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

From "A B C"
Jump to navigation Jump to search
m
m
Line 4: Line 4:
 
[...]
 
[...]
 
===Hardware===
 
===Hardware===
−
<table width="33%" align="center">
+
<table width="90%" align="left">
 
<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>
Line 11: Line 11:
  
 
===Systems and Tools===
 
===Systems and Tools===
−
<table width="33%">
+
<table width="90%" align="left">
 
<tr class="s1"><td class="l1">[[Unix]]</td></tr>
 
<tr class="s1"><td class="l1">[[Unix]]</td></tr>
−
<tr class="s2"><td class="l2">[[Network Configuration]]</td></tr>
+
<tr class="s2"><td class="l1">[[Network Configuration]]</td></tr>
−
<tr class="s1"><td class="l3">[[Apache]]</td></tr>
+
<tr class="s1"><td class="l1">[[Apache]]</td></tr>
−
<tr class="s2"><td class="l4">[[MySQL]]</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="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>
Line 21: Line 21:
  
  
−
<table width="33%">
+
===Programming===
−
<tr class="sh"><td>Programming</td></tr>
+
<table width="90%" align="left">
−
<tr class="s1"><td>[[IDE|IDE (Integrated Development Environment)]]</td></tr>
+
<tr class="s1"><td class="l1">[[IDE|IDE (Integrated Development Environment)]]</td></tr>
−
<tr class="s2"><td>[[Regular Expressions]]</td></tr>
+
<tr class="s2"><td class="l1">[[Regular Expressions]]</td></tr>
−
<tr class="s1"><td>[[Screenscraping]]</td></tr>
+
<tr class="s1"><td class="l1">[[Screenscraping]]</td></tr>
−
<tr class="s2"><td>[[Perl]]</td></tr>
+
<tr class="s2"><td class="l1">[[Perl]]</td></tr>
−
<tr class="s1"><td>[[BioPerl]]</td></tr>
+
<tr class="s1"><td class="l1">[[BioPerl]]</td></tr>
−
<tr class="s2"><td>[[PHP]]</td></tr>
+
<tr class="s2"><td class="l1">[[PHP]]</td></tr>
−
<tr class="s1"><td>[[Relational database principles]]</td></tr>
+
<tr class="s1"><td class="l1">[[Relational database principles]]</td></tr>
−
<tr class="s2"><td>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>Graphical output <!-- (PNG and SVG) --></td></tr>
+
<tr class="s1"><td class="l1">Graphical output <!-- (PNG and SVG) --></td></tr>
−
<tr class="s2"><td>[[Autonomous agents]]</td></tr>
+
<tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr>
 
</table>
 
</table>
  
  
−
<table width="33%">
+
===Algorithms===
−
<tr class="sh"><td>Algorithms on Sequences</td></tr>
+
<table width="90%" align="left">
−
<tr class="s1"><td>[[Dynamic Programming]]</td></tr>
+
<tr class="sh"><td class="l1">Algorithms on Sequences</td></tr>
−
<tr class="s2"><td>[[Multiple Sequence Alignment]]</td></tr>
+
<tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr>
−
<tr class="s1"><td>[[Genome Assembly]]</td></tr>
+
<tr class="s2"><td class="l2">[[Multiple Sequence Alignment]]</td></tr>
−
<tr class="sh"><td>Algorithms on Structures</td></tr>
+
<tr class="s1"><td class="l2">[[Genome Assembly]]</td></tr>
−
<tr class="s1"><td>[[Docking]]</td></tr>
+
 
−
<tr class="s2"><td>Protein Structure Prediction <!-- ''ab initio'' --></td></tr>
+
<tr><td class="sp">&nbsp;</td></tr>
−
<tr class="sh"><td>Algorithms on Trees</td></tr>
+
 
−
<tr class="s1"><td>Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --></td></tr>
+
<tr class="sh"><td class="l1">Algorithms on Structures</td></tr>
−
<tr class="sh"><td>Algorithms on Networks</td></tr>
+
<tr class="s1"><td class="l2">[[Docking]]</td></tr>
−
<tr class="s1"><td>Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) --></td></tr>
+
<tr class="s2"><td class="l2">Protein Structure Prediction <!-- ''ab initio'' --></td></tr>
−
<tr class="s2"><td>[[Dijkstras Algorithm]]</td></tr>
+
 
−
<tr class="s1"><td>[[Floyd Warshall Algorithm]]</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>
 
</table>
  
  
−
<table width="33%">
+
===Communication and collaboration===
−
<tr class="sh"><td>Communication and collaboration</td></tr>
+
<table width="90%" align="left">
−
<tr class="s1"><td>[[MediaWiki]]</td></tr>
+
<tr class="s1"><td class="l1">[[MediaWiki]]</td></tr>
−
<tr class="s2"><td>[[HTML essentials]]</td></tr>
+
<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr>
−
<tr class="s1"><td>[[HTML 5]]</td></tr>
+
<tr class="s1"><td class="l1">[[HTML 5]]</td></tr>
−
<tr class="s2"><td>[[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>[[CGI]]</td></tr>
+
<tr class="s1"><td class="l1">[[CGI]]</td></tr>
 
</table>
 
</table>
  
  
−
<table width="33%">
+
===Statistics===
−
<tr class="sh"><td>Statistics
+
<table width="90%" align="left">
−
<tr class="s1"><td>[[Pattern discovery]]</td></tr>
+
<tr class="s1"><td class="l1">[[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="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>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="s1"><td>Cluster metrics <!-- (Cluster quality metrics (Akaike, BIC)–when and how) --></td></tr>
+
<tr class="s2"><td class="l1">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 class="l1">[[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 class="l1">Machine learning <!-- (Classification problems: Neural Networks, HMMs, SVM..) --></td></tr>
−
<tr class="s2"><td>[[R]]</td></tr>
+
<tr class="s1"><td class="l1">[[R]]</td></tr>
−
<tr class="s1"><td>- R plotting</td></tr>
+
<tr class="s2"><td class="l2">R plotting</td></tr>
−
<tr class="s2"><td>- [[R programming]]</td></tr>
+
<tr class="s1"><td class="l2">[[R programming]]</td></tr>
−
<tr class="s1"><td>- R EDA</td></tr>
+
<tr class="s2"><td class="l2">R EDA</td></tr>
−
<tr class="s2"><td>- R regression</td></tr>
+
<tr class="s1"><td class="l2">R regression</td></tr>
−
<tr class="s1"><td>- R PCA</td></tr>
+
<tr class="s2"><td class="l2">R PCA</td></tr>
−
<tr class="s2"><td>- R Clustering</td></tr>
+
<tr class="s1"><td class="l2">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 class="l2">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 class="l2">R hypothesis testing</td></tr>
−
<tr class="s1"><td>- [[Bioconductor]]</td></tr>
+
<tr class="s2"><td class="l2">[[Bioconductor]]</td></tr>
 
</table>
 
</table>
  
−
 
+
===Applications===
−
<table width="33%">
+
<table width="90%" align="left">
−
<tr class="sh"><td>Applications</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="s1"><td>[[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>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>[[HMMER]]</td></tr>
+
<tr class="s2"><td class="l1">High-throughput sequencing</td></tr>
−
<tr class="s2"><td>High-throughput sequencing</td></tr>
+
<tr class="s1"><td class="l1">Functional annotation <!-- GFF --></td></tr>
−
<tr class="s1"><td>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>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>
 
</table>
 
</td></tr></table>
 
</td></tr></table>
  
 
</div>
 
</div>

Revision as of 03:15, 19 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

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
Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=User:Boris/Temp/APB&oldid=5587"