Title: 'European Bioconductor Meeting 2017' output: html_document: toc: true toc_float: true

European Bioconductor Meeting 2017

• Conference webpage: https://Bioconductor.github.io/EuroBioc2017/ and short URL http://bit.ly/EuroBioc2017
• Where: Betty and Gordon Moore Library, University of Cambridge, UK
• When: Conference 5 - 6 December 2017 - Special interest group sessions 4 December
• On twitter: #EuroBioC2017
• Public etherpad: https://public.etherpad-mozilla.org/p/2017-12-04-EuroBioC
• On youtube: Tuesday 5/12 and Wednesday 6/12.

Introduction

The 2017 edition of the European Bioconductor meeting will be held in the Betty and Gordon Moore Library, Centre for Mathematical Sciences, at the University of Cambridge, UK.

The meeting is aimed at biologists, bioinformaticians, 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.

This will be a 3-day event. The main conference will be on Tuesday 5 and Wednesday 6 December 2017. The conference will feature invited talks as well as contributed flashlight sessions. We will also have special interest group (SIG) sessions on Monday 4th December, in the afternoon (see details below).

Registation for the conference is now closed.

Final Schedule

Live video and slides can be found beside the speaker's name. Slides and videos for Flashlight talks are linked below.

Confirmed speakers

• Martin Morgan, Roswell Park Cancer Institute and Bioconductor project. New approaches to the analysis and comprehension of high-throughput genomic data.
• Sara-Jane Dunn, Microsoft Research. Applying automated reasoning to uncover genetic programs.
• Vincent J. Carey, Harvard Medical School. Semantically rich interfaces to remote large data.
• Kasper D. Hansen, Johns Hopkins University. A large subset of the human epigenetic machinery demonstrates co-expression and severe intolerance to loss-of-function variation.
• Leopold Parts, Wellcome Trust Sanger Institute. Deep learning for microscopy images.
• Sophie Rabe, EMBL Heidelberg. Image based drug profiling in co-cultures with EBImage.
• Catalina Vallejos, Alan Turing Institute. BASiCS: dealing with technical and biological noise in single-cell expression data.
• Gabriella Rustici, University of Cambridge. Building bioinformatics training capacity and coordination in Europe.
• Levi Waldron, City University of New York. Multi-omics methods and resources for Bioconductor.
• Lukas Weber, University of Zurich. Statistical methods for differential discovery in high-dimensional cytometry data.
• Thomas Ingraham, F1000Research. Updates on the Bioconductor Gateway.
• Lori Shepherd, Roswell Park Cancer Institute. Bioconductor packages for cached file management.

Flashlight Talks

Flashlights are intended to be short presentations covering a single topic e.g. a new package or a particular technical problem you have encountered. Each talk has been allotted 10 minutes and presenters should aim for approximately 6 slides. The following rules will apply in these sessions in order to keep things flowing:

• There will be a warning at 9 minutes.
• Flashlight talks will be interrupted (possibly mid-syllable) at the 10 minute mark regardless of how many slides the speaker has left.
• At this point the next talk will be set up on the computer, allowing the next speaker to get going immediately that their time begins.
• To keep on schedule, there will be no time for questions. Save your quesions until one of the tea breaks or lunch!

Speakers, please share you slides with your session chair in the tea/lunch break preceding your session. Presentations will be transferred to a single computer to ensure smooth running of the session. It's safest to use a PDF.

Session I: Chair, Aaron Lun

• Simon Anders, University of Heidelberg, LinkedCharts and rlc, video
• Federico Marini, Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Interactivity and reproducibility: RNA-seq analysis, the ideal way, video
• Parham Solaimani, BeDataDriven, Renjin, video, slides
• Charlotte Soneson, University of Zurich, Towards unified quality verification of synthetic count data with countsim QC, video, slides
• Koen Van den Berge, Ghent University, Unlocking RNA-seq tools for zero inflation and single cell applications using ZINB-WaVE observation weight, video, slides
• Sokratis Kariotis, University of Sheffield, From gene expression to pathway fingerprints and correlation networks, video, slides

Session II: Chair, Rory Stark

• Laure Cougnaud, OpenAnalytics, Easy unsupervised visualizations of high dimensional genomic data via dimensional reduction methods with the esetVis package, video, slides
• Rachel Lyne, University of Cambridge, InterMineR: R Client Library for InterMine, video, slides
• Koustav Pal, IFOM - FIRC Institute of Molecular Oncology, HiCLegos - store, retrieve and plot Hi-C data, video, slides
• Davis McCarthy, EMBL-EBI, Slalom: scalable and versatile factor analysis for single-cell RNA-seq, video, slides
• Anna Sozanska, University of Cambridge, SpideR: R package for Search, Integration and Retrieval of Big Data, video, slides
• Kirsten Van Hoorde, OpenAnalytics, How to automate analysis workflow via reproducible reports (using an R template package) for recurrent standardized data: a case study, video, slides

Session III: Chair, Laurent Gatto

• Johannes Rainer, Eurac Research, Enabling analysis of large scale metabolomics/proteomics data: on-the-fly data access in MSnbase, video, slides
• Sebastien Gibb, University Medicine Greifswald, topdownr - Systematic Optimisation of Protein Sequencing for Top-Down Proteomics, video, slides
• Constantin Ahlmann-Eltze, University Heidelberg, Differential Detection for Label-free Mass Spec Data, video, slides
• Oliver Crook, University of Cambridge, A Bayesian Framework for Spatial Proteomics, video, slides
• Jing Tang, University of Helsinki, Modelling drug combinations for cancer, video, slides
• Junyan Lu, European Molecular Biology Laboratory, Workflow for high-throughput drug sensitivity screen, video, slides

Session IV: Chair, Aaron Lun

• Kaur Alasoo, University of Tartu, Annotation preprocessing improves the detection of genetic effects on transcript usage, video, slides
• Robert Castelo, Pompeu Fabra University, The analysis of genetic interactions from gene expression data, video, slides
• Bernet Gel, Germans Trias i Pujol Research Institute , KaryoploteR plot any data on any genome, video, slides
• Rory Stark, University of Cambridge, CRUK Cambridge Institute, In development: a package for deep learning of omics data, video, [slides](https://github.com/Bioconductor/EuroBioc2017/raw/master/flashlight/sessionIV/BioC Euro Dev 2017 Stark.pdf)
• Petr Smirnov, University of Toronto, PharmacoGx: Analysis of High Throughput Pharmacogenomics Studies, video, [slides](https://github.com/Bioconductor/EuroBioc2017/raw/master/flashlight/sessionIV/EuroBioC2017 – Flashlight Talk - Final.pdf)
• Anna Gogleva, Sainsbury Laboratory Cambridge University, SecretSanta: flexible pipelines for automated prediction of secreted proteins, video, slides

Special Interest Groups

We invite participants to form groups dedicated to discuss or work on topics of interest on Monday afternoon. We have booked rooms for the respective groups. The topics are set by one group leader, and are advertised in advance of the event on the conference page.

To create a special interest group, open an issue describing the topic. The issue title should start with SIG: followed by a short but descriptive title. Describe the topic in the main body of the issue in as much detail as necessary, including the name of the topic leader, a chair and a scribe (to report, see below), possible or desired outputs (could be code, a piece of documentation, or general discussion), and possible outcomes. Any interested participants are invited to use the issue to ask questions and/or express their interest in participating.

Reporting: At the end of the SIG session, we ask that each group prepares a short summary of their session, which will be coordinated by a chair (who may or may not be the person that suggested the topic) and a scribe. These outputs will be presented and discussed during the conference.

Social activities

The SIG sessions on Monday (4th December) will be followed by an informal get-together in a pub. Participants are encouraged to attend, though you will have to buy your own drinks.

There will also be a conference dinner on Tuesday evening (5th December), held in Robinson College. This will be provided for free for conference participants.

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 2017 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, poster sessions, social activities, or online.

Meeting locations

Information on how to get to Cambridge can be found here.

The meeting itself is taking place in the Betty and Gordon Moore Library, Centre for Mathematical Sciences, at the University of Cambridge, UK., the full address of which is:

Betty and Gordon Moore library,
Wilberforce Road,
Cambridge,
CB3 0WA

The conference dinner will be in Robinson College, which is a short walk from the conference venue.

Robinson College,
Grange Road,
Cambridge,
CB3 9AN

These two locations are shown on the map below.

Accommodation

A number of rooms have been reserved in Robinson College, which is a few minutes walk from the conference venue. Details on how to reserve a room (including a discount code for this conference) will be sent in a confirmation email.

Otherwise, there are a number of hotels to the north of the city that are both fairly cheap should be relatively easy to travel to the venue from. These include:

• The Holiday Inn (http://www.hicambridgehotel.co.uk/). You can use the Citi8 bus service from Cambridge Road to Victoria Road, which is a short walk from the conference venue.
• Travel Lodge (https://www.travelodge.co.uk/)
• Premier Inn (http://www.premierinn.com/). You can use the Guided Bus 'B' route from Orchard Park to the Shire Hall stop, which is a short walk from the conference venue.

Another alternative is the Cambridge Central Travel Lodge, which is close to the Uni 4 bus route that stops outside the conference venue

• Travel Lodge Cambridge Central (https://www.travelodge.co.uk/)

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 2016 and 2015 editions.

Organising committee

• Mark Dunning <Mark.Dunning_AT_cruk.cam.ac.uk>
• Laurent Gatto <lg39_AT_cam.ac.uk>
• Aaron Lun <Aaron.Lun_AT_cruk.cam.ac.uk>

Sponsors

If you are interested in supporting this meeting, please contact the organisers.