Difference between revisions of "User:Boris/Temp/APB"

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<div id="APB">
 
<div id="APB">
  
−
<table width="40%"><tr><td>
+
<table width="40%"><tr><td class="l1">&nbsp;</td><td>
  
 
===Hardware===
 
===Hardware===
−
<table width="90%" align="left">
+
<table width="100%">
 
<tr class="s1"><td class="l1">High performance computing <!-- (... at the bench: GPUs, FPGAs, Clusters) --></td></tr>
 
<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 class="s2"><td class="l1">Cloud computing</td></tr>
 +
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</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 automation]]</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Program installation]]</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">[[wget]]</td></tr></table>
 +
</div>
 +
</td></tr>
  
−
===Systems and Tools===
 
−
<table width="90%" align="left">
 
−
<tr class="s1"><td class="l1">[[Unix]]</td></tr>
 
 
<tr class="s2"><td class="l1">[[Network Configuration]]</td></tr>
 
<tr class="s2"><td class="l1">[[Network Configuration]]</td></tr>
 
<tr class="s1"><td class="l1">[[Apache]]</td></tr>
 
<tr class="s1"><td class="l1">[[Apache]]</td></tr>
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<tr class="s1"><td class="l1">[[Tools for the bioinformatics lab]]</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 class="s2"><td class="l1">[[GBrowse|GBrowse and LDAS]]</td></tr>
 +
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</table>
−
 
  
 
===Programming===
 
===Programming===
−
<table width="90%" align="left">
+
<table width="100%" >
 
<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>
 
<tr class="s1"><td class="l1">[[Screenscraping]]</td></tr>
 
<tr class="s1"><td class="l1">[[Screenscraping]]</td></tr>
−
<tr class="s2"><td class="l1">[[Perl]]</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">[[Perl: Object oriented programming]]</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">[[Perl: Ugly programming]]</td></tr></table>
 +
</div>
 +
</td></tr>
 +
 
 
<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>
 
</table>
 
</table>
−
 
  
 
===Algorithms===
 
===Algorithms===
−
<table width="90%" align="left">
+
<table width="100%" >
 
<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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===Communication and collaboration===
 
===Communication and collaboration===
−
<table width="90%" align="left">
+
<table width="100%" >
 
<tr class="s1"><td class="l1">[[MediaWiki]]</td></tr>
 
<tr class="s1"><td class="l1">[[MediaWiki]]</td></tr>
 
<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr>
 
<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr>
Line 70: Line 96:
 
<tr class="s2"><td class="l1">[[SADI|SADI Semantic Automated Discovery and Integration]]</td></tr>
 
<tr class="s2"><td class="l1">[[SADI|SADI Semantic Automated Discovery and Integration]]</td></tr>
 
<tr class="s1"><td class="l1">[[CGI]]</td></tr>
 
<tr class="s1"><td class="l1">[[CGI]]</td></tr>
 +
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</table>
−
 
  
 
===Statistics===
 
===Statistics===
−
<table width="90%" align="left">
+
<table width="100%" >
 
<tr class="s1"><td class="l1">[[Pattern discovery]]</td></tr>
 
<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="s2"><td class="l1">Correlation <!-- (Covariance matrices and their interpretation, application to large problems, collaborative filtering, MIC and MINE) --></td></tr>
Line 81: Line 107:
 
<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 <!-- (Classification problems: Neural Networks, HMMs, SVM..) --></td></tr>
 
<tr class="s2"><td class="l1">Machine learning <!-- (Classification problems: Neural Networks, HMMs, SVM..) --></td></tr>
−
<tr class="s1"><td class="l1">[[R]]</td></tr>
+
 
−
<tr class="s2"><td class="l2">R plotting</td></tr>
+
<tr class="s1"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[R]]
−
<tr class="s1"><td class="l2">[[R programming]]</td></tr>
+
<div class="mw-collapsible-content">
−
<tr class="s2"><td class="l2">R EDA</td></tr>
+
<table width="100%"><tr class="s2"><td class="l2">R plotting</td></tr></table>
−
<tr class="s1"><td class="l2">R regression</td></tr>
+
<table width="100%"><tr class="s1"><td class="l2">[[R programming]]</td></tr></table>
−
<tr class="s2"><td class="l2">R PCA</td></tr>
+
<table width="100%"><tr class="s2"><td class="l2">R EDA</td></tr></table>
−
<tr class="s1"><td class="l2">R Clustering</td></tr>
+
<table width="100%"><tr class="s1"><td class="l2">R regression</td></tr></table>
−
<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 width="100%"><tr class="s2"><td class="l2">R PCA</td></tr></table>
−
<tr class="s1"><td class="l2">R hypothesis testing</td></tr>
+
<table width="100%"><tr class="s1"><td class="l2">R Clustering</td></tr></table>
−
<tr class="s2"><td class="l2">[[Bioconductor]]</td></tr>
+
<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="s1"><td class="l2">R hypothesis testing</td></tr></table>
 +
<table width="100%"><tr class="s2"><td class="l2">[[Bioconductor]]</td></tr></table>
 +
</div>
 +
</td></tr>
 +
 
 +
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</table>
  
 
===Applications===
 
===Applications===
−
<table width="90%" align="left">
+
<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">[[Data 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>
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<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) --></td></tr>
 +
<tr><td class="sp">&nbsp;</td></tr>
 
</table>
 
</table>
 
</td></tr></table>
 
</td></tr></table>
  
 
</div>
 
</div>

Latest revision as of 12:44, 27 September 2015

 

Hardware

High performance computing
Cloud computing
 

Systems and Tools

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

Programming

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
Perl: Object oriented programming
Perl: Ugly programming
BioPerl
PHP
Data modelling
BioPython
Graphical output
Autonomous agents

Algorithms

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
SADI Semantic Automated Discovery and Integration
CGI
 

Statistics

Pattern discovery
Correlation
Clustering methods
Cluster metrics
The Map Equation
Machine learning
R
R plotting
R programming
R EDA
R regression
R PCA
R Clustering
R Classification
R hypothesis testing
Bioconductor
 

Applications

Data integration
Text mining
HMMER
High-throughput sequencing
Functional annotation
Microarray analysis
 
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