BioC Developers Workshop 2011

This workshop is for Bioconductor contributors and at people who wish to contribute packages to the Bioconductor programme.

The aim of the meeting is to foster the exchange of technical expertise, to keep contributors up to speed with the latest developments and to coordinate related efforts.

Topics

New developments in Bioconductor core packages and infrastructure
Next Generation Data handling and analysis
Tools and techniques for the management of proteomics datasets
Reproducible research and software engineering

Thursday 8th December
08.30 – 09.30	Registration
Session 1 Applications
09.40 – 09.50	Welcome and introduction
09.50 – 10.15	“DiffBind”	Rory Stark
10.15 – 10.40	“DEXSeq”	Simon Anders
10.40 – 11.00	“Annotating the genome with Bioc”	Crispin Miller
Session 2 Writing R packages
11.00 – 11.20	Coffee
11.20 – 12.00	“What’s in a package?” Basics of package structure What’s in a NAMESPACE S4 classes and methods Bioc software, data experiment and annotation packages	Martin Morgan
12.00 – 12.40	Flashlight session 1
12.40 – 14.00	Lunch
Session 3 Dealing with large data
14.00 – 15.40	"rhdf5 - Storing data in HDF5"	Bernd Fischer
	"Handling large datasets in R"	Benilton Carvalho
	"Representation and analysis with high volume data"	Vince Carey
	"Reproducible research in Bioconductor for the larger dataset"	Andy Lynch
15.40 – 16.00	Coffee
16.00 – 16.30	Session 3 continued.
16.30 – 17.00	Flashlight session 2

Friday 9th December
Session 4 Proteomics
09.00 – 11.00	“Quantitative labelled MS2 proteomics: from data structure to QC”	Laurent Gatto
	“Estimation of relative protein abundances in multiple iTraq experiments”	Ingo Ruczinski and Shelley Herbich
	“MetShot: High throughput acquisition and processing of tandem mass spectra”	Steffen Neumann
	“Utilisation of lock-mass data to improve raw data”	Paul Benton
	Future plans
11.00 – 11.20	Coffee
Session 5 Writing better R packages
11.20 – 12.00	“Better practices” Vignettes, examples and tests Bioc package guidelines Classes and methods for re-use Bioc release and devel branches Managing package development: subversion, git and friends
Session 6 New developments in core packages/R
12.00 – 12.40	Bioc: annotations and variants; paired and complicated reads R: parallel; 64 bit integers; yearly releases
12.40 – 14.00	Lunch
14.00 – 14.25	“Developments in edgeR & Repitools: count data, epigenomics and integrative analyses”	Mark Robinson
14.25 – 15.00	“Analysis of shotgun bisulphate sequencing of cancer samples”	Kasper Daniel Hansen
Session 7
15.00 – 15.40	Future Directions
15.40 – 16.00	Coffee
16.00 – 16.30	“Genetic Interactions: Computational methods for image- based genotyping and reverse genetics.”	Wolfgang Huber