BioC 2011

European Developers' Workshop

Manchester UK, 8th - 9th December 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

The Manchester Museum

The University of Manchester
Oxford Road
Manchester
M13 9PL

 

Midland Hotel

+44161 236 3333‎

Peter Street
Manchester
M60 2DS

Approx 1.2 miles away

The Palace Hotel

+44161 288 1111

Oxford St
Manchester
M60 7HA

Approx 1 mile away

Holiday Inn Express

0843 208 3005

2 Oxford Rd
Manchester
M1 5QA

Approx 0.8 miles away
 
 

Novotel – Conference Hotel

+44161 235 2200

21 Dickinson Street
Manchester
M1 4LX

Approx 1.2 miles away

Ibis

+44161 234 0600‎

96 Portland St
Manchester
M1 4GX

Approx 1.5 miles away

Willowbank Hotel

+44161 224 0461

340 Wilmslow Road
Manchester
M14 6AF

Approx 2.5 miles away
 

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