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

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<div id="APB">
 
<div id="APB">
  
 +
[...]
 +
<table width="33%">
 +
<tr class="sh"><td>Hardware</td></tr>
 +
<tr class="s1"><td>High performance computing <!-- (... at the bench: GPUs, FPGAs, Clusters) --></td></tr>
 +
<tr class="s2"><td>Cloud computing</td></tr>
 +
</table>
  
−
;Hardware
 
−
* High performance computing <!-- (... at the bench: GPUs, FPGAs, Clusters) -->
 
−
* Cloud computing
 
  
−
; Systems and Tools
+
<table width="33%">
−
* [[Unix]]
+
<tr class="sh"><td>Systems and Tools</td></tr>
−
* [[Network Configuration]]
+
<tr class="s1"><td>[[Unix]]</td></tr>
−
* [[Apache]]
+
<tr class="s2"><td>[[Network Configuration]]</td></tr>
−
* [[MySQL]]
+
<tr class="s1"><td>[[Apache]]</td></tr>
−
* [[Tools for the bioinformatics lab]]
+
<tr class="s2"><td>[[MySQL]]</td></tr>
−
* [[GBrowse|GBrowse and LDAS]]
+
<tr class="s1"><td>[[Tools for the bioinformatics lab]]</td></tr>
 +
<tr class="s2"><td>[[GBrowse|GBrowse and LDAS]]</td></tr>
 +
</table>
  
−
;Programming
 
−
* [[IDE|IDE (Integrated Development Environment)]]
 
−
* [[Regular Expressions]]
 
−
* [[Screenscraping]]
 
−
* [[Perl]]
 
−
* [[BioPerl]]
 
−
* [[PHP]]
 
−
* [[Relational database principles]]
 
−
* BioPython <!-- (scope, highlights, installation, use, support) -->
 
−
* Graphical output <!-- (PNG and SVG) -->
 
−
* [[Autonomous agents]]
 
  
−
:; Algorithms on Sequences
+
<table width="33%">
−
** [[Dynamic Programming]]
+
<tr class="sh"><td>Programming</td></tr>
−
** [[Multiple Sequence Alignment]]
+
<tr class="s1"><td>[[IDE|IDE (Integrated Development Environment)]]</td></tr>
−
** [[Genome Assembly]]
+
<tr class="s2"><td>[[Regular Expressions]]</td></tr>
−
:; Algorithms on Structures
+
<tr class="s1"><td>[[Screenscraping]]</td></tr>
−
** [[Docking]]
+
<tr class="s2"><td>[[Perl]]</td></tr>
−
** Protein Structure Prediction <!-- ''ab initio'' -->
+
<tr class="s1"><td>[[BioPerl]]</td></tr>
−
:; Algorithms on Trees
+
<tr class="s2"><td>[[PHP]]</td></tr>
−
** Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) -->
+
<tr class="s1"><td>[[Relational database principles]]</td></tr>
−
:; Algorithms on Networks
+
<tr class="s2"><td>BioPython <!-- (scope, highlights, installation, use, support) --></td></tr>
−
** Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) -->
+
<tr class="s1"><td>Graphical output <!-- (PNG and SVG) --></td></tr>
−
*** [[Dijkstras Algorithm]]
+
<tr class="s2"><td>[[Autonomous agents]]</td></tr>
−
*** [[Floyd Warshall Algorithm]]
+
</table>
  
−
;Communication and collaboration
 
−
* [[MediaWiki]]
 
−
* [[HTML essentials]]
 
−
* [[HTML 5]]
 
−
* [[SADI|SADI Semantic Automated Discovery and Integration]]
 
−
* [[CGI]]
 
  
−
; Statistics
+
<table width="33%">
−
* [[Pattern discovery]]
+
<tr class="sh"><td>Algorithms on Sequences</td></tr>
−
* Correlation <!-- (Covariance matrices and their interpretation, application to large problems, collaborative filtering, MIC and MINE) -->
+
<tr class="s1"><td>[[Dynamic Programming]]</td></tr>
−
* 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) -->
+
<tr class="s2"><td>[[Multiple Sequence Alignment]]</td></tr>
−
* Cluster metrics <!-- (Cluster quality metrics (Akaike, BIC)–when and how) -->
+
<tr class="s1"><td>[[Genome Assembly]]</td></tr>
−
* [[Map equation|The Map Equation]]
+
<tr class="sh"><td>Algorithms on Structures</td></tr>
−
* Machine learning <!-- (Classification problems: Neural Networks, HMMs, SVM..) -->
+
<tr class="s1"><td>[[Docking]]</td></tr>
−
* [[R]]
+
<tr class="s2"><td>Protein Structure Prediction <!-- ''ab initio'' --></td></tr>
−
** R plotting
+
<tr class="sh"><td>Algorithms on Trees</td></tr>
−
** [[R programming]]
+
<tr class="s1"><td>Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --></td></tr>
−
** R EDA
+
<tr class="sh"><td>Algorithms on Networks</td></tr>
−
** R regression
+
<tr class="s1"><td>Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) --></td></tr>
−
** R PCA
+
<tr class="s2"><td>[[Dijkstras Algorithm]]</td></tr>
−
** R Clustering
+
<tr class="s1"><td>[[Floyd Warshall Algorithm]]</td></tr>
−
** R Classification <!-- Phrasing inquiry as a classification problem, dealing with noisy data, machine learning approaches to classification, implementation in R) -->
+
</table>
−
** R hypothesis testing
 
−
** [[Bioconductor]]
 
  
−
;Applications
+
 
−
* [[Data integration]] <!-- Add BioMart: Biodata integration, and data-mining of complex, related, descriptive data -->
+
<table width="33%">
−
* Text mining <!-- (Use cases, tasks and metrics, taggers, vocabulary mapping, Practicals: R-support, Python/Perl support, others...) -->
+
<tr class="sh"><td>Communication and collaboration</td></tr>
−
* [[HMMER]]
+
<tr class="s1"><td>[[MediaWiki]]</td></tr>
−
* High-throughput sequencing
+
<tr class="s2"><td>[[HTML essentials]]</td></tr>
−
* Functional annotation <!-- GFF -->
+
<tr class="s1"><td>[[HTML 5]]</td></tr>
−
* 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) -->
+
<tr class="s2"><td>[[SADI|SADI Semantic Automated Discovery and Integration]]</td></tr>
 +
<tr class="s1"><td>[[CGI]]</td></tr>
 +
</table>
 +
 
 +
 
 +
<table width="33%">
 +
<tr class="sh"><td>Statistics
 +
<tr class="s1"><td>[[Pattern discovery]]</td></tr>
 +
<tr class="s1"><td>Correlation <!-- (Covariance matrices and their interpretation, application to large problems, collaborative filtering, MIC and MINE) --></td></tr>
 +
<tr class="s1"><td>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>Cluster metrics <!-- (Cluster quality metrics (Akaike, BIC)–when and how) --></td></tr>
 +
<tr class="s2"><td>[[Map equation|The Map Equation]] </td></tr>
 +
<tr class="s1"><td>Machine learning <!-- (Classification problems: Neural Networks, HMMs, SVM..) --></td></tr>
 +
<tr class="s2"><td>[[R]]</td></tr>
 +
<tr class="s1"><td>- R plotting</td></tr>
 +
<tr class="s2"><td>- [[R programming]]</td></tr>
 +
<tr class="s1"><td>- R EDA</td></tr>
 +
<tr class="s2"><td>- R regression</td></tr>
 +
<tr class="s1"><td>- R PCA</td></tr>
 +
<tr class="s2"><td>- R Clustering</td></tr>
 +
<tr class="s1"><td>- R Classification <!-- Phrasing inquiry as a classification problem, dealing with noisy data, machine learning approaches to classification, implementation in R) --></td></tr>
 +
<tr class="s2"><td>- R hypothesis testing</td></tr>
 +
<tr class="s1"><td>- [[Bioconductor]]</td></tr>
 +
</table>
 +
 
 +
 
 +
<table width="33%">
 +
<tr class="sh"><td>Applications</td></tr>
 +
<tr class="s1"><td>[[Data integration]] <!-- Add BioMart: Biodata integration, and data-mining of complex, related, descriptive data --></td></tr>
 +
<tr class="s2"><td>Text mining <!-- (Use cases, tasks and metrics, taggers, vocabulary mapping, Practicals: R-support, Python/Perl support, others...) --></td></tr>
 +
<tr class="s1"><td>[[HMMER]]</td></tr>
 +
<tr class="s2"><td>High-throughput sequencing</td></tr>
 +
<tr class="s1"><td>Functional annotation <!-- GFF --></td></tr>
 +
<tr class="s2"><td>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>
 +
</table>
  
 
</div>
 
</div>

Revision as of 18:23, 18 September 2012

[...]

Hardware
High performance computing
Cloud computing


Systems and Tools
Unix
Network Configuration
Apache
MySQL
Tools for the bioinformatics lab
GBrowse and LDAS


Programming
IDE (Integrated Development Environment)
Regular Expressions
Screenscraping
Perl
BioPerl
PHP
Relational database principles
BioPython
Graphical output
Autonomous agents


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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