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

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<div id="CSB">
+
<div id="APB">
  
−
== Timetable and syllabus ==
+
<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>
  
−
<table>
+
===Systems and Tools===
 +
<table width="100%">
  
−
<tr class="st">
+
<tr class="s1"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Unix]]
−
<td colspan="5">'''I n t r o d u c t i o n'''</td>
+
<div class="mw-collapsible-content">
−
</tr>
+
<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>
  
−
<tr class="sh">
+
<tr class="s2"><td class="l1">[[Network Configuration]]</td></tr>
−
<td class="sc">'''Week'''</td>
+
<tr class="s1"><td class="l1">[[Apache]]</td></tr>
−
<td class="sc">'''Date'''</td>
+
<tr class="s2"><td class="l1">[[MySQL]]</td></tr>
−
<td class="sc">'''Topics'''</td>
+
<tr class="s1"><td class="l1">[[Tools for the bioinformatics lab]]</td></tr>
−
<td class="sc">'''Activities'''</td>
+
<tr class="s2"><td class="l1">[[GBrowse|GBrowse and LDAS]]</td></tr>
−
<td class="sc">'''Assignment'''</td>
+
<tr><td class="sp">&nbsp;</td></tr>
−
</tr>
+
</table>
  
−
<tr class="s1">
+
===Programming===
−
<td class="sc">1</td>
+
<table width="100%" >
−
<td class="sc">Jan. 9 - 14</td>
+
<tr class="s1"><td class="l1">[[IDE|IDE (Integrated Development Environment)]]</td></tr>
−
<td class="sc">
+
<tr class="s2"><td class="l1">[[Regular Expressions]]</td></tr>
−
<div class="table-intro-text">Computational Biology aims to bring biology from its descriptive beginnings to a truly predictive science, based on consistent and well understood principles. In the systems biology field of computational biology, we deal primarily with large-scale, cross-sectional data, its relationships and hierarchies.</div>
+
<tr class="s1"><td class="l1">[[Screenscraping]]</td></tr>
−
* Course Organisation
 
−
* [[CSB_Introduction|Introduction to Computational Systems Biology]]
 
−
</td>
 
−
<td class="sc">&mdash;</td>
 
−
<td class="sc">[[CSB_Assignment_Week_1|Assignment&nbsp;1]]</td>
 
−
</tr>
 
  
−
<!-- ===================    THEME    ===================  -->
+
<tr class="s2"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[Perl]]
−
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
+
<div class="mw-collapsible-content">
−
<tr class="st">
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl basic programming]]</td></tr></table>
−
<td colspan="5">'''D a t a'''</td>
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl hash example]]</td></tr></table>
−
</tr>
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl LWP example]]</td></tr></table>
−
<tr class="sh">
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl MySQL introduction]]</td></tr></table>
−
<td class="sc">'''Week'''</td>
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl OBO parser]]</td></tr></table>
−
<td class="sc">'''Date'''</td>
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl basic programming]]</td></tr></table>
−
<td class="sc">'''Topics'''</td>
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl programming exercises 1]]</td></tr></table>
−
<td class="sc">'''Activities'''</td>
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl programming exercises 2]]</td></tr></table>
−
<td class="sc">'''Assignment'''</td>
+
<table width="100%"><tr class="s1"><td class="l2">[[Perl programming Data Structures]]</td></tr></table>
−
</tr>
+
<table width="100%"><tr class="s2"><td class="l2">[[Perl references]]</td></tr></table>
−
<!-- ===================    /THEME  ===================  -->
+
<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 class="sc">2</td>
+
<tr class="s2"><td class="l1">[[PHP]]</td></tr>
−
<td class="sc">Jan. 16 - 21</td>
+
<tr class="s1"><td class="l1">[[Data modelling]]</td></tr>
−
<td class="sc">
+
<tr class="s2"><td class="l1">BioPython <!-- (scope, highlights, installation, use, support) --></td></tr>
−
<div class="table-intro-text">In principle, most of the data of interest to us is freely available on the Web, in public repositories. However, the number of databases and associated Web services is large and in constant flux and integrating the data has its own issues. The most important issue is the question of how to define ''function'' and make this concept computable; from this arises the central role that ontologies play in the field.</div>
+
<tr class="s1"><td class="l1">Graphical output <!-- (PNG and SVG) --></td></tr>
−
* [[CSB_Web_tools|CSB on the Web: Databases and services]]
+
<tr class="s2"><td class="l1">[[Autonomous agents]]</td></tr>
−
* [[Data_integration|Data integration]]
+
</table>
−
* [[CSB_Ontologies|GO, OMIM and other phenotype databases]]
 
−
* [[Function_prediction|Prediction of function]]
 
−
</td>
 
−
<td class="sc">Quiz 1</td>
 
−
<td class="sc">[[CSB_Assignment_Week_2|Assignment&nbsp;2]]</td>
 
−
</tr>
 
  
−
<tr class="s1">
+
===Algorithms===
−
<td class="sc">3</td>
+
<table width="100%" >
−
<td class="sc">Jan. 23 - 28</td>
+
<tr class="sh"><td class="l1">Algorithms on Sequences</td></tr>
−
<td class="sc">
+
<tr class="s1"><td class="l2">[[Dynamic Programming]]</td></tr>
−
<div class="table-intro-text">The large volume of data in any given systems biology experiment basically precludes the manual, gene-by-gene analysis of results. Questions arise regarding computational strategies for ''gene lists'', especially the statistical tools and strategies we have at our disposal, and a minimum set of programming and automation skills.</div>
+
<tr class="s2"><td class="l2">[[Multiple Sequence Alignment]]</td></tr>
−
* Lists of genes - a common outcome of high-throughput experiments
+
<tr class="s1"><td class="l2">[[Genome Assembly]]</td></tr>
−
** [[CSB Gene lists|Gene lists]]
 
−
** [[Enrichment|Enrichment analysis]]
 
−
** [[GSEA|The GSEA approach]]
 
−
* Statistics
 
−
** [[Statistics|Principles of Statistics in molecular biology]]
 
−
** [[R]]
 
−
** [[Bioconductor]]
 
−
** [[Clustering|Clustering and Classification]]
 
−
** [[EDA|Exploratory Data Analysis]]
 
−
** [[Data_mining|Data mining]]
 
−
* Programming
 
−
** [[Informal_programming|Informal programming]]
 
−
** [[IDE|Using an IDE (Integrated Development Environments)]]
 
−
</td>
 
−
<td class="sc">Quiz 2, project concept due</td>
 
−
<td class="sc">[[CSB_Assignment_Week_3|Assignment&nbsp;3]]</td>
 
−
</tr>
 
  
 +
<tr><td class="sp">&nbsp;</td></tr>
  
−
<!-- ===================    THEME    ===================  -->
+
<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 class="sc">'''Week'''</td>
 
−
<td class="sc">'''Date'''</td>
 
−
<td class="sc">'''Topics'''</td>
 
−
<td class="sc">'''Activities'''</td>
 
−
<td class="sc">'''Assignment'''</td>
 
−
</tr>
 
−
<!-- ===================    /THEME  ===================  -->
 
  
−
<tr class="s2">
+
<tr class="sh"><td class="l1">Algorithms on Trees</td></tr>
−
<td class="sc">4</td>
+
<tr class="s1"><td class="l2">Computing with trees <!-- Bayesian approaches for phylogenetic trees, tree comparison) --></td></tr>
−
<td class="sc">Jan. 30 - Feb. 3</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text">Genome sequencing brought the first complete overview of the information underlying life; the associated concept of the ''transcriptome'' - a description of which portion of the genome is expressed at what time - is the most basic ''functional'' description of this information.</div>
 
−
* [[Genomics|Genome]]
 
−
* [[Transcriptome|Transcriptome]]
 
−
</td>
 
−
<td class="sc">Quiz 3</td>
 
−
<td class="sc">[[CSB_Assignment_Week_4|Assignment&nbsp;4]]</td>
 
−
</tr>
 
  
−
<tr class="s1">
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td class="sc">5</td>
 
−
<td class="sc">Feb. 6 - 10</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text">Many more holistic, or cross-sectional descriptions of the molecular composition and assembly of the cell are being worked on.</div>
 
−
*  [[Proteome|Proteome]]
 
−
*  [[Metabolome|Metabolome]]
 
−
*  [[Glycome|Glycome]]
 
−
*  [[Lipidome|Lipidome]]
 
−
</td>
 
−
<td class="sc">Quiz 4, project outline due</td>
 
−
<td class="sc">[[CSB_Assignment_Week_5|Assignment&nbsp;5]]</td>
 
−
</tr>
 
  
−
<!-- ===================    THEME    ===================  -->
+
<tr class="sh"><td class="l1">Algorithms on Networks</td></tr>
−
<tr><td colspan="5" class="sp">&nbsp;</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="st">
+
<tr class="s2"><td class="l3">[[Dijkstras Algorithm]]</td></tr>
−
<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 class="s1"><td class="l3">[[Floyd Warshall Algorithm]]</td></tr>
−
</tr>
+
</table>
  
−
<tr class="sh">
 
−
<td class="sc">'''Week'''</td>
 
−
<td class="sc">'''Date'''</td>
 
−
<td class="sc">'''Theme'''</td>
 
−
<td class="sc">'''Activities'''</td>
 
−
<td class="sc">'''Assignment'''</td>
 
−
</tr>
 
−
<!-- ===================    /THEME  ===================  -->
 
  
−
<tr class="s1">
+
===Communication and collaboration===
−
<td class="sc">6</td>
+
<table width="100%" >
−
<td class="sc">Feb. 13 - 17</td>
+
<tr class="s1"><td class="l1">[[MediaWiki]]</td></tr>
−
<td class="sc">
+
<tr class="s2"><td class="l1">[[HTML essentials]]</td></tr>
−
<div class="table-intro-text">Fundamentally, ''-omics'' descriptions provide us with lists of components. However, to understand how things work, we need to address the ''relationships'' of the components - how things are put together: the molecular blueprints. At its most basic level, this is the question of molecular interactions in the cell.  A quantitative description of molecular interactions relies heavily on the mathematical discipline of ''graph theory''. ''Cytoscape'' is a visualization and analysis platform for molecular interactions. </div>
+
<tr class="s1"><td class="l1">[[HTML 5]]</td></tr>
−
* [[Graph_theory|Graph theory]]
+
<tr class="s2"><td class="l1">[[SADI|SADI Semantic Automated Discovery and Integration]]</td></tr>
−
* [[Cytoscape|Cytoscape]]
+
<tr class="s1"><td class="l1">[[CGI]]</td></tr>
−
</td>
+
<tr><td class="sp">&nbsp;</td></tr>
−
<td class="sc">Quiz 5</td>
+
</table>
−
<td class="sc">[[CSB_Assignment_Week_6|Assignment&nbsp;6]]</td>
 
−
</tr>
 
  
−
<tr class="s2">
+
===Statistics===
−
<td class="sc">&nbsp;</td>
+
<table width="100%" >
−
<td class="sc">Feb. 20 - 24</td>
+
<tr class="s1"><td class="l1">[[Pattern discovery]]</td></tr>
−
<td colspan="3">''Reading Week - School closed''</td>
+
<tr class="s2"><td class="l1">Correlation <!-- (Covariance matrices and their interpretation, application to large problems, collaborative filtering, MIC and MINE) --></td></tr>
−
</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="s2"><td class="l1">Cluster metrics <!-- (Cluster quality metrics (Akaike, BIC)–when and how) --></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="s1">
+
<tr class="s1"><td class="l1 mw-collapsible mw-collapsed" data-expandtext="Expand subtopics" data-collapsetext="Collapse">[[R]]
−
<td class="sc">7</td>
+
<div class="mw-collapsible-content">
−
<td class="sc">Feb. 27 - Mar. 2</td>
+
<table width="100%"><tr class="s2"><td class="l2">R plotting</td></tr></table>
−
<td class="sc">
+
<table width="100%"><tr class="s1"><td class="l2">[[R programming]]</td></tr></table>
−
<div class="table-intro-text">Here we focus on the biological objects of "Interaction Science".</div>
+
<table width="100%"><tr class="s2"><td class="l2">R EDA</td></tr></table>
−
* [[Interactome|The Interactome]]
+
<table width="100%"><tr class="s1"><td class="l2">R regression</td></tr></table>
−
* [[Interaction_databases|Interaction databases]]
+
<table width="100%"><tr class="s2"><td class="l2">R PCA</td></tr></table>
−
* [[Pathways_and_Networks|Pathways and Networks]]
+
<table width="100%"><tr class="s1"><td class="l2">R Clustering</td></tr></table>
−
* [[Interaction_prediction|Interaction prediction]]
+
<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>
−
</td>
+
<table width="100%"><tr class="s1"><td class="l2">R hypothesis testing</td></tr></table>
−
<td class="sc">Quiz 6</td>
+
<table width="100%"><tr class="s2"><td class="l2">[[Bioconductor]]</td></tr></table>
−
<td class="sc">[[CSB_Assignment_Week_7|Assignment&nbsp;7]]</td>
+
</div>
−
</tr>
+
</td></tr>
  
−
<!-- ===================    THEME    ===================  -->
+
<tr><td class="sp">&nbsp;</td></tr>
−
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
+
</table>
−
<tr class="st">
 
−
<td colspan="5">'''S y s t e m s'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sh">
 
−
<td class="sc">'''Week'''</td>
 
−
<td class="sc">'''Date'''</td>
 
−
<td class="sc">'''Topics'''</td>
 
−
<td class="sc">'''Activities'''</td>
 
−
<td class="sc">'''Assignment'''</td>
 
−
</tr>
 
−
<!-- ===================    /THEME  ===================  -->
 
−
 
 
−
<tr class="s1">
 
−
<td class="sc">8</td>
 
−
<td class="sc">Mar. 5 - 9</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text">Several key networked systems exist in the cell. Here we discuss their paradigms, how they are constructed from experimental data and examples of how they can be organized in databases.</div>
 
−
* [[Gene_regulatory_networks|Gene regulatory networks]]
 
−
* [[Metabolic_networks|Metabolic networks]]
 
−
* [[Signal_transduction_networks|Signal transduction networks]]
 
−
* [[Developmental_networks|Developmental networks]]
 
−
* Pathway and network databases
 
−
** [[KEGG]]
 
−
** [[BioCYC]]
 
−
</td>
 
−
<td class="sc">Quiz 7</td>
 
−
<td class="sc">[[CSB_Assignment_Week_8|Assignment&nbsp;8]]</td>
 
−
</tr>
 
−
 
 
−
<tr class="s2">
 
−
<td class="sc">9</td>
 
−
<td class="sc">Mar. 12 - 16</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text">Information theory has proven to be one of the cornerstones of biological analysis. A good example of its power and utility is the definition of systems in large-scale biological datasets.</div>
 
−
* [[CSB_Mutual information|Extracting systems from ''-omics'' datasets through mutual information]]
 
−
</td>
 
−
<td class="sc">Quiz 8</td>
 
−
<td class="sc">[[CSB_Assignment_Week_9|Assignment&nbsp;9]]</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td class="sc">10</td>
 
−
<td class="sc">Mar. 19 - 23</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text">Life is not static, only death is. Yet, the dynamic nature of biological systems is often overlooked.</div>
 
−
* [[Systems dynamics|Systems dynamics]]
 
−
</td>
 
−
<td class="sc">Quiz 9, project final submission due</td>
 
−
<td class="sc">[[CSB_Assignment_Week_10|Assignment&nbsp;10]]</td>
 
−
</tr>
 
−
 
 
−
<!-- ===================    THEME    ===================  -->
 
−
<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 class="sc">'''Week'''</td>
 
−
<td class="sc">'''Date'''</td>
 
−
<td class="sc">'''Theme'''</td>
 
−
<td class="sc">'''Activities'''</td>
 
−
<td class="sc">'''Assignment'''</td>
 
−
</tr>
 
−
<!-- ===================    /THEME  ===================  -->
 
−
 
 
−
<tr class="s1">
 
−
<td class="sc">11</td>
 
−
<td class="sc">Mar. 26 - 30</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text">The notion that computational biology will at some time become predictive is tied to the idea that we will be able to model the cell's systems. Many approaches exist, each with its own strengths and weaknesses; how to integrate such models - preferrably across multiple scales -  is a question of its own.</div>
 
−
* [[CSB_modelling_principles|Modelling principles]]
 
−
* [[CSB_modelling_methods|Modelling methods]]
 
−
* [[CSB_model_representations|Model representations]]
 
−
* [[CSB_modelling_examples|Modelling examples]]
 
−
</td>
 
−
<td class="sc">&mdash;</td>
 
−
<td class="sc">[[CSB_Assignment_Week_11|Assignment&nbsp;11]]</td>
 
−
</tr>
 
−
 
 
−
<tr class="s2">
 
−
<td class="sc">12</td>
 
−
<td class="sc">Apr. 2 - 6</td>
 
−
<td class="sc">
 
−
<div class="table-intro-text">Do we really ''understand'' systems biology? Computational Synthetic Biology is the ultimate test.</div>
 
−
* [[Computational Synthetic Biology]]
 
−
</td>
 
−
<td class="sc">&mdash;</td>
 
−
<td class="sc">[[CSB_Assignment_Week_12|Assignment&nbsp;12]]</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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