Difference between revisions of "Applied Bioinformatics Main Page"

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== The Courses ==
 
== The Courses ==
  
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:
+
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.
  
* 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.
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{{Vspace}}
* 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.
 
  
 
<div class="alert">
 
<div class="alert">
Continue [[BCB410_2012|'''here''']] for the current BCB410 course page ...
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Continue [[BCB410|'''here''']] for the current BCB410H course page ...
 
</div>
 
</div>
  
 +
{{Vspace}}
 +
 +
<div class="alert">
 +
Continue [[BCB330|'''here''']] for guidelines on BCB330Y and BCB430Y projects with me ...
 +
</div>
 +
 +
 +
{{Vspace}}
  
 
==Topics==
 
==Topics==
  
<table width="40%"><tr><td class="l1">&nbsp;</td><td>
+
<table width="60%"><tr><td class="l1">&nbsp;</td><td>
  
 
===Hardware===
 
===Hardware===
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<div class="mw-collapsible-content">
 
<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="s2"><td class="l2">[[Unix system administration]]</td></tr></table>
<table width="100%"><tr class="s1"><td class="l2">[[Unix automation]]</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">[[Program installation]]</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">[[wget]]</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>
 
</div>
 
</td></tr>
 
</td></tr>
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===Programming===
 
===Programming===
 
<table width="100%" >
 
<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="s1"><td class="l1">[[IDE|IDE (Integrated Development Environment)]]</td></tr>
 
<tr class="s2"><td class="l1">[[Regular Expressions]]</td></tr>
 
<tr class="s2"><td class="l1">[[Regular Expressions]]</td></tr>
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<table width="100%"><tr class="s2"><td class="l2">[[Perl references]]</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="s1"><td class="l2">[[Perl simulation]]</td></tr></table>
<table width="100%"><tr class="s2"><td class="l2">[[Perl: Object oriented programming]]</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: Ugly programming]]</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>
 
</td></tr>
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<tr class="s1"><td class="l1">[[BioPerl]]</td></tr>
 
<tr class="s1"><td class="l1">[[BioPerl]]</td></tr>
 
<tr class="s2"><td class="l1">[[PHP]]</td></tr>
 
<tr class="s2"><td class="l1">[[PHP]]</td></tr>
<tr class="s1"><td class="l1">[[Relational database principles]]</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="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="s1"><td class="l1">Graphical output <!-- (PNG and SVG) --></td></tr>
 
<tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr>
 
<tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr>
 +
<tr class="s1"><td class="l1">CVS / Git</td></tr>
 +
 
</table>
 
</table>
  
 
===Algorithms===
 
===Algorithms===
 
<table width="100%" >
 
<table width="100%" >
 +
<tr class="sh"><td class="l1">General Algorithms</td></tr>
 +
<tr class="s1"><td class="l2">[[Optimization]]</td></tr>
 +
 +
<tr><td class="sp">&nbsp;</td></tr>
 +
 
<tr class="sh"><td class="l1">Algorithms on Sequences</td></tr>
 
<tr class="sh"><td class="l1">Algorithms on Sequences</td></tr>
 
<tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr>
 
<tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr>
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<tr class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr>
 
<tr class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr>
 
</table>
 
</table>
 
  
 
===Communication and collaboration===
 
===Communication and collaboration===
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<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr>
 
<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr>
 
<tr class="s1"><td class="l1">[[HTML 5]]</td></tr>
 
<tr class="s1"><td class="l1">[[HTML 5]]</td></tr>
<tr class="s2"><td class="l1">[[SADI|SADI Semantic Automated Discovery and Integration]]</td></tr>
+
<tr class="s2"><td class="l1">CSS</td></tr>
<tr class="s1"><td class="l1">[[CGI]]</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>
 
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</table>
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<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="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="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 metrics <!-- (Cluster quality metrics (Akaike, BIC)–when and how) --></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="s1"><td class="l1">[[Map equation|The Map Equation]] </td></tr>
<tr class="s2"><td class="l1">[[Machine learning]]</td></tr>
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<tr class="s2"><td class="l1">[[BIO Machine learning|Machine learning]]</td></tr>
 
<tr class="s1"><td class="l1">[[Information theory]]</td></tr>
 
<tr class="s1"><td class="l1">[[Information theory]]</td></tr>
  
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<table width="100%"><tr class="s2"><td class="l2">R PCA</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="s1"><td class="l2">R Clustering</td></tr></table>
<table width="100%"><tr class="s2"><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 Gene expression clustering]]</td></tr></table>
<table width="100%"><tr class="s1"><td class="l2">R hypothesis testing</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">[[Bioconductor]]</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>
</td></tr>
+
<tr class="s1"><td class="l1">Bayesian inference</td></tr>
  
 
<tr><td class="sp">&nbsp;</td></tr>
 
<tr><td class="sp">&nbsp;</td></tr>
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===Applications===
 
===Applications===
 
<table width="100%" >
 
<table width="100%" >
<tr class="s1"><td class="l1">[[Data integration]] <!-- Add BioMart: Biodata integration, and data-mining of complex, related, descriptive data --></td></tr>
+
<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="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="s1"><td class="l1">[[HMMER]]</td></tr>
 
<tr class="s2"><td class="l1">[[High-throughput sequencing]]</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="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) --></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>
 
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</table>
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{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}}
 
{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}}
  
 
+
-->
 
== Resources ==
 
== Resources ==
 
;Course related
 
;Course related
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;Contents related
 
;Contents related
*The '''[[VMD]]''' tutorial
+
*'''[[UCSF_Chimera|Chimera]]'''
 
*A '''[[Stereo Vision]]''' tutorial
 
*A '''[[Stereo Vision]]''' tutorial
 +
*[[Workshops]] taught elsewhere
  
 
+
<!--
 
<table width="100%" padding="10" border="1">
 
<table width="100%" padding="10" border="1">
 
<tr>
 
<tr>

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
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
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