamics
  • Ab initio structure prediction
 Quiz 7 Assignment 8

 

G e n o m e s

 

Week Date Topics Activities Assignment
9 Nov. 5 - 11
...
  • Genome sequencing and annotation
 Quiz 8 Assignment 9
10 Nov. 12 - 18
...
  • Fall break - no class on Tuesday, Nov. 13
  • SNPs
  • Human genomics
 Quiz 9, project final submission due Assignment 10

 

P h y l o g e n i e s

 

Week Date Topics Activities Assignment
11 Nov. 19 - 25
...
  • Phylogenetic analysis principles
  • Phylogenetic tree building
 Quiz 10 Assignment 11
12 Nov. 26 - Dec. 2
...
  • Phylogenetic data interpretation
  • Functional annotation and Function prediction
 Quiz 11 Assignment 12
- Dec. 4
...
  • Exam review
 Quiz 12  

 

Lecture slides 2012

None yet.




Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=Bioinformatics_Main_Page&oldid=5402"