European Bioconductor Developers' Meeting
12th-13th January 2015, Heidelberg
This is an archive website for a past meeting. For the upcoming meeting in December 2015 see here.
The meeting is aimed at bioinformaticians, programmers and software engineers who contribute to the Bioconductor project, or are interested in developing packages for Bioconductor. The goals are to:
- foster the exchange of technical expertise,
- keep contributors up to date with the latest developments,
- coordinate any related efforts.
Sponsored by RADIANT
We aim to have a mixture of scientific and technical presentations, with the themes of this year's meeting including:
- single cell genomics and transcriptomics
- causal inference and multi-type data
- personal genomes
- Tools and Infrastructure
- news from the Bioc core, Bioconductor 3.0
- the package review process
- the MultiAssays infrastructure for multi-omics experiments
- new developments in online vignettes
- Topics contributed by Participants
European Molecular Biology Laboratory
ATC building room "Courtyard A+B"
The meeting will start 12:00 on Monday 12th January with a buffet lunch, and end around 17:00 on Tuesday 13th January. There will be a group dinner on Monday evening. For a detailed schedule see below.
The registration for the meeting is now closed!
To be put on a waiting list (in case someone drops out) please follow the instructions below.
Please confirm your attendance by email to aoles at embl.de with the subject "Registration for the European Bioconductor Developers' Meeting". In the body of your mail please specify your full name and affiliation. Additionally, please provide briefly a description of your interest in the Bioconductor project (e.g. name existing packages you maintain or develop, planned contributions, or other types if interest). Also, please state if you are interested in presenting something; talks/posters will be selected dependent on availability of time slots and session topics.
If you have any specific dietary requirements, please include them in your registration email.
Registration places are limited. Preference will be given to active developers (package maintainers and authors) who register before 30 November 2014. Subsequently, remaining places will be allocated on a first-come first-serve basis.
Monday, 12th January
- 11:45 Registration – ATC building room "Courtyard A+B"
- 12:00 Buffet lunch
- 13:00 Session I, chair: Wolfgang Huber
- 13:00 Martin Morgan – Bioconductor: Status and Recent Developments (30 min)
- 13:30 Levi Waldron – Integrative analysis of multiple genomic assays (30 min)
- 14:00 Peter Hickey – Genomic tuples and DNA methylation patterns (15 min)
- 14:15 Alexander Bertram – Exploiting many-core architectures with R on Renjin (15 min)
- 14:30 Coffee break
- 15:00 Session II, chair: Martin Morgan
- 15:00 Benedikt Brors – Tertiary analysis of cancer genome sequencing data (30 min)
- 15:30 Moritz Gerstung – Prognostic stratification of AML using random effects models (30 min)
- 16:00 Helen Lindsay – crispRvariants: a toolkit for studying targeted mutations (15 min)
- 16:15 Julian Gehring – Dynamic and reproducible reports (15 min)
- 16:30 Coffee break
- 17:00 Discussion: Future directions and needs for Bioconductor
- 19:30 Dinner Downtown
Tuesday, 13th January
- 9:00 Session III, chair: Rory Stark
- 9:00 Julien Gagneur – A statistical model for signal detection and bias correction in ChIP-Seq dat (30 min)
- 9:30 Antti Honkela – Fast and accurate approximate inference of transcript expression from RNA-seq data with BitSeq (15 min)
- 9:45 Małgorzata Oleś – Multi-omics with Bioconductor: genomics of drug sensitivity in blood cancer (15 min)
- 10:00 Davide Risso – Removing unwanted variation from RNA-seq data (15 min)
- 10:15 Coffee break
- 10:45 Session IV, chair: Vincent Carey
- 10:45 Laurent Gatto – Combining experimental and annotation data to predict protein sub-cellular localisation (30 min)
- 11:15 Bernd Fischer – RBDmap: Detection and prediction of RNA-binding sites on proteins using mass spectrometry and Bioconductor (30 min)
- 11:45 Christian Panse – specL: Prepare peptide spectrum matches for use in targeted proteomics (15 min)
- 12:00 Lunch
- 13:00 Session V, chair: Levi Waldron
- 13:00 Vincent J. Carey – Statistical modeling with large collections of variants (30 min)
- 13:30 Andrzej Oleś – Image processing and analysis using EBImage and RBioFormats (15 min)
- 13:45 Federico Marini – Cell tracking in intravital fluorescence microscopy with the flowcatchR package (15 min)
- 14:00 Thomas Siegmund An interactive platform for multivariate transcriptomics (15 min)
- 14:15 Maarten van Iterson – MethylAid: Visual and interactive quality control of large Illumina 450k data sets (15 min)
- 14:30 Coffee break
- 15:00 Session VI, chair: Laurent Gatto
- 15:00 Rory Stark – Checking gene expression signatures against random and known signatures with SigCheck (15 min)
- 15:15 Fabian Schmich – Deconvoluting off-target confounded RNA interference screens with the gespeR package (15 min)
- 15:30 Ludwig Geistlinger – Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis (15 min)
- 15:45 Matteo Carrara – Chimera: a Bioconductor package for secondary analysis of fusion products (15 min)
- 16:00 Discussion
- 16:30 Coffee break
- 17:00 GenomicRanges Workshop
Participants are encouraged to make their own travel and accommodation arrangements.
In addition, the top choices at TripAdvisor are all recommendable. However, Kurpfalzhof and Hotel Heidelberg are far out of town and are not recommended unless you're driving.
For those arriving by train, it is recommended that you go to Heidelberg Hauptbahnhof and take a taxi to EMBL (~15 Euro) as public transport for this journey is slow and cumbersome.
As well as the information below, the EMBL website provides comprehensive information on traveling to EMBL.
Either take the train or the Lufthansa Shuttle that goes to the Crowne Plaza hotel. From there, either take a taxi or bus 39 to EMBL.
From Stuttgart, train is feasible (usually with two changes, in Stuttgart Central and in Mannheim).
Baden-Baden and Hahn
For Baden-Baden and Hahn, there are shuttle buses.
For questions, please contact firstname.lastname@example.org .