Bioconductor Developer Meeting Europe - 17.-18. 11. 2010

Thanks to our sponsors: ENFIN, CancerPathways, Novartis Molecular Diagnostics, Mango Solutions.

Wed 17 Nov
9.00 Welcome & Introductions
   Wolfgang Huber

9.20 - 10.10 New developments in Bioconductor core packages and infrastructure 
   Martin Morgan
   Vince Carey

10.30 - 12.30 Visualisation
   Simon Urbanek: iPlots eXtreme - high-performance interactive graphics for analysis of large data in R
   Michael Lawrence: Qt & R
   Crispin Miller, Michael Okoniewski: xmap, GoogleMaps API
   Gregoire Pau: Exploration of high-throughput image-based assays with imageHTS
   Wolfgang Huber: interactive reports with DHTML, SVG, Javascript

12.30 - 14.00 Lunch

14.00 - 15.30 Flashlight talks (90 min) 
*Sequencing* (n=7)
Jonathan Cairns	          BayesPeak - Bayesian analysis of ChIP-seq data
Simon Anders              DESeq for Alternative Splicing
Michal Okoniewski	  New functions on alternative splicing
Misha Kapushesky          An RNA-Seq analysis pipeline
Anna Lesniewska		  RNAseq-related topic
Stefanie Tauber		  Analysis of a NGS time course experiment
Oscar Reina Garcia	  High-Throughput Sequencing data analysis with R and Bioconductor 	

16.00 - 16.20 Reference classes in R 
   Martin Morgan

16.20 - 17.30 Flashlight talks (70 min)
*Genotyping (n=2)*
Ingo Ruczinski	          Genotype and DNA copy number estimation (SNPchip, VanillaICE)	
David Clayton             New developments in snpMatrix

*Statistics (n=3)*
Robert Castelo	          Network inference with 'qpgraph': recent developments and future challenges
Jesper Ryge		  Circular statistics for eletrophysiology recordings
Maarten van Iterson	  SSPA - Pilot data based sensitivity analysis for high-dimensional data

17.30 - 18.00 Wrap Up, Discussion, Emerging topics

18.30 Bus leaves from EMBL (bus stop)
19.00 Bus arrives in downtown (Neckarmuenzplatz)

19.30 Workshop Dinner in Roter Ochsen, downtown Heidelberg, sponsored by Mango Solutions and 
      Novartis Molecular Diagnostics.

Thu 18 Nov
9.00 - 10.00 Reproducible Research in Practice
     Friedrich Leisch		
     Vince Carey        Experimental data packages
     Misha Kapushesky   R Cloud and R Wiki; 
                        Flashlight: ScalaR - a new implementation of R in scala

10.30 - 12.30 Proteomics and metabolomics
   Introduction (Laurent Gatto)
   Steffen Neumann: XCMS 
   Bernd Fischer: Label-free differential quantification for proteomics
   Laurent Gatto: MSnbase (including QC)
   Laurent Gatto: protein localisation with pRoloc
   Crispin Miller and Simon Perkins: ProtIO - data import from standard packages such as Mascot.
   Florian Breitwieser: MIAPE:MSI
   Yue Fan: DIGE gels with digeR by a graphical user interface R package for analyzing 2D-DIGE data

12.30 - 14.00 Lunch

14.00-17.00 Flashlight talks (180 min)
*Arrays (n=5)*
Mike Smith	          beadarray 2.0 - Improved flexibility in the processing  of raw data from Illumina BeadArrays
Fabrice Berger            affyILM - estimating gene expression levels for Affymetrix genechips with physical chemistry
Wolfgang Raffelsberger    GxTools - Automating transcriptome analysis
Julian Gehring	          Identifying Loci of Enhanced Significance in Tiling Microarray Data
Leonardo Collado-Torres	  Transcription initiation mapping and transcription unit identification in E. coli

*GSEA* (n=2)
Daniela Beisser	          BioNet - Routines for the functional analysis of biological networks
Xin Wang	          Gene set enrichment and network analysis of high-throughput RNAi screen data using HTSanalyzeR

*Imaging (n=1)*
Xian Zhang	          Phenotypic dissimilarity analysis for high-content screening

*Scalability and performance* (n=3)          
Martin Morgan             Parallelisation 
Bernd Fischer             Using netcdf
Michal Piotrowski         Parallelisation and SPRINT 

17.00 - 18.00 Loose Ends, Discussion