Munich
 
The 2018 edition of the European Bioconductor Meeting will be hosted at the Technical University of Munich, Germany, on 6-7 December 2018.
Where: TUM-IAS Building, Lichtenbergstrasse 2a, Garching
When: 6 - 7 December 2018
Conference booklet
On twitter: #EuroBioc2018
 
Introduction:
The meeting is aimed at biologists, bioinformaticians, statisticians, programmers and software engineers who use or contribute to the Bioconductor project, or are interested in using Bioconductor. The goals are to:
foster the exchange of technical expertise
keep contributors up to speed with the latest developments coordinate any related efforts.
The main conference will be on Thursday 6 and Friday 7 December 2018. The day before, attendees are welcome to join the STRATOS topic group 9 “high-dimensional data” for a keynote talk by Lisa Meier McShane.
 
Key dates:
Oct 17: Abstract deadline
Oct 29: Notice of acceptance
Nov 21: Registration deadline
Dec 5 (evening): STRATOS meeting
Dec 6-7: European Bioconductor Meeting
 
Confirmed invited speakers:
Keegan Korthauer, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health
Fanny Perraudeau, Whole Biome, San Francisco
Bernd Bischl, LMU, Munich
 
Preliminary schedule:
Joint meeting with the STRATOS topic group 9 “high-dimensional data”

Wed 5 Dec
Schellingstr. 3 (Munich centre, near Geschwister-Scholl-Platz), lecture hall S005
17:00 - 18:00
Lisa Meier McShane Reproducibility of omics research: shared responsibilities and consequences of ignorance
18:00 - 19:00
Introduction to the STRATOS initiative
19:00 -
Informal get-together in some brewery
EuroBioc 2018
 
Thu 6 Dec
TUM-IAS Building, Lichtenbergstrasse 2a, Garching
09:00 - 09:15
Registration
09:15 - 09:30
Welcome and introduction
09:30 - 10:00
Bernd Bischl mlr3: Towards an object-oriented, configurable ML pipeline system in R6
10:00 - 10:30
Session I
10:00 - 10:15
Lukas Weber: HDCytoData package: High-dimensional cytometry benchmark datasets in Bioconductor formats
10:15 - 10:30
Elena Landoni: Normalization and batch correction effects on class comparison analysis with high throughput data: a simulation study
10:30 - 11:00
Coffee break
11:00 - 12:15
Session II - Visualization
11:00 - 11:15
Nemanja Vucic: Using R/Shiny implementation of Bioconductor packages on the Cancer Genomic Cloud platform
11:15 - 11:30
Federico Marini: iSEE: data exploration made easy & reproducible
11:30 - 11:45
Svetlana Ovchinnikova / Simon Anders: R/LinkedCharts: A novel approach for simple but powerful interactive data analysis
11:45 - 12:00
Laurent Gatto / Lisa Breckels: Interactive visualisation of spatial proteomics data
12:00 - 12:15
Phil Cheng: TCGA Browser
12:15 - 13:30
Lunch
13:30 - 14:00
Martin Morgan Update from the Bioconductor core team
14:00 - 15:00
Session III - Epigenomics
14:00 - 14:15
Shijie Zheng: Identification of differentially methylated cell-types in Epigenome-Wide Association Studies
14:15 - 14:30
Jonas Ibn-Salem: sevenC: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
14:30 - 14:45
Markus List: Analysing large-scale epigenomic data with DeepBlue
14:45 - 15:00
Yadollah Shahryary Dizaji: MethylStar: An efficient and flexible pipeline for population-level analysis of Whole Genome Bisulfite Sequencing (WGBS) data
15:00 - 15:15
Alexander Gosdschan: methylKit, a package for DNA methylation analysis from high-throughput bisulfite sequencing data
15:15 - 15:45
Coffee break
15:45 - 17:00
Session IV - Proteomics
15:45 - 16:00
Christian Panse: rawDiag: access orbitrap data on the fast lane
16:00 - 16:15
Nils Kurzawa: TPP: a Bioconductor package for analysis of thermal proteome profiling experiments
16:15 - 16:30
Markus Gruber: MS-EmpiRe - Mass Spectrometry analysis using Empirical and Replicate based statistics
16:30 - 16:45
Helena Crowell: Differential discovery in CyTOF data with CATALYST & diffcyt
16:45 - 17:00
Constantin Ahlmann-Eltze: Empirical Bayesian Modeling for Mass Spectrometry Data
18:00 - 19:00
Free time (Christmas market)
19:30 -
Dinner at Hofbrauhaus (self-funded)
 
Fri 7 Dec
TUM-IAS Building, Lichtenbergstrasse 2a, Garching
09:00 - 09:30
Keegan Korthauer Practical recommendations for controlling false discoveries in computational biology
09:30 - 10:15
Session V
09:30 - 09:45
Ruizhu Huang: The tree aggregation
09:45 - 10:00
Thomas Girke: signatureSearch: Gene Expression Signature Search Methods for Discovering Novel Modes of Action of Drugs and Other Cellular Perturbations
10:00 - 10:15
Ludwig Geistlinger: Towards a gold standard for benchmarking gene set enrichment analysis
10:15 - 10:45
Coffee break
10:45 - 12:00
Session VI - Multiomics
10:45 - 11:00
Vince Carey: Hybrid data architectures for multiomic experiments
11:00 - 11:15
Johannes Rainer: ensembldb: coordinate mapping between the genome, exome, transcriptome and proteome
11:15 - 11:30
Laurent Gatto: A Grammar of Omics Data Manipulation
11:30 - 11:45
Leo Lahti: A roadmap for microbiome bioinformatics in R
11:45 - 12:00
Katarzyna Wreczycka: Genomation: a toolkit to summarize, annotate and visualize genomic intervals
12:00 - 13:30
Lunch
13:30 - 14:00
Fanny Perraudeau Unlocking RNA-seq tools for zero-inflation and single cell applications using ZINB-WaVE observation weights
14:00 - 15:30
Session VII - RNA
14:00 - 14:15
Clara Benoit-Pilven: kissDE retrieves condition-specific variants in RNA-Seq data from model and non-model species
14:15 - 14:30
Charlotte Soneson: A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
14:30 - 14:45
Christian Mertes: OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data
14:45 - 15:00
Svetozar Nesic: Targeted synthetic datasets to benchmark allele specific expression algorithms
15:00 - 15:15
Marijke Van Moerbeke: A Random Effects Model for the Identification of Differential Splicing (REIDS) Using Exon and HTA Arrays
15:15 - 15:30
Ziga Avsec: Kipoi: accelerating the community exchange and reuse of predictive models for genomics
15:30 - 15:35
Wrap-up and closing
 
Accommodation
Motel One Munich-Sendlinger Tor. This is located in the city centre close to the Sendlinger Tor underground station.
Motel One Munich-Garching. This is located outside the city centre but closer to the conference venue. The Garching-Hochbruck station is right outside the hotel.
 
Getting to the venue
By public transport (U-Bahn), the venue can be reached in approximately 30 minutes from the city centre. You need to get off at the last stop of the U6 Line (Garching-Forschungszentrum).
 
Social Activities
Wed. 5 Dec. evening. There will be a talk by Lisa McShane at Ludwig-Maximilians University (LMU) from 5-6pm, followed by a presentation of the STRATOS initiative. This is an opportunity for the two groups to meet. We plan to go for some beer and food downtown afterward (self-funded).
Thur. 6 Dec. evening we will visit the Christmas market in the city centre and have a dinner party (self-funded) at the brewery Hofbrauhaus afterwards.
Sat. 8 Dec. If the snow condition allows it, some organizers will go skiing in Garmisch, a ski resort near Munich. Everyone is welcome to join. Here some information from last year about a train & ski-pass offer.
 
Code of conduct
Bioconductor is built on the free and open exchange of scientific ideas, and the contributions of our diverse user community. In this spirit, EuroBioc 2018 is dedicated to providing a harassment-free conference experience for everyone. Harassment of any form (verbal, physical, sexual, or other) will not be tolerated in talks, workshops, social activities, or online.
Reach out to conference organizers (This email address is being protected from spambots. You need JavaScript enabled to view it.) or our on-site response team with any concern (Anne-Laure Boulesteix or Julien Gagneur).
 
Previous meetings
If you have not previously attended any European Bioconductor meetings, you can get an idea about the topics and talks by looking at the programmes from the 2017, and 2015 editions.
 
Organising committee
Wolfgang Huber, European Microbiology Laboratory (EMBL), Heidelberg
Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo
Mark Robinson, University of Zurich
Julien Gagneur, Technical University of Munich
Anne-Laure Boulesteix, Ludwig-Maximilians Universitaet, Munich
Fabian Theis, Helmholtz Zentrum Munich