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

@@ Line 16: / Line 16: @@
 == 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.
+{{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">
+Continue [[BCB410|'''here''']] for the current BCB410H course page ...
+</div>
+{{Vspace}}
 <div class="alert">
-Continue [[BCB410_2013|'''here''']] for the current BCB410 course page ...
+Continue [[BCB330|'''here''']] for guidelines on BCB330Y and BCB430Y projects with me ...
 </div>
-&nbsp;
-&nbsp;
+{{Vspace}}
 ==Topics==
@@ Line 64: / Line 67: @@
 ===Programming===
 <table width="100%" >
-<tr class="s2"><td class="l1">[[Software Development|Software Development <small>(in a small-scale research context)</small>]]</td></tr>
+<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>
@@ Line 90: / Line 94: @@
 <tr class="s1"><td class="l1">[[BioPerl]]</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="s1"><td class="l1">Graphical output <!-- (PNG and SVG) --></td></tr>
@@ Line 147: / Line 151: @@
 <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]]</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>
@@ Line 159: / Line 163: @@
 <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 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">[[Regular Expressions]]</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>
@@ Line 171: / Line 176: @@
 ===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>
@@ Line 176: / Line 183: @@
 <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) --></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>
@@ Line 188: / Line 195: @@
 {{#lst:Computational_Systems_Biology_Main_Page|CSB_main_grading}}
+-->
 == Resources ==
 ;Course related
@@ Line 195: / Line 202: @@
 ;Contents related
-*The '''[[VMD]]''' tutorial
+*'''[[UCSF_Chimera|Chimera]]'''
 *A '''[[Stereo Vision]]''' tutorial
+*[[Workshops]] taught elsewhere
+<!--
 <table width="100%" padding="10" border="1">
 <tr>

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

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Search

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