Educators:
David Ellinghaus (Associated partner - CAU)

Date:
March 6, 2018 Time: 08:30 - 16:30

Location:
Kiel, Am Botanischen Garten 1-9, Room E49
This course is designed for 15 participants. If we receive (a lot) more applications, we will choose participants based on the relevance of their application and/or a first-come-first-serve basis.

Contents:
Over the past decade, genetic epidemiology studies have progressed from studying single genetic variants in candidate genes to investigating millions of common genetic variants in genome-wide association studies (GWAS). Nowadays GWAS studies are moving forward to genome-wide rare variant association studies, gene-gene (GxG) and gene-environment (GxE) interaction studies as well as cross-phenotype studies including several 10k and sometimes even >100k genetic samples.

Learning goals:
In this one day course we will give guidance for planning of SNP array genotyping and will provide best-practices for large-scale quality control, variant annotation and association analysis of GWAS data. In the practical part of the course will work on real-world data sets and show how to automatically and manually analyze large case-control sample sets and how to annotate phenotype-associated genomic regions.

Prerequisites:
None

Keywords:
genome-wide association studies (GWAS); SNP genotype quality control; association testing

Deadline:
This registration closes on February 12th 2018.

Contact:
David Ellinghaus, This email address is being protected from spambots. You need JavaScript enabled to view it.

Registration:
https://docs.google.com/forms/d/e/1FAIpQLSd28nNXl9ykvgB1bxFrfuJslLsbuEV9TyIZ111ko9ZfJ76xbQ/viewform?usp=sf_link

Educators:
RBC Freiburg

Date:
26.02.-02.03.2018

Location:
Uni Freiburg

Contents:
1-week full-day hands-on workshop in Freiburg. Topics:
- Galaxy Introduction
- Data analysis of RNA-seq, ChIP-seq, Exome-seq, MethylC-seq data
 
Learning goals:
Using Galaxy for data analysis of HTS data. Topics:
- Quality control
- Mapping
- Differential expression analysis
- Workflow design
- Statistics
- Visualization.

Prerequisites:
No. Beginner training course!

Keywords:
Galaxy, NGS, HTS,  RNA-seq, ChIP-seq, Exome-seq, MethylC-seq

Tools:
Galaxy

Contact:
Freiburg Galaxy Team: http://galaxy.uni-freiburg.de/

Registration:
https://drive.google.com/open?id=1qnFUCHvyvBHt5OA97puq9sQ83yp8nKSg-EiUQznN4Jw

For more information: This email address is being protected from spambots. You need JavaScript enabled to view it.

Educators:
Julianus Pfeuffer, CIBi, FU Berlin
Timo Sachsenberg, CIBi, EKU Tübingen

Date:
9-12 January 2018

Location:
Ghent, Belgium

Contents:
OpenMS is a C++ library and framework for computational mass spectrometry. At times, the large code-base (and C++) might overwhelm novel developers. This project is intended to give a gentle introduction on how to find your way through the OpenMS codebase, how to implement your own tools and algorithms, or how to integrate novel third-party tools to interact in complex workflows. We also show how Python (pyOpenMS) bindings are provided for novel algorithms.

Learning goals:
Creating an OpenMS tool that can be fully integrated into a workflow system. Basic understanding of OpenMS concepts and functionality.

Prerequisites:
The course is targeted to bioinformaticians with a programming background. Ideally, participants have basic experience with C++.

Keywords:
workflows, proteomics, metabolomics, mass spectrometry, KNIME, OpenMS

Tools:
OpenMS, KNIME

Registration:
http://uahost.uantwerpen.be/eubic18/

Contact:
Timo Sachsenberg
This email address is being protected from spambots. You need JavaScript enabled to view it., +49-7071-29-70461, http://uahost.uantwerpen.be/eubic18/hackathon.html

Educators:
RBC Freiburg, de.NBI-epi Freiburg

Date:
Mon 8 January 2018 to Fri 12 January 2018

Location:
Oslo, Norway

Contents:
Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community.
 
Learning goals: 
Installation, configuration, customization, and extension of the own Galaxy servers.

Prerequisites:
Admin expertise

Keywords:
Galaxy

Tools:
Galaxy tools

Contact:
This email address is being protected from spambots. You need JavaScript enabled to view it.

Registration:
https://www.elixir-europe.org/events/european-galaxy-administrator-workshop

Educators:
Marc Höppner (Associated partner - CAU)

Date:
March 5, 2018 - 08:30 - 16:30

Location:
Kiel, Am Botanischen Garten 1-9, Room E49

Contents:
The constant drop in sequencing prices and the development of easy-to-use assembly programs makes it possible, even for small groups, to embark on a de novo genome project to obtain the full sequence of their species of interest. However, automatically annotating all genetic features in a eukaryotic genome, especially in non-model species with few or no sequenced closely related species, remains a challenge and standard pipelines still do not exist.

Learning goals:
In this one day course participants will learn about these challenges and the current strategies that can be used to try to obtain the most complete set of genes from a de novo assembled eukaryotic genome. We will also discuss how additional data, such as RNA-seq, assembled transcriptomes or proteomic data, can be used to improve the annotation, which can inform decisions on how best to spend the budget during a genome project. The practical part of the course will explain how to automatically and manually annotate a genomic region and how that information can be immediately translated into biologically relevant data for the species of interest.

Prerequisites:
None

Keywords:
eukaryotic genome, annotation, RNAseq proteomic data, assembly

Contact:
Marc Höppner, This email address is being protected from spambots. You need JavaScript enabled to view it.

This course is designed for 15 participants. If we receive (a lot) more applications, we will choose participants based on the relevance of their application and/or a first-come-first-serve basis.

Deadline: This registration closes on February 12th 2018

Registration: https://goo.gl/forms/Iq2omSUYWqGfFWPT2