Difference between revisions of "User:Boris/Temp/APB"
< User:Boris | Temp
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| Line 3: | Line 3: | ||
;Hardware | ;Hardware | ||
| − | * | + | * High performance computing <!-- (... at the bench: GPUs, FPGAs, Clusters) --> |
| − | * | + | * Cloud computing |
; Systems and Tools | ; Systems and Tools | ||
| Line 11: | Line 11: | ||
* [[Apache]] | * [[Apache]] | ||
* [[MySQL]] | * [[MySQL]] | ||
| − | * [[Tools for the bioinformatics lab]] | + | * [[Tools for the bioinformatics lab]] |
| − | * [[GBrowse]] | + | * [[GBrowse|GBrowse and LDAS]] |
;Programming | ;Programming | ||
| − | * [[IDE|IDE (Integrated Development Environment)]] | + | * [[IDE|IDE (Integrated Development Environment)]] |
* [[Regular Expressions]] | * [[Regular Expressions]] | ||
* [[Screenscraping]] | * [[Screenscraping]] | ||
| Line 22: | Line 22: | ||
* [[PHP]] | * [[PHP]] | ||
* [[Relational database principles]] | * [[Relational database principles]] | ||
| − | * | + | * BioPython <!-- (scope, highlights, installation, use, support) --> |
| − | * | + | * Graphical output <!-- (PNG and SVG) --> |
* [[Autonomous agents]] | * [[Autonomous agents]] | ||
:; Algorithms on Sequences | :; Algorithms on Sequences | ||
| − | ** [[Dynamic Programming]] | + | ** [[Dynamic Programming]] |
** [[Multiple Sequence Alignment]] | ** [[Multiple Sequence Alignment]] | ||
| − | ** [[Genome Assembly]] | + | ** [[Genome Assembly]] |
:; Algorithms on Structures | :; Algorithms on Structures | ||
** [[Docking]] | ** [[Docking]] | ||
| − | ** | + | ** Protein Structure Prediction <!-- ''ab initio'' --> |
:; Algorithms on Trees | :; Algorithms on Trees | ||
| − | ** | + | ** Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --> |
:; Algorithms on Networks | :; Algorithms on Networks | ||
| − | ** | + | ** Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) --> |
*** [[Dijkstras Algorithm]] | *** [[Dijkstras Algorithm]] | ||
*** [[Floyd Warshall Algorithm]] | *** [[Floyd Warshall Algorithm]] | ||
| Line 42: | Line 42: | ||
;Communication and collaboration | ;Communication and collaboration | ||
* [[MediaWiki]] | * [[MediaWiki]] | ||
| − | |||
* [[HTML essentials]] | * [[HTML essentials]] | ||
* [[HTML 5]] | * [[HTML 5]] | ||
* [[SADI|SADI Semantic Automated Discovery and Integration]] | * [[SADI|SADI Semantic Automated Discovery and Integration]] | ||
| − | * [[CGI]] | + | * [[CGI]] |
; Statistics | ; Statistics | ||
* [[Pattern discovery]] | * [[Pattern discovery]] | ||
| − | * | + | * Correlation <!-- (Covariance matrices and their interpretation, application to large problems, collaborative filtering, MIC and MINE) --> |
| − | * | + | * 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) --> |
| − | * | + | * Cluster metrics <!-- (Cluster quality metrics (Akaike, BIC)–when and how) --> |
| − | * [[Map equation|The Map Equation]] | + | * [[Map equation|The Map Equation]] |
| − | * | + | * Machine learning <!-- (Classification problems: Neural Networks, HMMs, SVM..) --> |
* [[R]] | * [[R]] | ||
| − | ** | + | ** R plotting |
| − | ** [[R programming]] | + | ** [[R programming]] |
| − | ** | + | ** R EDA |
| − | ** | + | ** R regression |
| − | ** | + | ** R PCA |
| − | ** | + | ** R Clustering |
| − | ** | + | ** R Classification <!-- Phrasing inquiry as a classification problem, dealing with noisy data, machine learning approaches to classification, implementation in R) --> |
| − | ** | + | ** R hypothesis testing |
| − | ** [[Bioconductor]] | + | ** [[Bioconductor]] |
;Applications | ;Applications | ||
| − | * [[Data integration]] | + | * [[Data integration]] <!-- Add BioMart: Biodata integration, and data-mining of complex, related, descriptive data --> |
| − | * | + | * Text mining <!-- (Use cases, tasks and metrics, taggers, vocabulary mapping, Practicals: R-support, Python/Perl support, others...) --> |
* [[HMMER]] | * [[HMMER]] | ||
| − | * | + | * High-throughput sequencing |
| − | * | + | * Functional annotation <!-- GFF --> |
| − | * | + | * 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) --> |
</div> | </div> | ||
Revision as of 17:46, 18 September 2012
- Hardware
- High performance computing
- Cloud computing
- Systems and Tools
- Programming
- IDE (Integrated Development Environment)
- Regular Expressions
- Screenscraping
- Perl
- BioPerl
- PHP
- Relational database principles
- BioPython
- Graphical output
- Autonomous agents
- Algorithms on Sequences
- Algorithms on Structures
- Docking
- Protein Structure Prediction
- Algorithms on Trees
- Computing with trees
- Algorithms on Networks
- Network metrics
- Communication and collaboration
- 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
