Difference between revisions of "Applied Bioinformatics Main Page"

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Applied Bioinformatics
 
Applied Bioinformatics
  
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<small>'''This is our main tool to coordinate information, activities and projects in University of Toronto's bioinformatics course BCH441'''. If you are not one of our students, you can still browse this site, however only users with a login account can edit or contribute or edit material. If you are here because you are interested in general aspects of bioinformatics or computational biology, you may want to review the [http://en.wikipedia.org/wiki/Bioinformatics Wikipedia article on bioinformatics], or visit [http://www.openwetware.org/wiki/Wikiomics Wikiomics]. Contact boris.steipe(at)utoronto.ca with any questions you may have.</small>
+
<small>'''These wiki pages are provided to coordinate information, activities and projects in the applied bioinformatics courses 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 [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>
  
−
== The Course ==
 
  
−
<div style="padding: 5px; background: #C3CBF7;  border:solid 1px #AAAAAA;">
+
__TOC__
−
I am in the process of repairing the original course Wiki and many of the pages are still arbitrarily outdated.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.
 
−
<br>
 
−
<span style="font-size:80%;">Contact Boris Steipe for all matters of urgency. November 11. 2011</span>
 
−
</div>
 
  
−
===Organization===
 
−
;Dates
 
  
−
:Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00
+
== The Courses ==
−
:Tutorial sessions: Mondays, 12:00 to 13:00  for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.
 
  
−
;Location
+
This material is variably being used in my undergraduate courses BCH441 (Bioinformatics), BCB410 (Applied Bioinformatics), BCB420 (Computational Systems Biology), their graduate course cognates BCH1441 and JTB2020, and other workshops I teach.
−
:MSB 2173 (Medical Sciences Building)  
 
  
−
;General
+
{{Vspace}}
−
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>)
+
<div class="alert">
 +
Continue [[BCB410|'''here''']] for the current BCB410H course page ...
 +
</div>
  
−
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].
+
{{Vspace}}
  
 +
<div class="alert">
 +
Continue [[BCB330|'''here''']] for guidelines on BCB330Y and BCB430Y projects with me ...
 +
</div>
  
−
===Grading and Activities===
 
  
 +
{{Vspace}}
  
−
<table cellpadding="5">
+
==Topics==
  
−
<tr class="sh">
+
<table width="60%"><tr><td class="l1">&nbsp;</td><td>
−
<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>
+
===Hardware===
 +
<table width="100%">
 +
<tr class="s1"><td class="l1">High performance computing <!-- (... at the bench: GPUs, FPGAs, Clusters) --></td></tr>
 +
<tr class="s2"><td class="l1">Cloud computing</td></tr>
 +
<tr><td class="sp">&nbsp;</td></tr>
 +
</table>
  
−
<tr class="s1">
+
===Systems and Tools===
−
<td>[[Assignments|'''5 Assignments''']]</td>
+
<table width="100%">
−
<td>15 marks <small>(5 x 3)</small></td>
 
−
<td>10 marks <small>(5 x 2)</small></td>
 
−
</tr>
 
  
−
<tr class="s2">
+
<tr class="s1"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Unix]]
−
<td>[[Quizzes|'''5 In-class quizzes''']]</td>
+
<div class="mw-collapsible-content">
−
 
+
<table width="100%"><tr class="s2"><td class="l2">[[Unix system administration]]</td></tr></table>
−
<td>35 marks <small>(5 x 7)</small></td>
+
<table width="100%"><tr class="s1"><td class="l2">[[Unix commandline tools]]</td></tr></table>
−
<td>25 marks <small>(5 x 5)</small></td>
+
<table width="100%"><tr class="s2"><td class="l2">[[Unix automation]]</td></tr></table>
−
</tr>
+
<table width="100%"><tr class="s1"><td class="l2">[[Program installation]]</td></tr></table>
−
 
+
<table width="100%"><tr class="s2"><td class="l2">[[wget]]</td></tr></table>
−
<tr class="s1">
+
</div>
−
<td>[[Open project|'''Open project''']]</td>
+
</td></tr>
−
<td>7 marks</td>
 
−
<td>5 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s2">
 
−
<td>[[Participation|'''"Classroom" participation''']]</td>
 
−
<td>3 marks</td>
 
−
<td>3 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>[[Graduate project|'''Graduate project''']]</td>
 
−
<td>&nbsp;</td>
 
−
<td>17 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s2">
 
−
<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">
 
−
<td>'''Total'''</td>
 
−
<td>100 marks</td>
 
−
<td>100 marks</td>
 
−
</tr>
 
  
 +
<tr class="s2"><td class="l1">[[Network Configuration]]</td></tr>
 +
<tr class="s1"><td class="l1">[[Apache]]</td></tr>
 +
<tr class="s2"><td class="l1">[[MySQL]]</td></tr>
 +
<tr class="s1"><td class="l1">[[Tools for the bioinformatics lab]]</td></tr>
 +
<tr class="s2"><td class="l1">[[GBrowse|GBrowse and LDAS]]</td></tr>
 +
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</table>
  
 +
===Programming===
 +
<table width="100%" >
 +
<tr class="s1"><td class="l1">[[Software Development|Software Development <small>(in a small-scale research context)</small>]]</td></tr>
 +
<tr class="s2"><td class="l1">[[SPN|SPN <small>(Structured Process Notation)</small>]]</td></tr>
 +
<tr class="s1"><td class="l1">[[IDE|IDE (Integrated Development Environment)]]</td></tr>
 +
<tr class="s2"><td class="l1">[[Regular Expressions]]</td></tr>
 +
<tr class="s1"><td class="l1">[[Screenscraping]]</td></tr>
  
−
;A note on marking
+
<tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Perl]]
−
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>
+
<div class="mw-collapsible-content">
−
 
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl basic programming]]</td></tr></table>
−
== Assignments ==
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl hash example]]</td></tr></table>
−
 
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl LWP example]]</td></tr></table>
−
<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl MySQL introduction]]</td></tr></table>
−
[[Assignment 5]] has been posted.
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl OBO parser]]</td></tr></table>
−
<br>
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl basic programming]]</td></tr></table>
−
<span style="font-size:60%;">Due Monday, Dec. 5.</span>
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl programming exercises 1]]</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Perl programming exercises 2]]</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">[[Perl programming Data Structures]]</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Perl references]]</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">[[Perl simulation]]</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Regular Expressions]]</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">[[Perl: Object oriented programming]]</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Perl: Ugly programming]]</td></tr></table>
 
</div>
 
</div>
 +
</td></tr>
  
−
== Temporary links for material ==
+
<tr class="s1"><td class="l1">[[BioPerl]]</td></tr>
 +
<tr class="s2"><td class="l1">[[PHP]]</td></tr>
 +
<tr class="s1"><td class="l1">[[Data modelling]]</td></tr>
 +
<tr class="s2"><td class="l1">BioPython <!-- (scope, highlights, installation, use, support) --></td></tr>
 +
<tr class="s1"><td class="l1">Graphical output <!-- (PNG and SVG) --></td></tr>
 +
<tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr>
 +
<tr class="s1"><td class="l1">CVS / Git</td></tr>
  
−
===Lecture slides===
+
</table>
−
*[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>]
 
  
−
===Lecture recordings===
+
===Algorithms===
−
*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>]
+
<table width="100%" >
−
*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>]
+
<tr class="sh"><td class="l1">General Algorithms</td></tr>
−
*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>]
+
<tr class="s1"><td class="l2">[[Optimization]]</td></tr>
−
*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>]
 
−
*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>]
 
−
*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>]
 
−
*Thursday, 13. October 2011: (Parkinson)
 
−
*Monday, 17. October 2011:  (Parkinson)
 
−
*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>]
 
  
−
*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>]
+
<tr><td class="sp">&nbsp;</td></tr>
−
*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>]
 
−
*Monday, 14. November 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-11-14_Topic-16.mp4  Lecture 16 Phylogenetic Analysis II <small>(mp4, 18.5 MB)</small>]
 
−
*Thursday, 17. November 2011: Lecture 17 Comparative Genomics (Parkinson)
 
−
*Monday, 21. November 2011: Lecture 18 Computational Systems Biology (Parkinson)
 
−
*Thursday, 24. November 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-11-24_Topic-19.mp4  Lecture 19 Exploratory Data Analysis <small>(mp4, 20.0 MB)</small>]
 
  
 +
<tr class="sh"><td class="l1">Algorithms on Sequences</td></tr>
 +
<tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr>
 +
<tr class="s2"><td class="l2">[[Multiple Sequence Alignment]]</td></tr>
 +
<tr class="s1"><td class="l2">[[Genome Assembly]]</td></tr>
  
−
*Monday, 28. November 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-11-28_Topic-20a.mp4 Lecture 20 Protein structure prediction II: ''ab initio'' <small>(mp4, 15.5 MB)</small>]
+
<tr><td class="sp">&nbsp;</td></tr>
−
*Thursday, 1. December 2011: [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/2011-12-01_Topic-20b.mp4 Lecture 20 ''cont.'' <small>(mp4, 13.2 MB)</small>]
 
−
*Monday, 6. December 2011: Outlook: Computational Systems Biology
 
  
 +
<tr class="sh"><td class="l1">Algorithms on Structures</td></tr>
 +
<tr class="s1"><td class="l2">[[Docking]]</td></tr>
 +
<tr class="s2"><td class="l2">Protein Structure Prediction <!-- ''ab initio'' --></td></tr>
  
 +
<tr><td class="sp">&nbsp;</td></tr>
  
 +
<tr class="sh"><td class="l1">Algorithms on Trees</td></tr>
 +
<tr class="s1"><td class="l2">Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --></td></tr>
  
−
<!--
+
<tr><td class="sp">&nbsp;</td></tr>
−
== Organization ==
 
  
−
;Dates
+
<tr class="sh"><td class="l1">Algorithms on Networks</td></tr>
−
:''Lectures'': Monday and Thursday, 12:00 to 13:00
+
<tr class="s1"><td class="l2">Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) --></td></tr>
−
:''Tutorial sessions'': Mondays, 13:00 to 14:00 <small>&nbsp;&nbsp;for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.</small>
+
<tr class="s2"><td class="l3">[[Dijkstras Algorithm]]</td></tr>
 +
<tr class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr>
 +
</table>
  
−
;Location
+
===Communication and collaboration===
−
:MSB 2173 (Medical Sciences Building)
+
<table width="100%" >
 +
<tr class="s1"><td class="l1">[[MediaWiki]]</td></tr>
 +
<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr>
 +
<tr class="s1"><td class="l1">[[HTML 5]]</td></tr>
 +
<tr class="s2"><td class="l1">CSS</td></tr>
 +
<tr class="s1"><td class="l1">[[SADI|SADI and SHARE <small>- a Semantic Web Service framework</small>]]</td></tr>
 +
<tr class="s2"><td class="l1">[[CGI]]</td></tr>
 +
<tr><td class="sp">&nbsp;</td></tr>
 +
</table>
  
−
See the [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/ Course Web page] for general information.
+
===Statistics===
 +
<table width="100%" >
 +
<tr class="s1"><td class="l1">[[Pattern discovery]]</td></tr>
 +
<tr class="s2"><td class="l1">Correlation <!-- (Covariance matrices and their interpretation, application to large problems, collaborative filtering, MIC and MINE) --></td></tr>
 +
<tr class="s1"><td class="l1">Clustering methods <!-- (Algorithms and choice (including: hierarchical, model-based and partition clustering, graphical methods (MCL), flow based methods (RRW) and spectral methods). Implementation in R if possible) --></td></tr>
 +
<tr class="s2"><td class="l1">Cluster quality metrics <!-- (Cluster metrics (Akaike, BIC)–when and how) --></td></tr>
 +
<tr class="s1"><td class="l1">[[Map equation|The Map Equation]] </td></tr>
 +
<tr class="s2"><td class="l1">[[BIO Machine learning|Machine learning]]</td></tr>
 +
<tr class="s1"><td class="l1">[[Information theory]]</td></tr>
  
−
We are recommending '''[http://www.garlandscience.com/textbooks/0815340249.asp Understanding Bioinformatics]''', Zvelebil &amp; 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>
+
<tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[R]]
−
 
+
<div class="mw-collapsible-content">
−
== Grading and Activities ==
+
<table width="100%"><tr class="s1"><td class="l2">[[R tutorial|Introductory tutorial to '''R''']]</td></tr></table>
−
 
+
<table width="100%"><tr class="s2"><td class="l2">[[R plotting]]</td></tr></table>
−
<table cellpadding="5">
+
<table width="100%"><tr class="s1"><td class="l2">[[R programming]]</td></tr></table>
−
 
+
<table width="100%"><tr class="s2"><td class="l2">R EDA</td></tr></table>
−
<tr class="sh">
+
<table width="100%"><tr class="s1"><td class="l2">R regression</td></tr></table>
−
<td>'''Activity'''</td>
+
<table width="100%"><tr class="s2"><td class="l2">R PCA</td></tr></table>
−
<td>'''Weight'''<br><small>(Undergraduates)</small></td>
+
<table width="100%"><tr class="s1"><td class="l2">R Clustering</td></tr></table>
−
<td>'''Weight'''<br><small>(Graduates)</small></td>
+
<table width="100%"><tr class="s2"><td class="l2">[[R Gene expression clustering]]</td></tr></table>
−
</tr>
+
<table width="100%"><tr class="s1"><td class="l2">R Classification <!-- Phrasing inquiry as a classification problem, dealing with noisy data, machine learning approaches to classification, implementation in R) --></td></tr></table>
−
 
+
<table width="100%"><tr class="s2"><td class="l2">R hypothesis testing</td></tr></table>
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
+
<table width="100%"><tr class="s1"><td class="l2">[[Bioconductor]]</td></tr></table>
−
 
+
<table width="100%"><tr class="s2"><td class="l2">[[Regular Expressions]]</td></tr></table>
−
<tr class="s0">
+
</div>
−
<td>[[Assignments|'''5 Assignments''' (drop 1)]]</td>
+
<tr class="s1"><td class="l1">Bayesian inference</td></tr>
−
<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>
 
−
<td>10 marks</td>
 
−
<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>&nbsp;</td>
 
−
<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>
 
  
 +
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</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.
+
===Applications===
−
 
+
<table width="100%" >
−
== Lecture Schedule ==
+
<tr class="s1"><td class="l1">[[BLAST scripting]]</td></tr>
−
<small>This section is currently under construction.</small>
+
<tr class="s2"><td class="l1">[[Chimera programming]]</td></tr>
−
 
+
<tr class="s1"><td class="l1">[[Data integration|Biological data access and integration]] <!-- Add BioMart: Biodata integration, and data-mining of complex, related, descriptive data --></td></tr>
−
 
+
<tr class="s2"><td class="l1">Text mining <!-- (Use cases, tasks and metrics, taggers, vocabulary mapping, Practicals: R-support, Python/Perl support, others...) --></td></tr>
−
<table cellpadding="5">
+
<tr class="s1"><td class="l1">[[HMMER]]</td></tr>
−
 
+
<tr class="s2"><td class="l1">[[High-throughput sequencing]]</td></tr>
−
<tr class="st">
+
<tr class="s1"><td class="l1">Functional annotation <!-- GFF --></td></tr>
−
<td colspan="7">'''I n t r o d u c t i o n'''</td>
+
<tr class="s2"><td class="l1">Microarray analysis <!-- (... in R: differential expression and multiple testing; Loading and normalizing data, calculating differential expression, LOWESS, the question of significance, FWERs: Bonferroni and FDR; SAM and LIMMA) Expand to RNAseq--></td></tr>
−
</tr>
+
<tr><td class="sp">&nbsp;</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>
 
−
<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>
 
</table>
 +
</td></tr></table>
  
−
==In depth...==
 
  
−
* [[Glossary]]
 
−
* [[Mutation Data Matrices]]
 
−
* [http://en.wikipedia.org/wiki/List_of_standard_amino_acids Amino acids]
 
  
−
--><!-- * [[Database Identifiers]] --><!--
+
<!--  
 +
{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_organization}}
  
−
&nbsp;
+
{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}}
  
 +
-->
 
== Resources ==
 
== Resources ==
 
;Course related
 
;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
 
*[[Netiquette]] for the Group mailing list
−
*Previous [[Exam_questions]]
 
−
*[[Feedback_2007|2007 course feedback]]
 
−
*[[Feedback_2008|2008 course feedback]]
 
  
  
−
&nbsp;<br>
 
 
;Contents related
 
;Contents related
−
*The '''[[VMD]]''' tutorial
+
*'''[[UCSF_Chimera|Chimera]]'''
 
*A '''[[Stereo Vision]]''' tutorial
 
*A '''[[Stereo Vision]]''' tutorial
−
*[http://biodatabase.org/index.php/Main_Page MetaDatabase]
+
*[[Workshops]] taught elsewhere
−
*[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>
 
−
 
 
−
 
 
−
 
 
−
-->
 
−
 
 
  
 
<!--
 
<!--
−
;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.
 
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*[[Help:Editing| Editing:]] Editing principles and Wiki markup syntax for the Course Wiki pages
 
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*[[Feedback]]: Share your views on the course, suggest improvements.
 
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−
 
−
 
−
 
−
&nbsp;<br>
 
−
 
 
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<tr>
 
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 +
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[[Category:Applied Bioinformatics]]
 +
 +
</div>

Latest revision as of 16:38, 1 May 2017

Applied Bioinformatics

Welcome to the Applied Bioinformatics Course Wiki.

These wiki pages are provided to coordinate information, activities and projects in the applied bioinformatics courses 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.



The Courses

This material is variably being used in my undergraduate courses BCH441 (Bioinformatics), BCB410 (Applied Bioinformatics), BCB420 (Computational Systems Biology), their graduate course cognates BCH1441 and JTB2020, and other workshops I teach.


 

Continue here for the current BCB410H course page ...


 

Continue here for guidelines on BCB330Y and BCB430Y projects with me ...


 

Topics

 

Hardware

High performance computing
Cloud computing
 

Systems and Tools

Unix
Unix system administration
Unix commandline tools
Unix automation
Program installation
wget
Network Configuration
Apache
MySQL
Tools for the bioinformatics lab
GBrowse and LDAS
 

Programming

Software Development (in a small-scale research context)
SPN (Structured Process Notation)
IDE (Integrated Development Environment)
Regular Expressions
Screenscraping
Perl
Perl basic programming
Perl hash example
Perl LWP example
Perl MySQL introduction
Perl OBO parser
Perl basic programming
Perl programming exercises 1
Perl programming exercises 2
Perl programming Data Structures
Perl references
Perl simulation
Regular Expressions
Perl: Object oriented programming
Perl: Ugly programming
BioPerl
PHP
Data modelling
BioPython
Graphical output
Autonomous agents
CVS / Git

Algorithms

General Algorithms
Optimization
 
Algorithms on Sequences
Dynamic Programming
Multiple Sequence Alignment
Genome Assembly
 
Algorithms on Structures
Docking
Protein Structure Prediction
 
Algorithms on Trees
Computing with trees
 
Algorithms on Networks
Network metrics
Dijkstras Algorithm
Floyd Warshall Algorithm

Communication and collaboration

MediaWiki
HTML essentials
HTML 5
CSS
SADI and SHARE - a Semantic Web Service framework
CGI
 

Statistics

Pattern discovery
Correlation
Clustering methods
Cluster quality metrics
The Map Equation
Machine learning
Information theory
R
Introductory tutorial to R
R plotting
R programming
R EDA
R regression
R PCA
R Clustering
R Gene expression clustering
R Classification
R hypothesis testing
Bioconductor
Regular Expressions
Bayesian inference
 

Applications

BLAST scripting
Chimera programming
Biological data access and integration
Text mining
HMMER
High-throughput sequencing
Functional annotation
Microarray analysis
 


Resources

Course related


Contents related
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