Difference between revisions of "Applied Bioinformatics Main Page"

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

Netiquette for the Group mailing list

Contents related

Chimera
A Stereo Vision tutorial
Workshops taught elsewhere

Difference between revisions of "Applied Bioinformatics Main Page"

Latest revision as of 16:38, 1 May 2017

Contents

The Courses

Topics

Hardware

Systems and Tools

Programming

Algorithms

Communication and collaboration

Statistics

Applications

Resources

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Sections

Tools

@@ Line 1: / Line 1: @@
-<div style="padding: 5px; background: #327378;  border:solid 1px #AAAAAA; font-size:300%;font-weight:bold; color:#FFFFFF">
+<div id="APB">
+<div class="b1">
 Applied Bioinformatics
@@ Line 9: / Line 10: @@
 <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 ==
-{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_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>
+{{Vspace}}
+<div class="alert">
+Continue [[BCB330|'''here''']] for guidelines on BCB330Y and BCB430Y projects with me ...
+</div>
+{{Vspace}}
+==Topics==
+<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>
+===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>
+<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>
+===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>
+<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>
+</table>
+===Algorithms===
+<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="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>
+<tr><td class="sp">&nbsp;</td></tr>
+<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>
+<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>
+===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>
-{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}}
+===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>
+<tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[R]]
+<div class="mw-collapsible-content">
+<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 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>
+<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>
+<tr class="s1"><td class="l1">Bayesian inference</td></tr>
-== Topics and exercises ==
+<tr><td class="sp">&nbsp;</td></tr>
-* GPU and Cloud computing
+</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>
-&nbsp;
+<!--
+{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_organization}}
+{{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}}
+-->
 == Resources ==
 ;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
-*Previous [[Exam_questions]]
-*[[Feedback_2007|2007 course feedback]]
-*[[Feedback_2008|2008 course feedback]]
-&nbsp;<br>
 ;Contents related
-*The '''[[VMD]]''' tutorial
+*'''[[UCSF_Chimera|Chimera]]'''
 *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>
 <table width="100%" padding="10" border="1">
 <tr>
@@ Line 73: / Line 217: @@
 </table>
+-->
 [[Category:Applied Bioinformatics]]
+</div>