Difference between revisions of "Applied Bioinformatics Main Page"

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Applied Bioinformatics
 
Applied Bioinformatics
  
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<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>
 
<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 ==
 
  
−
BCB410H1F is the undergraduate course code and JTB2020H1S is the course code for graduate students. However the delivery and scope of the courses is very different:
+
__TOC__
  
−
* BCB410 is intended for students in the Bioinformatics and Computational Biology Specialist Program. Therefore I assume that all students are very familiar with a wide variety of computer science related topics and their practical application.
 
−
* JTB2020 is designed for students in the Collaborative PhD Program in Bioinformatics and Genome Biology. These students have a wide variety of backgrounds and prior experience. They participate in  the [[Computational_Systems_Biology_Main_Page|Computational Systems Biology Course]] and go through a number of targeted exercises in applied bioinformatics to add as much material to their knowledge- and skill set as can reasonably be acquired in a single term.
 
  
 +
== The Courses ==
  
−
===Organization===
+
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.
  
 +
{{Vspace}}
  
 +
<div class="alert">
 +
Continue [[BCB410|'''here''']] for the current BCB410H course page ...
 +
</div>
  
−
;Dates
+
{{Vspace}}
  
−
:Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00
+
<div class="alert">
−
:Tutorial sessions: Mondays, 12:00 to 13:00  for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.  
+
Continue [[BCB330|'''here''']] for guidelines on BCB330Y and BCB430Y projects with me ...
 +
</div>
  
−
;Location
 
−
: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>)
+
==Topics==
  
−
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].
+
<table width="60%"><tr><td class="l1">&nbsp;</td><td>
  
 +
===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>
  
−
===Grading and Activities===
+
===Systems and Tools===
 +
<table width="100%">
  
 +
<tr class="s1"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Unix]]
 +
<div class="mw-collapsible-content">
 +
<table width="100%"><tr class="s2"><td class="l2">[[Unix system administration]]</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">[[Unix commandline tools]]</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Unix automation]]</td></tr></table>
 +
<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>
 +
</div>
 +
</td></tr>
  
−
<table cellpadding="5">
+
<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>
  
−
<tr class="sh">
+
===Programming===
−
<td><b>Activity</b></td>
+
<table width="100%" >
−
<td><b>Weight</b><br><small>(Undergraduates)</small></td>
+
<tr class="s1"><td class="l1">[[Software Development|Software Development <small>(in a small-scale research context)</small>]]</td></tr>
−
<td><b>Weight</b><br><small>(Graduates)</small></td>
+
<tr class="s2"><td class="l1">[[SPN|SPN <small>(Structured Process Notation)</small>]]</td></tr>
−
</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>
 +
 
 +
<tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Perl]]
 +
<div class="mw-collapsible-content">
 +
<table width="100%"><tr class="s1"><td class="l2">[[Perl basic programming]]</td></tr></table>
 +
<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>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Perl MySQL introduction]]</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">[[Perl OBO parser]]</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Perl basic programming]]</td></tr></table>
 +
<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>
 +
</td></tr>
 +
 
 +
<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>
  
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
+
</table>
  
−
<tr class="s1">
+
===Algorithms===
−
<td>[[Assignments|'''5 Assignments''']]</td>
+
<table width="100%" >
−
<td>15 marks <small>(5 x 3)</small></td>
+
<tr class="sh"><td class="l1">General Algorithms</td></tr>
−
<td>10 marks <small>(5 x 2)</small></td>
+
<tr class="s1"><td class="l2">[[Optimization]]</td></tr>
−
</tr>
 
  
−
<tr class="s2">
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td>[[Quizzes|'''5 In-class quizzes''']]</td>
 
  
−
<td>35 marks <small>(5 x 7)</small></td>
+
<tr class="sh"><td class="l1">Algorithms on Sequences</td></tr>
−
<td>25 marks <small>(5 x 5)</small></td>
+
<tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr>
−
</tr>
+
<tr class="s2"><td class="l2">[[Multiple Sequence Alignment]]</td></tr>
 +
<tr class="s1"><td class="l2">[[Genome Assembly]]</td></tr>
  
−
<tr class="s1">
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td>[[Open project|'''Open project''']]</td>
 
−
<td>7 marks</td>
 
−
<td>5 marks</td>
 
−
</tr>
 
  
−
<tr class="s2">
+
<tr class="sh"><td class="l1">Algorithms on Structures</td></tr>
−
<td>[[Participation|'''"Classroom" participation''']]</td>
+
<tr class="s1"><td class="l2">[[Docking]]</td></tr>
−
<td>3 marks</td>
+
<tr class="s2"><td class="l2">Protein Structure Prediction <!-- ''ab initio'' --></td></tr>
−
<td>3 marks</td>
 
−
</tr>
 
  
−
<tr class="s1">
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td>[[Graduate project|'''Graduate project''']]</td>
 
−
<td>&nbsp;</td>
 
−
<td>17 marks</td>
 
−
</tr>
 
  
−
<tr class="s2">
+
<tr class="sh"><td class="l1">Algorithms on Trees</td></tr>
−
<td>[[Exam questions|'''Final exam''']]</td>
+
<tr class="s1"><td class="l2">Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --></td></tr>
−
<td>40 marks</td>
 
−
<td>40 marks</td>
 
−
</tr>
 
  
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
+
<tr><td class="sp">&nbsp;</td></tr>
−
<tr class="s1">
 
−
<td>'''Total'''</td>
 
−
<td>100 marks</td>
 
−
<td>100 marks</td>
 
−
</tr>
 
  
 +
<tr class="sh"><td class="l1">Algorithms on Networks</td></tr>
 +
<tr class="s1"><td class="l2">Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) --></td></tr>
 +
<tr class="s2"><td class="l3">[[Dijkstras Algorithm]]</td></tr>
 +
<tr class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr>
 
</table>
 
</table>
  
 +
===Communication and collaboration===
 +
<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>
  
−
;A note on marking
+
===Statistics===
−
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>
+
<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>
  
−
== Assignments ==
+
<tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[R]]
−
 
+
<div class="mw-collapsible-content">
−
<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
+
<table width="100%"><tr class="s1"><td class="l2">[[R tutorial|Introductory tutorial to '''R''']]</td></tr></table>
−
[[Assignment 5]] has been posted.
+
<table width="100%"><tr class="s2"><td class="l2">[[R plotting]]</td></tr></table>
−
<br>
+
<table width="100%"><tr class="s1"><td class="l2">[[R programming]]</td></tr></table>
−
<span style="font-size:60%;">Due Monday, Dec. 5.</span>
+
<table width="100%"><tr class="s2"><td class="l2">R EDA</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">R regression</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">R PCA</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">R Clustering</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[R Gene expression clustering]]</td></tr></table>
 +
<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>
 +
<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>
 
</div>
 
</div>
 +
<tr class="s1"><td class="l1">Bayesian inference</td></tr>
  
 +
<tr><td class="sp">&nbsp;</td></tr>
 +
</table>
  
 +
===Applications===
 +
<table width="100%" >
 +
<tr class="s1"><td class="l1">[[BLAST scripting]]</td></tr>
 +
<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>
 +
<tr class="s1"><td class="l1">[[HMMER]]</td></tr>
 +
<tr class="s2"><td class="l1">[[High-throughput sequencing]]</td></tr>
 +
<tr class="s1"><td class="l1">Functional annotation <!-- GFF --></td></tr>
 +
<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><td class="sp">&nbsp;</td></tr>
 +
</table>
 +
</td></tr></table>
  
  
−
=== Add this material ===
 
−
* GPU and Cloud computing
 
  
 +
<!--
 +
{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_organization}}
  
 +
{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}}
  
−
 
+
-->
−
==In depth...==
 
−
 
 
−
* [[Glossary]]
 
−
* [[Mutation Data Matrices]]
 
−
* [http://en.wikipedia.org/wiki/List_of_standard_amino_acids Amino acids]
 
−
* [[Database Identifiers]]
 
−
 
 
−
&nbsp;
 
−
 
 
 
== 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.
 
−
*[[Help:Editing| Editing:]] Editing principles and Wiki markup syntax for the Course Wiki pages
 
−
*[[Sandbox]]: A page for your editing experiments. Content added to this page will not stay permanently.
 
−
*[[Feedback]]: Share your views on the course, suggest improvements.
 
−
-->
 
−
 
−
 
−
 
−
&nbsp;<br>
 
−
 
 
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<table width="100%" padding="10" border="1">
 
<tr>
 
<tr>
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</table>
 
</table>
  
 +
-->
  
 +
[[Category:Applied Bioinformatics]]
  
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<syntaxhighlight lang="php">
+
</div>
−
<?php
 
−
    $v = "string";    // sample initialization
 
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html text
 
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<?
 
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    echo $v;        // end of php code
 
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?>
 
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</syntaxhighlight>
 

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
Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=Applied_Bioinformatics_Main_Page&oldid=9089"