European Bioconductor Developers' Meeting 2016

Basel Switzerland, 6-7th December 2016


OVERVIEW

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: 

TOPICS

We aim to have a mix of scientific and technical presentations, with the themes of this year's meeting including: 

On twitter:  #EuroBioC2016

REGISTRATION

Registration seats are limited. Preference will be given to active developers (package maintainers and authors) who register before 4 November 2016. Subsequently, remaining seats will be allocated on a first-come first-serve basis.  

REGISTRATION IS NOW CLOSED - for questions please contact Robert Ivanek

PROGRAM

Download an archive of the presentations here .

Tuesday December 6, 2016

08:30 - 09:00 Registration
Session I, chairman: Florian Hahne
09:00 - 10:00 TALK Martin Morgan: "Package review process"
10:00 - 10:15 FLT1 Andrzej Oles: "Authoring R Markdown documents with BiocStyle"
10:15 - 10:30 FLT2 Jitao David Zhang: "ribios, a suite of R packages dedicated to high-performance and pipelineable bioinformatics analysis"
10:30 - 10:45 FLT3 Mike Smith: "BiocWorkflowTools package"
10:45 - 11:05 FLT4 Wolfgang Huber: "More powerful FDR control with data-driven hypothesis weighting"
11:05 - 11:30 Coffee break
Session II, chairman: Mark Robinson
11:30 - 11:45 FLT5 Federico Marini: "Development of Applications for Interactive and Reproducible Research: the pcaExplorer Case Study"
11:45 - 12:00 FLT6 Phil Cheng: "TCGA browser package"
12:15 - 12:30 FLT7 Nuno Agostinho: "Shiny application for the integrated analysis of alternative splicing from large transcriptomic datasets (TCGA)"
12:30 - 12:45 FLT8 Carles Hernandez-Ferrer: "rexposome: A Bioconductor package for characterizing multiple environmental factors and its association with different omics biomarkers and disease"
12:45 - 13:00 FLT9 Davis McCarthy: "scater: pre-processing, quality control, normalisation and visualisation for single-cell RNA-seq data"
13:00 - 14:00 Lunch
Session III, chairman: Charlotte Soneson
14:15 - 14:30 FLT10 Laurent Gatto: "MSnbase2 - disk access is the limit"  https://github.com/lgatto/EuroBioc2016-Basel-MSnbase2/
14:30 - 14:45 FLT11 Witold Wolski: "bibliospec: Reading Mass Spectrometric Search Results"
14:45 - 15:00 FLT12 Cancelled
15:00 - 16:00 KEYNOTE I Anne-Laure Boulesteix: "Towards evidence-based computational statistics: lessons from clinical research on the role and design of real-data benchmark studies"
The goal of medical research is to develop interventions that are in some sense superior, with respect to patient outcome, to interventions currently in use. Similarly, the goal of research in methodological computational statistics is to develop data analysis tools that are themselves superior to the existing tools. The methodology of the evaluation of medical interventions continues to be discussed extensively in the literature and it is now well accepted that medicine should be at least partly "evidence based". Although we statisticians are convinced of the importance of unbiased, well-thought-out study designs and evidence-based approaches in the context of clinical research, we tend to ignore these principles when designing our own studies for evaluating statistical methods in the context of our methodological research. In this talk, I draw an analogy between clinical trials and real-data-based benchmarking experiments in methodological statistical science, with datasets playing the role of patients and methods playing the role of medical interventions, as suggested in the technical report by Boulesteix, Wilson & Hapfelmeier (2016, https://epub.ub.uni-muenchen.de/29889/). Through this analogy, I discuss the concept of "evidence-based" statistical research, its limitations and its impact on the design and interpretation of real-data-based benchmark experiments as well as potential implications for Bioconductor development.
16:00 - 16:30 Coffee Break
Session IV, chairman: Michael Stadler
16:30 - 16:45 FLT13 Raffaele Calogero: "PAMR-SC: Subpopulation classification in single-cell sequencing"
16:45 - 17:00 FLT14 Helena Crowell: "CATALYST package (Cytometry dATa AnaLYSis Tools)"
17:00 - 18:00 KEYNOTE II Niko Beerenwinkel: "Modeling cancer evolution from genomic data"
Cancer progression is an evolutionary process characterized by the accumulation of mutations and responsible for tumor growth, clinical progression, and drug resistance development. Evolutionary theory can be used to describe the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular profiling data. We present recent approaches to modeling the evolution of cancer, including population genetics models of tumorigenesis, phylogenetic methods of intra-tumor subclonal diversity, and probabilistic graphical models of tumor progression, and we discuss their relevance for personalized medicine in general and for precision oncology in particular.
19:00 Dinner in Restaurant Löwenzorn

 

Wednesday December 7, 2016

Session V, chairman: Vincent Carey
09:00 - 09:15 FLT15 Andrea Komljenovic: "BgeeDB package"
09:15 - 09:30 FLT16 Julien Roux: "BgeeDB package"
09:30 - 09:45 FLT17 Michal Okoniewski: "Connecting to genomic data in Parquet using SparkR"
09:45 - 10:00 FLT18 Johannes Rainer: "Extending ensembldb: MySQL backend and protein annotations"
10:00 - 10:20 FLT19 Parham Solaimani: "Supporting Bioconductor packages in Renjin"
10:20 - 10:30 FLT20 Levi Waldron: "curatedMetagenomicData"
10:30 - 10:45 FLT21 Vince Carey: "Recent Developments in MultiAssayExperiment"
10:45 - 11:00 Discussion Session
11:00 - 11:30 Coffee Break
Session VI, chairman: Wolfgang Huber
11:30 - 13:00 Discussion Session
13:00 - 14:00 Lunch
14:00 - 15:30 Wrap up

 

SUPPORT/SPONSORSHIP
   

 

ACCOMMODATION

Participants are encouraged to make their own travel and accommodation arrangements.

Basel’s hotels offer accommodation for every taste and need. From traditional top-of-the-line hotels to youth hostels, from highly
modern design hotels to the family atmosphere of a bed & breakfast, you’ll find what you’re looking for. 

The hotels in Basel are centrally located. All attractions, museums, restaurants and bars, as well as diverse opportunities for shopping are therefore easy to reach on foot or by public transport. When checking in as a guest at a hotel in Basel, you will receive a Mobility Ticket which gives you free use of public transport during your stay. 

TripAdvisor Basel

LOCATION and TRAVEL INFORMATION

Department of Biomedicine (ZLF Building)
University of Basel
Hebelstrasse 20
CH-4053 Basel
Switzerland
map

Situated in Switzerland at the heart of Europe, Basel is one of the continent’s most convenient locations for major events.  Basel is easily accessible from many European cities by plane or high-speed trains. Approximate travel times to the meeting location (DBM, Hebelstrasse):

CONTACT INFORMATION

For questions, please contact Florian Hahne (florian.hahne'at'novartis.com) or Robert Ivanek (robert.ivanek'at'unibas.ch)