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

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<div id="CSB">
+
<div id="APB">
  
−
[[User:Boris/CSB_Page_template]]
+
<table width="40%"><tr><td class="l1">&nbsp;</td><td>
  
 +
===Hardware===
 +
<table width="100%">
 +
<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><td class="sp">&nbsp;</td></tr>
 +
</table>
  
−
== Timetable and syllabus ==
+
===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>
  
−
<table>
+
<tr class="s2"><td class="l1">[[Network Configuration]]</td></tr>
 +
<tr class="s1"><td class="l1">[[Apache]]</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="s2"><td class="l1">[[GBrowse|GBrowse and LDAS]]</td></tr>
 +
<tr><td class="sp">&nbsp;</td></tr>
 +
</table>
  
−
<tr class="st">
+
===Programming===
−
<td colspan="5">'''I n t r o d u c t i o n'''</td>
+
<table width="100%" >
−
</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="s1"><td class="l1">[[Screenscraping]]</td></tr>
  
−
<tr class="sh">
+
<tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Perl]]
−
<td>'''Week'''</td>
+
<div class="mw-collapsible-content">
−
<td>'''Date'''</td>
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl basic programming]]</td></tr></table>
−
<td>'''Lecturer'''</td>
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl hash example]]</td></tr></table>
−
<td>'''Contents'''</td>
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl LWP example]]</td></tr></table>
−
<td>'''Activities'''</td>
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl MySQL introduction]]</td></tr></table>
−
</tr>
+
<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">
+
<tr class="s1"><td class="l1">[[BioPerl]]</td></tr>
−
<td>1</td>
+
<tr class="s2"><td class="l1">[[PHP]]</td></tr>
−
<td>Jan. 9 - 14</td>
+
<tr class="s1"><td class="l1">[[Data modelling]]</td></tr>
−
<td>Steipe</td>
+
<tr class="s2"><td class="l1">BioPython <!-- (scope, highlights, installation, use, support) --></td></tr>
−
<td>
+
<tr class="s1"><td class="l1">Graphical output <!-- (PNG and SVG) --></td></tr>
−
* [[CSB_Introduction|Introduction to Computational Systems Biology]]
+
<tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr>
−
* [[CSB_Web_tools|CSB on the Web: Databases and services]]
+
</table>
−
* Course Organisation
 
−
</td>
 
−
<td>&mdash;</td>
 
−
</tr>
 
  
−
<!-- ===================    TOPIC    ===================  -->
+
===Algorithms===
−
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
+
<table width="100%" >
−
<tr class="st">
+
<tr class="sh"><td class="l1">Algorithms on Sequences</td></tr>
−
<td colspan="5">'''F u n c t i o n a l &nbsp; A n n o t a t i o n'''</td>
+
<tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr>
−
</tr>
+
<tr class="s2"><td class="l2">[[Multiple Sequence Alignment]]</td></tr>
−
<tr class="sh">
+
<tr class="s1"><td class="l2">[[Genome Assembly]]</td></tr>
−
<td>'''Week'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Contents'''</td>
 
−
<td>'''Activities'''</td>
 
−
</tr>
 
−
<!-- ===================    /TOPIC  ===================  -->
 
  
−
<tr class="s1">
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td>2</td>
 
−
<td>Jan. 16 - 21</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* [[CSB_Databases|GO, OMIM and other phenotype databases]]
 
−
* [[Data_mining|Data mining]]
 
−
* [[Data_integration|Data integration: Loose coupling, combining datasets to improve annotation quality, evidence combination]]
 
−
* [[Function_prediction|Prediction of function]]
 
−
</td>
 
−
<td>Quiz 1</td>
 
−
</tr>
 
  
−
<!-- ===================    TOPIC    ===================  -->
+
<tr class="sh"><td class="l1">Algorithms on Structures</td></tr>
−
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
+
<tr class="s1"><td class="l2">[[Docking]]</td></tr>
−
<tr class="st">
+
<tr class="s2"><td class="l2">Protein Structure Prediction <!-- ''ab initio'' --></td></tr>
−
<td colspan="5">'''''"-omics"'''''</td>
 
−
</tr>
 
  
−
<tr class="sh">
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td>'''Week'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Contents'''</td>
 
−
<td>'''Activities'''</td>
 
−
</tr>
 
−
<!-- ===================    /TOPIC  ===================  -->
 
  
−
<tr class="s1">
+
<tr class="sh"><td class="l1">Algorithms on Trees</td></tr>
−
<td>3</td>
+
<tr class="s1"><td class="l2">Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --></td></tr>
−
<td>Jan. 23 - 28</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* Working with -ome scale data
 
−
** [[R_and_Bioconductor|R and Bioconductor]]
 
−
** [[Clustering|Clustering and partitioning]]
 
−
** [[Enrichment|Enrichment analysis]]
 
−
** [[Informal_programming|Informal programming with perl/php/MySQL/]]
 
−
** [[IDE|IDE - Komodo]], [http://en.wikipedia.org/wiki/KDevelop KDevelop] (also Eclipse, except no Perl)
 
−
</td>
 
−
<td>Quiz 2, project concept due</td>
 
−
</tr>
 
  
−
<tr class="s2">
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td>4</td>
 
−
<td>Jan. 30 - Feb. 3</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* [[Genomics|Genomics]]
 
−
* [[Transcriptome|The transcriptome]]
 
−
</td>
 
−
<td>Quiz 3</td>
 
−
</tr>
 
  
−
<tr class="s1">
+
<tr class="sh"><td class="l1">Algorithms on Networks</td></tr>
−
<td>5</td>
+
<tr class="s1"><td class="l2">Network metrics <!-- (Degree distributions, Centrality metrics, other metrics on topology, small-world- vs. random-geometric controversy) --></td></tr>
−
<td>Feb. 6 - 10</td>
+
<tr class="s2"><td class="l3">[[Dijkstras Algorithm]]</td></tr>
−
<td>Steipe</td>
+
<tr class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr>
−
<td>
+
</table>
−
*  [[Proteome|Proteome]]
 
−
*  [[Interactome|Interactome]]
 
−
*  [[Metabolome|Metabolome]]
 
−
*  [[Glycome|Glycome]]
 
−
*  [[Lipidome|Lipidome]]
 
−
</td>
 
−
<td>Quiz 4, project outline due</td>
 
−
</tr>
 
  
−
<!-- ===================    TOPIC    ===================  -->
 
−
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
 
−
<tr class="st">
 
−
<td colspan="5">'''I n t e r a c t i o n s , &nbsp;  P a t h w a y s &nbsp;  a n d &nbsp;  N e t w o r k s'''</td>
 
−
</tr>
 
  
−
<tr class="sh">
+
===Communication and collaboration===
−
<td>'''Week'''</td>
+
<table width="100%" >
−
<td>'''Date'''</td>
+
<tr class="s1"><td class="l1">[[MediaWiki]]</td></tr>
−
<td>'''Lecturer'''</td>
+
<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr>
−
<td>'''Contents'''</td>
+
<tr class="s1"><td class="l1">[[HTML 5]]</td></tr>
−
<td>'''Activities'''</td>
+
<tr class="s2"><td class="l1">[[SADI|SADI Semantic Automated Discovery and Integration]]</td></tr>
−
</tr>
+
<tr class="s1"><td class="l1">[[CGI]]</td></tr>
−
<!-- ===================    /TOPIC  ===================  -->
+
<tr><td class="sp">&nbsp;</td></tr>
 +
</table>
  
−
<tr class="s1">
+
===Statistics===
−
<td>6</td>
+
<table width="100%" >
−
<td>Feb. 13 - 17</td>
+
<tr class="s1"><td class="l1">[[Pattern discovery]]</td></tr>
−
<td>Steipe</td>
+
<tr class="s2"><td class="l1">Correlation <!-- (Covariance matrices and their interpretation, application to large problems, collaborative filtering, MIC and MINE) --></td></tr>
−
<td>
+
<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>
−
* [[Cytoscape|Cytoscape]]
+
<tr class="s2"><td class="l1">Cluster metrics <!-- (Cluster quality metrics (Akaike, BIC)–when and how) --></td></tr>
−
* [[Graph_theory|Graph theory]], graph types and metrics; small-world or random-geometric, date-hubs and party-hubs
+
<tr class="s1"><td class="l1">[[Map equation|The Map Equation]] </td></tr>
−
</td>
+
<tr class="s2"><td class="l1">Machine learning <!-- (Classification problems: Neural Networks, HMMs, SVM..) --></td></tr>
−
<td>Quiz 5</td>
 
−
</tr>
 
  
−
<tr class="s2">
+
<tr class="s1"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[R]]
−
<td>&nbsp;</td>
+
<div class="mw-collapsible-content">
−
<td>Feb. 20 - 24</td>
+
<table width="100%"><tr class="s2"><td class="l2">R plotting</td></tr></table>
−
<td colspan="3">''Reading Week - School closed''</td>
+
<table width="100%"><tr class="s1"><td class="l2">[[R programming]]</td></tr></table>
−
</tr>
+
<table width="100%"><tr class="s2"><td class="l2">R EDA</td></tr></table>
 +
<table width="100%"><tr class="s1"><td class="l2">R regression</td></tr></table>
 +
<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="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 class="s1">
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td>7</td>
+
</table>
−
<td>Feb. 27 - Mar. 2</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* [[PPI|The biology of protein-protein interactions]]; physical vs. genetic interactions
 
−
* [[Interaction_databases|Interaction databases]]
 
−
* [[Interaction_prediction|Interaction prediction]], Interologs
 
−
</td>
 
−
<td>Quiz 6</td>
 
−
</tr>
 
−
 
 
−
<!-- ===================    TOPIC    ===================  -->
 
−
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
 
−
<tr class="st">
 
−
<td colspan="5">'''S y s t e m s'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sh">
 
−
<td>'''Week'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Contents'''</td>
 
−
<td>'''Activities'''</td>
 
−
</tr>
 
−
<!-- ===================    /TOPIC  ===================  -->
 
−
 
 
−
<tr class="s1">
 
−
<td>8</td>
 
−
<td>Mar. 5 - 9</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* [[Gene_regulatory_networks|Gene regulatory networks]]
 
−
* [[Signal_transduction_networks|Signal transduction networks]]
 
−
* [[Metabolic_networks|Metabolic networks]]
 
−
* [[KEGG]], [[BioCYC]]
 
−
</td>
 
−
<td>Quiz 7</td>
 
−
</tr>
 
−
 
 
−
<tr class="s2">
 
−
<td>9</td>
 
−
<td>Mar. 12 - 16</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* [[CSB_Regulatory_network_extraction|Extracting regulatory networks from gene expression data]]
 
−
* [[CSB_Mutual information|Extracting systems from -omics datasets through mutual information]]
 
−
</td>
 
−
<td>Quiz 8</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>10</td>
 
−
<td>Mar. 19 - 23</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* [[CSB_Structural_network_analysis|Structural network analysis]] http://www.csb.ethz.ch/research/structural
 
−
* [[Systems dynamics|Systems dynamics]] http://www.csb.ethz.ch/research/dynamic
 
−
</td>
 
−
<td>Quiz 9, project final submission due</td>
 
−
</tr>
 
−
 
 
−
<!-- ===================    TOPIC    ===================  -->
 
−
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
 
−
<tr class="st">
 
−
<td colspan="5">'''M o d e l s'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sh">
 
−
<td>'''Week'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Contents'''</td>
 
−
<td>'''Activities'''</td>
 
−
</tr>
 
−
<!-- ===================    /TOPIC  ===================  -->
 
−
 
 
−
<tr class="s1">
 
−
<td>11</td>
 
−
<td>Mar. 26 - 30</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* [[CSB_modelling methods|Modelling methods]]:
 
−
** ODEs, PDEs and their stochastic counterparts
 
−
** Petri Nets
 
−
** Cellular Automata)
 
−
** process calculi (pi-calculus, )
 
−
* [[CSB_model_representations|Model representations]] (SBML, CellML)
 
−
* [[CSB_Modelling|Modelling examples]](E-Cell, M-Cell, Virtual Cell)
 
−
</td>
 
−
<td>&mdash;</td>
 
−
</tr>
 
−
 
 
−
<tr class="s2">
 
−
<td>12</td>
 
−
<td>Apr. 2 - 6</td>
 
−
<td>Steipe</td>
 
−
<td>
 
−
* [[Constraint based modelling]], [[Flux balance analysis]]
 
−
* [[Computational Synthetic Biology]] http://www.csb.ethz.ch/research/synthetic
 
−
</td>
 
−
<td>&mdash;</td>
 
−
</tr>
 
  
 +
===Applications===
 +
<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="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="s1"><td class="l1">[[HMMER]]</td></tr>
 +
<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><td class="sp">&nbsp;</td></tr>
 
</table>
 
</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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