Fourth Consortium Meeting


Dates: 9th – 10th March 2017
Venue: ETH Zurich
Department of Biosystems Science and Engineering (D-BSSE)
Room: Misrock seminar room, ground floor (close to the building entrance).
Mattenstrasse 26
4058 Basel

How to go there: https://www.bsse.ethz.ch/department/locations.html

Thursday, March 9th 2017


08:15 Registration and coffee
09:00 – 09:10 Welcome. Wolfgang Huber and Niko Beerenwinkel

Session I, scientific presentations


(20’ presentation + 10’ discussion)

09:10 – 09:45 Differential discovery in high dimensional cytometry datasets.
Mark Robinson (University of Zurich)
09:45 – 10:20 Identifying early-branching genes from single cell expression data.
Magnus Rattray (University of Manchester)
10:20 – 10:35 Introduction to the SOUND project. Wolfgang Huber (EMBL Heidelberg)
10:35 – 11:00 Coffee break
11:00 – 11:30 Computational methods for genome-based precision oncology.
Niko Beerenwinkel (ETH Zurich)
11:30 – 12:00 Multi-omics opportunities and challenges in the management of advanced melanoma. Mitch Levesque (USZ)
12:00 – 13:30 Group photo and lunch

Session II, scientific presentations


13:30 – 14:00 Computational approaches for diagnosis of rare disorders using transcriptome sequencing. Julien Gagneur (TUM)
14:00 – 14:30 Systematic statistical analysis of multi-omics data identified novel disease genes. Holger Prokisch (TUM-MED)
14:30 – 15:00 Automatic parallelization of bioinformatic workflows: Challenges and results. Alexander Bertram (BDD)
15:00 – 15:20 Coffee break
15:20 – 15:50 Functional classification of disease by integration of drug perturbation phenotyping and multi-omics. Wolfgang Huber (EMBL Heidelberg)
15:50 – 16:20 High throughput screening to assess signaling dependency of primary blood cancer cells. Thorsten Zenz (DKFZ)
16:20 – 16:50 Computational infrastructure to support SOUND dissemination.
Martin Morgan (RPCI)
16:50 – 17:10 Break
17:10 – 17:40 Structured sparse models and outlier detection for multi-omics patient data analysis. Susana Vinga (IDMEC)
17:40 – 18:30 Steering Committee meeting (WP-leaders and their representatives)
20:00 Dinner at Kohlmanns. Am Barfüsserplatz im Stadtcasino.
Steinenberg 14, Basel.

Friday, March 10th 2017


Session III, parallel meetings

09:00 – 09:30 Open-source software for the standardised application of existing methods in ctDNA data analysis. Daniele Biasci (UCAM)
09:30 – 10:05 Translational Oncology at the National Center for Tumor Diseases Heidelberg. Christof von Kalle (NCT Heidelberg)
10:05 – 10:40 Data-driven Precision Oncology. Michael Krauthammer (Yale School of Medicine)
10:40 – 11:00 Coffee break
11:00 – 11:45 Scientific Advisory Board private meeting and preparation of the SAB report. Euler Meeting Raum P.60, building 1058, ground floor
11:45 – 12:15 SAB feedback and discussion with the consortium. All
12:15 – 12:30 Emerging topics
Lunch
14:00 Departure

 

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:

  • Foster the exchange of technical expertise
  • Keep contributors up to speed with the latest developments
  • Coordinate any related efforts

Topics

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

  • Strategies for processing large data problems
  • Interactive tools
  • Reproducibility in high-throughput research
  • Emerging biological applications and technologies
  • Flashlight talks

Register at: http://scicore.ch/events/eurobioc2016/

Next meetings

Fourth consortium meeting

Dates: 9 – 10 March 2017
Location:  Basel
Host: ETH Zurich

Fifth consortium meeting

Dates: 15 – 16 November 2017
Location: Heidelberg
Host: European Molecular Biology Laboratory (EMBL)

Sixth consortium meeting

Dates: Spring 2018
Location: Cambridge
Host: University of Cambridge

Seventh and final consortium meeting

Dates: 16 – 17 July 2018
Location: Heidelberg

Third Consortium Meeting


Dates: 15th – 16th September 2016
Venue: Technical University of Munich
TUM main building on Arcisstrasse 21, Munich
Room 0504.02.408, 2nd floor

Please use the building entrance no. IX starting from the Luisenstraße. As a reference, there is a supermarket on the opposite side of the street. The entrance IX is the first one after the redecorated part of the building. The meeting room belongs to Lehrstuhl für Ingenieurgeologie, led by Prof. Dr. K. Thuro.

Thursday, September 15th 2016


08:15 Registration and coffee
09:00 – 09:10 Welcome. Wolfgang Huber and Julien Gagneur

Session I, Scientific Work Packages


(25’ presentation + 10’ discussion)

09:10 – 09:45 Genetic diagnosis of Mendelian disorders via exome and RNA sequencing. Holger Prokisch (TUM-MED)
09:45 – 10:20 Genetic diagnosis of Mendelian disorders via RNA sequencing (part II). Christian Mertes (TUM)
10:20 – 10:50 Coffee break
10:50 – 11:25 Methods for liquid biopsies. Meltem Gurel (UCAM)
11:25 – 12:00 Developing a multi-omics in vitro toolbox for melanoma.
Sandra Freiberger (UHZ)
12:00 – 13:30 Group photo and lunch at Das Tresznjewski, Theresienstrasse 72, Munich

Session II


13:30 – 14:05 Genomic variant annotation workflow for clinical applications.
Thomas Thurnherr (ETH)
14:05 – 14:25 DegreeCox: a network-based regularisation method for survival analysis. André Veríssimo (IDMEC)
14:25 – 15:00 Genomics of Drug Sensitivity of Primary Cancer Cells.
Sascha Dietrich (UKL-HD)
15:00 – 15:30 Coffee break
15:30 – 15:50 The role of germline variants in leukemia. Vladislav Kim (EMBL)
15:50 – 16:10 Mechanistic study of CLL biology and drug response using ex-vivo drug testing and multi-omics technology. Junyan Lu (EMBL)
16:10 – 16:55 Systems biology approach to the analysis of pharmacogenomic data in psoriasis. Amy Foulkes (University of Manchester)
16:55 – 17:15 Break
17:15 – 18:00 Genetic dissection of innate immune responses.
Veit Hornung (GeneCenter, Ludwig-Maximillians-Universität Munich)
19:30 Dinner at Bachmaier Hofbräu, Leopoldstraße 50, Munich.
By bus: Line 150 direction “Tivolistraße” or line 154 direction “Arabellapark”.
Stop: “Giselastrasse”
By underground: U3 or U6 direction “Fröttmaning”.
Stop: “Giselastrasse”

Friday, September 16th 2016


Session III

08:45 – 09:30 Steering Committee Meeting (WP-leaders and their representatives)
09:30 – 10:15 Decoding temporal order and lineage choice of asynchronously differentiating cells from single cell gene expression data. Fabian J. Theis (Institute of Computational Biology, Helmholtz Center Munich & Mathematics, TUM)
10:15 – 10:50 Common data containers and interoperability and Reporting tools and workflows. Martin Morgan (RPCI)
10:50 – 11:20 Coffee break
11:20 – 11:55 Apply automatic parallelization to BioInformatic Workflows with Renjin. Parham Solaimani and Alexander Bertram (BDD)
11:55 – 12:05 Outlier detection using the rank product method. Susana Vinga (IDMEC)
12:05 – 12:30 Training and dissemination. Susana Vinga (IDMEC)
12:30 – 13:00 Emerging topics
Lunch at Löwenbräukeller, am Stiglmaierplatz, Nymphenburger Str. 2, Munich
14:30 Departure

 

Second Consortium Meeting

The second consortium meeting was hosted by our colleagues from IDMEC Lisbon. Principal investigators, postdocs and PhD students attended the meeting and presented recent results and progress in the work packages. All partners are well on track with their project aims and the atmosphere of sharing research developments was quite enthusiastic. The great atmosphere of Lisbon underpinned this successful meeting. The next one will take place in September 2016 in Munich.

SOUND consortium

SOUND consortium


Dates: 29th February – 1st March 2016
Venue: Instituto Superior Técnico (IDMEC), Lisbon

Monday, February 29th 2016


08:15 Registration and coffee
09:00 – 09:10 Welcome. Wolfgang Huber and Susana Vinga

Session I, Scientific Work Packages


(25’ presentation + 10’ discussion)

09:10 – 09:45 Methods for liquid biopsies. Meltem Gürel (UCAM)
09:45 – 10:20 Methods for genetic disorders. Christian Mertes (TUM)
10:20 – 10:50 Coffee break
10:50 – 11:25 Mitochondrial genetic disorders. Robert Kopajtich (TUM-MED)
Cross-cutting methods for oncology and genetics
11:25 – 11:40 Towards the molecular tumor board. Thomas Thurnherr (ETH)
11:40 – 11:55 Sparse models for high‐dimensional multi‐omics patient data. André Veríssimo (IDMEC)
11:55 – 13:30 Lunch and group photo

Session II


13:30 – 13:45 Robust regression and outlier detection. Eunice Carrasquinha (IDMEC)
13:45 – 14:20 Precision oncology in melanoma. Sandra Freiberger (UHZ)
14:20 – 15:05 Common data containers and interoperability and Reporting tools and workflows. Martin Morgan (RPCI)
15:05 – 15:35 Coffee break
15:35 – 15:50 Genome-wide generalized additive models. Georg Stricker (TUM)
15:50 – 16:15 Data driven hypothesis weighting and false discovery rates. Wolfgang Huber (EMBL)
16:15 – 16:35 Mechanistic study of drug response using ex-vivo drug testing and multi-omics technology. Junyan Lu (EMBL)
16:35 – 17:00 Genomics of drug sensitivity of primary cancer cells. Thorsten Zenz (UKL-HD)
17:00 – 17:15 Modulators of drug response identified by multivariate lasso regression. Malgorzata Oleś (EMBL)
20:00 Dinner

Tuesday, March 1st 2016


Session III

08:45 – 09:30 Steering Committee Meeting (WP-leaders and their representatives)
09:30 – 10:05 WP 9 Performance and software integration. Parham Solaimani Kartalaei (BDD)
10:05 – 10:40 WP 12 Training and dissemination. Susana Vinga (IDMEC)
10:40 – 11:10 Coffee break
11:10 – 11:30 Nomination of the Scientific Advisory Board Members
11:30 – 12:00 Emerging topics
12:00 – 12:30 Practical issues. Simone Bell
Lunch
14:30 Departure

 

Kick-Off Meeting

Dates: 10th – 11th September 2015
Venue: European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg
Room 202

Thursday, September 10th 2015


12:00pm Arrival and Buffet lunch at EMBL

Session I


13:00 – 13:15 Welcome and overview SOUND. Wolfgang Huber
13:15 – 13:35 Round Table – Introduction of the partners
  • European Molecular Biology Laboratory (EMBL), Heidelberg. Wolfgang Huber
  • Roswell Park Cancer Institute (RPCI), New York. Martin Morgan
  • Swiss Federal Institute of Technology (ETHZ), Zurich. Niko Beerenwinkel
  • University of Cambridge (UCAM). Simon Tavaré
  • Ludwig-Maximillians-Universität München (LMU). Julien Gagneur
  • Instituto de Engenharia Mecânica (IDMEC), Lisbon. Susana Vinga
  • BeDataDriven (BDD), The Hague. Alexander Bertram
  • Heidelberg University Medical School (UKL-HD). Thorsten Zenz
  • Hospital of the University Zurich (USZ). Mitch Levesque
  • Technische Universität München (TUM-MED). Holger Prokisch

Session II, Scientific Work Packages


(25’ presentation + 10’ discussion)

13:35 – 14:10 WP 1 Methods for high-throughput perturbation assays. Wolfgang Huber
14:10 – 14:20 WP 2 Methods for liquid biopsies. Simon Tavaré
14:20 – 14:30 APERIM Project. Zlatko Trajanoski
14:30 – 14.50 Coffee break and Group Photo
14:50 – 15:25 WP 3 Methods for genetic disorders. Julien Gagneur
15:25 – 16:00 WP 4 Cross-cutting methods for oncology and genetics. Niko Beerenwinkel
16:00 – 16:35 WP 5 Genomics of drug sensitivity of primary cancer cells. Thorsten Zenz
16:35 – 16:55 Coffee break
16:55 – 17:30 WP 6 Precision oncology in melanoma. Mitch Levesque
17:30 – 18:05 WP 7 Mitochondrial genetic disorders. Holger Prokisch
18:30 The EMBL-shuttle will bring the participants to the Heidelberg city center (Bismarckplatz)
20:00 Dinner at Restaurant S´Kastanie, Elisabethenweg 1, Heidelberg

Friday, September 11th 2015


Travel to EMBL by bus starting at “Bismarckplatz” (Platform G) and taking the Bus 39 direction “Königstuhl”. Duration: 22 minutes. Departure time e.g. 08:15h and every 30 minutes. Bus stop: EMBL.
Alternatively, take a taxi.

Session II (cont.)

9:00 – 9:50 WP 8 Common data containers and interoperability and WP 10 Reporting tools and workflows. Martin Morgan
9:50 – 10:25 WP 9 Performance and software integration. Alexander Bertram
10:25 – 10:45 Coffee break
10:45 – 11:05 WP 11 Benchmarking & validation. Simon Tavaré
11:05 – 11:40 WP 12 Training and dissemination. Susana Vinga
11:40 – 12:00 Election of the Innovation Board Members
12:00 – 12:35 Practical issues. Simone Bell
12:35 Lunch and Departure
13:30 The EMBL-shuttle will bring the participants to the Heidelberg city center