GCC2019: Full Schedule

The 2019 Galaxy Community Conference (GCC2019) was held in Freiburg, Germany, 1-8 July. There was one day of training, three days of mixed meeting and training, and then two to four days of CollaborationFest. The meeting featured joint & parallel sessions; invited, accepted, and lightning talks; poster and demo sessions; birds-of-a-feather meetups; social events; and training sessions every day.

Thanks to everyone who helped make GCC2019 a success!

10:00 CEST

Introduction to Galaxy Administration I

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/dagobah-training/Lobby

After attending this session you will be able to set up, configure, and administer a fairly polished Galaxy instance. Topics include:

deployment and platform options
using Ansible to install and configure your own server
customizing and extending your instance
defining and importing genomes, running data managers

Prerequisites

Knowledge and comfort with the Unix/Linux command line interface and a text editor: If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle

Speakers

Martin Čech

Dev and Trainer, free element

Galaxy Enthusiast

Enis Afgan

Research Scientist, Johns Hopkins University (JHU)

A long-standing member of the Galaxy community, spanning roles from system deployment to leadership.

Simon Gladman

University of Melbourne

Marius van den Beek

Penn State University

John Chilton

PSU

Nate Coraor

System Administrator, Galaxy Project, Penn State University

Helena Rasche

Monday July 1, 2019 10:00 - 12:00 CEST
Greece

A. Training, Admin / Dev

10:00 CEST

Introduction to Using Galaxy (Galaxy 101)

→ Slides

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/gcc2019-using-galaxy

This workshop will introduce the Galaxy user interface and how it can be used for reproducible data analysis. We will cover the basic features of Galaxy, including where to find tools, how to import and use your data, and an introduction to workflows. This session is recommended for anyone who has not used, or only rarely uses Galaxy.

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-using-galaxy

Prerequisites

Little or no experience using Galaxy
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

Speakers

Mo Heydarian

Galaxy Project, Johns Hopkins University

Jennifer Hillman-Jackson

Galaxy Project, Penn State University

Application Science Support Training at GalaxyProject.org

GCC 2019 Training Intro (101) pdf

Monday July 1, 2019 10:00 - 12:00 CEST
Germany

A. Training, Introduction / General

13:00 CEST

Beyond the Intro: Further Adventures in Using Galaxy

→ Slides

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/gcc2019-using-galaxy

This workshop continues where the Introduction to Galaxy session ends. Additional features of Galaxy will be introduced and several topics introduced in that first session will be explored in more detail. Topics covered will include

Uploading data via FTP
History management
Defining and using custom reference genomes
Using Tagging and Annotation to manage your Galaxy objects
More on workflow editing and management
More on sharing and publishing
Using Galaxy to help debug your analyses

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-using-galaxy

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

Speakers

Mo Heydarian

Galaxy Project, Johns Hopkins University

Jennifer Hillman-Jackson

Galaxy Project, Penn State University

Application Science Support Training at GalaxyProject.org

GCC 2019 Training Further (RNA) pdf

Monday July 1, 2019 13:00 - 15:00 CEST
Germany

A. Training, Introduction / General

13:00 CEST

Introduction to Galaxy Administration II

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/dagobah-training/Lobby

After attending this and the previous session you will be able to maintain and optimize a pretty good Galaxy instance Topics include:

upgrading to a new Galaxy release
configure nginX webserver with Galaxy
database overview and best practices
running tools in containers
users and groups and quotas
storage management and using heterogeneous storage services

Prerequisites

Knowledge and comfort with the Unix/Linux command line interface and a text editor: If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle
Knowledge of topics from or attendance at session I.

Speakers

Enis Afgan

Research Scientist, Johns Hopkins University (JHU)

A long-standing member of the Galaxy community, spanning roles from system deployment to leadership.

Simon Gladman

University of Melbourne

Martin Čech

Dev and Trainer, free element

Galaxy Enthusiast

Marius van den Beek

Penn State University

John Chilton

PSU

Nate Coraor

System Administrator, Galaxy Project, Penn State University

Helena Rasche

Monday July 1, 2019 13:00 - 15:00 CEST
Greece

A. Training, Admin / Dev

15:30 CEST

Analyzing Large / Complex Experimental Designs with Galaxy

→ Slides

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/gcc2019-using-galaxy

The slides to follow along are at

http://bit.ly/complextutorial

Learn how to successfully manage the analysis of large, complex experimental designs in Galaxy, from raw data intake through final summarized (and publishable) results. This workshop will focus on enhancements to Galaxy from the last few years that enable Galaxy to scale to handle large studies with tens of thousands of datasets.

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-using-galaxy

Prerequisites

Introduction to Galaxy or equivalent experience
Beyond the Intro: Further Adventures in Using Galaxy
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

Speakers

Daniel Blankenberg

Assistant Professor, Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute

Marius van den Beek

Penn State University

Mo Heydarian

Galaxy Project, Johns Hopkins University

Jennifer Hillman-Jackson

Galaxy Project, Penn State University

Application Science Support Training at GalaxyProject.org

GCC Analyzing Large Complex Experimental Designs with Galaxy pdf

Monday July 1, 2019 15:30 - 17:30 CEST
Germany

A. Training, Introduction / General

15:30 CEST

Introduction to Galaxy Administration III

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/dagobah-training/Lobby

After attending this and the previous 2 sessions you will be able to interconnect and troubleshoot a darn good Galaxy instance. Topics include:

exploring the Galaxy job configuration file
connecting Galaxy to compute clusters
polishing Galaxy on uWSGI application server
instance monitoring using Grafana
shared data management with CVMFS
when things go wrong: Galaxy server troubleshooting tips & examples

Prerequisites

Knowledge and comfort with the Unix/Linux command line interface and a text editor: If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle
Knowledge of topics from or attendance at session I and session II.

Speakers

Enis Afgan

Research Scientist, Johns Hopkins University (JHU)

A long-standing member of the Galaxy community, spanning roles from system deployment to leadership.

Simon Gladman

University of Melbourne

Martin Čech

Dev and Trainer, free element

Galaxy Enthusiast

John Chilton

PSU

Nate Coraor

System Administrator, Galaxy Project, Penn State University

Helena Rasche

Monday July 1, 2019 15:30 - 17:30 CEST
Greece

A. Training, Admin / Dev

13:19 CEST

Session 3: Training

Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

Tuesday July 2, 2019 13:19 - 14:50 CEST
Konzerthaus

A. Training

13:20 CEST

16S analysis with mothur

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-mothur

Speakers

Saskia Hiltemann

Erasmus MC

Metagenomics, Training materials, board games, CTF & security

Tuesday July 2, 2019 13:20 - 14:50 CEST
Belgium

A. Training, Metagenomics / Assembly

13:20 CEST

ChIP-seq data analysis

Introduction to ChIP-Seq analysis using Galaxy. What is a histone modification? How is a raw set of ChIP-seq data processed and analyzed?

Learning objectives

Assess the quality of a ChIP-seq experiment
Create coverage files
Call enriched regions or peaks

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-chipseq

Speakers

Leily Rabbani

Devon Ryan

Max Planck Institute of Immunobiology and Epigenetics (MPI-IE)

GalaxyCourse ChIP seq 2019 pdf

Tuesday July 2, 2019 13:20 - 14:50 CEST
Italy

A. Training, Epigenetics

13:20 CEST

EWAS data analysis for population epigenetics integrated into Galaxy - Epigenetics

Epigenetic aberrations which involve DNA modifications give researchers an interest to identify novel non-genetic factors responsible for complex human phenotypes such as height, weight, and disease. The goal of this session is to analyse differentially methylated regions in treatment resistant melanomas using Galaxy

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-ewas

Speakers

Krzysztof Poterlowicz

University of Bradford

Tuesday July 2, 2019 13:20 - 14:50 CEST
France

A. Training, Epigenetics

13:20 CEST

How to create a Galaxy Tool

→ Slides, Tutorial

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/creating-tools

A key bit of preparation:

please arrive with a working Planemo machine virtual machine appliance running. If you have a relatively updated Planemo already installed on your laptop - that can work also.

This session will walk bioinformaticians, developers, and admins through the process of taking a working script, app, or software and turning it into a Galaxy Tool. It will cover the basics of using Planemo, a command-line utility that assists in building and publishing Galaxy Tools. We will explore basics of wrapping, common parameters, tool linting, best practices, loading and modifying tools, citations, and publishing to Github and the Galaxy Tool Shed. Common tips and tricks will be discussed as well as insights from experienced tool developers.

Prerequisites

Introduction to Galaxy or equivalent experience
Knowledge and comfort with the Unix/Linux command line interface and a text editor: If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle
We will pass out USB sticks with a virtual machine for tool development on it, but ideally you'd arrive with this already working - instructions for downloading and installing this can be found in the Planemo documentation.
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

Speakers

John Chilton

PSU

Nicola Soranzo

Earlham Institute

Tuesday July 2, 2019 13:20 - 14:50 CEST
Greece

A. Training, Admin / Dev

13:20 CEST

Quality control of HTS data

Often the first step in high throughput sequencing data analysis is quality control. How reliable is the data? Does it have GC bias, or inaccuracies at the read ends, or contamination, or barcode corruption, or any number of other conditions that need to be detected and dealt with before the science begins. This workshop will provide hands-on experience performing quality control checks and how to get your data analysis-ready using Galaxy.
If you are unfamiliar with high throughput sequencing data, then this is a good introduction to HTS data.

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-hts-qc

Tuesday July 2, 2019 13:20 - 14:50 CEST
Germany

A. Training, Introduction / General

13:20 CEST

Variant calling I - from sequenced reads to variant lists

What exactly is variant calling?
How can I use Galaxy to call variants from my (exome-, whole-genome-)sequenced samples?

Learning objectives

Perform simple variant calling workflows including sequencing data quality control, read mapping and variant calling
Learn about different variant callers available for Galaxy and their strengths and weaknesses

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-variant-calling

Speakers

Wolfgang Maier

Member of the Galaxy Europe team, University of Freiburg

University of Freiburg

Tuesday July 2, 2019 13:20 - 14:50 CEST
Spain

A. Training, Transciptomics / Genome Variation

15:49 CEST

Session 5: Training

Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

Tuesday July 2, 2019 15:49 - 17:20 CEST
Konzerthaus

A. Training

15:50 CEST

Hi-C analysis

Why is a Hi-C) analysis useful?
What is 'chromosome conformation capture'?
What are main steps in order to generate and plot a Hi-C contact matrix?

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-hic

Speakers

Leily Rabbani

Joachim Wolff

Albert-Ludwigs-University Freiburg

Tuesday July 2, 2019 15:50 - 17:20 CEST
Italy

A. Training, Epigenetics

15:50 CEST

Machine Learning with Galaxy - Predict age from RNA-seq dataset

What is machine learning?
Why is it useful?
What are its different approaches?
How can we predict age from RNA-seq dataset?

Learning objectives

Provide the basics of machine learning and its variants
Learn how to do classification using the training and test data
Learn how to use Galaxy's machine learning tools

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-machine-learning

Speakers

Alireza Khanteymoori

Postdoc Researcher, University of Freiburg

Jeremy Goecks

Associate Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University

Anup Kumar

PhD candidate, University of Freiburg

Age prediction training presentation pdf

Tuesday July 2, 2019 15:50 - 17:20 CEST
Germany

A. Training, Diverse Communities

15:50 CEST

Metatranscriptomics and multi-omics functional microbiome analysis

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

Training Material for this workshop:

Functional microbiome analysis which estimates the functional groups expressed by microbial community, enables researchers to look beyond taxonomic composition and correlation with the condition under study. Using microbial community RNASeq data and subsequent metatranscriptomics workflows to elucidate the functional complement of the microbiome is gaining interest in the field.

The training workshop will introduce researchers to the basic concepts and tools from the published ASaiM workflow (Batut et al, GigaScience (2018), 7 (6), http://dx.doi.org/10.1093/gigascience/giy057). Attendees will also be able to run the workflow on small test datasets. Lastly, workshop trainers will update attendees of latest developments in galaxy tools and workflows for functional microbiome and multi-omics analysis.

Schedule:

Introduction to Functional Microbiome and multi-omics analysis
- Introduction to functional microbiome analysis.
- Metagenomics, metatranscriptomics and metaproteomics methods
- Inputs for the metatranscriptomics GTN training
Metatranscriptomics analysis using ASaiM workflow Part 1
- Inputs and tools used in ASaiM workflow
- Running the ASaiM workflow
Metatranscriptomics analysis using ASaiM workflow Part 2
- Understanding the outputs from the ASaiM workflow
Discussion and Q&A about functional microbiome and multi-omics analysis
- Recent advances in Galaxy workflows
- Q&A from attendees and future directions.

Prerequisites

Basic knowledge and interest in microbiome analysis.
Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-metatranscriptomics

Speakers

Timothy J. Griffin

Professor, University of Minnesota

Bérénice Batut

Post-doc, University of Freiburg

Ray Sajulga

University of Minnesota

Pratik Jagtap

Research Assistant Professor, University of Minnesota

Metaproteomics . DIA . Proteogenomics

Tuesday July 2, 2019 15:50 - 17:20 CEST
Belgium

A. Training, Metagenomics / Assembly

15:50 CEST

Scripting Galaxy through BioBlend

→ Slides

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/bioblend

Galaxy has an always-growing API that allows for external programs to upload and download data, manage histories and datasets, run tools and workflows, and even perform admin tasks. This session will cover various approaches to access the API, in particular using the BioBlend Python library.

Prerequisites

Knowledge and comfort with the Unix/Linux command line interface and a text editor: If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle
Basic understanding of Galaxy from a developer point of view.
Python programming.
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

Speakers

Marius van den Beek

Penn State University

Nicola Soranzo

Earlham Institute

Tuesday July 2, 2019 15:50 - 17:20 CEST
Greece

A. Training, Introduction / General, Admin / Dev

15:50 CEST

Variant Calling II - causative variant discovery

Why is a simple list of variants for a sample not enough?
How can I explore called variants and compare them across samples?
How can I link variants to phenotypes, i.e., identify causative variants?

Learning objectives

Use joint variant calling to facilitate variant comparison across samples
Filter, annotate and report lists of variants
Discover variant inheritance and linkage patterns

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
Variant calling I - from sequenced reads to variant lists or variant calling
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-variant-calling

Speakers

Wolfgang Maier

Member of the Galaxy Europe team, University of Freiburg

University of Freiburg

Tuesday July 2, 2019 15:50 - 17:20 CEST
Spain

A. Training, Transciptomics / Genome Variation

13:19 CEST

Session 9: Training

Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

Wednesday July 3, 2019 13:19 - 14:50 CEST
Konzerthaus

A. Training

13:20 CEST

Galaxy Code Architecture

How is the Galaxy code structured?
What do the various other projects related to Galaxy do?
What happens when I start Galaxy?

Learning objectives

Explore various aspects of the Galaxy codebase
Understand the various top-level files and modules in Galaxy
Understand how dependencies work in Galaxy's frontend and backend

Prerequisites

A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

Speakers

John Chilton

PSU

Nate Coraor

System Administrator, Galaxy Project, Penn State University

Wednesday July 3, 2019 13:20 - 14:50 CEST
Greece

A. Training, Admin / Dev

13:20 CEST

Single cell RNA-seq analysis

Mapping of single cell data, cluster analysis, diff. gene expression, workflows for standard platforms (10x, CELSeq2...)

This session focuses on the pre-processing of FASTQ data into a final Count Matrix

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

There will also be a scRNA BoF dinner/drinks on Monday at 18:00. The meeting point will be at the entrance of the Konzerthaus.

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-singlecell

Speakers

Alex Ostrovsky

Johns Hopkins University

Mehmet Tekman

Post Doc, University of Freiburg

Single-Cell, Developing Wrappers with Emacs

Wednesday July 3, 2019 13:20 - 14:50 CEST
Germany

A. Training, Transciptomics / Genome Variation

13:20 CEST

The RNA workbench, best practices for RNA and high-throughput sequencing bioinformatics in Galaxy - RNA and transcriptomics

Learn best practices for RNA and high-throughput sequencing bioinformatics in Galaxy using tools available in the RNA Workbench:

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-rnaworkbench

Speakers

Joerg Fallmann

Florian Eggenhofer

Postdoc, University of Freiburg (ALU)

University of Freiburg (ALU)

Wednesday July 3, 2019 13:20 - 14:50 CEST
France

A. Training, Transciptomics / Genome Variation

13:20 CEST

Train the Galaxy Trainer

This workshop will introduce:

using Galaxy as a training tool
Determining aim and audience
- e.g. single topic; string of related topics;
- e.g. response to specific request for training; or general upskilling people in Galaxy bioinformatics
setting up appropriate infrastructure
- usegalaxy.* resources
- TIaaS
- Your own
The available materials
- GTN tutorials
- and/or write your own; including how to contribute it to GTN
- Customising materials for your needs (Slides, language etc.)
Distributed workshops
- In practice
- Local facilitators vs lead trainers
- Using Zoom / Skype / other video conferencing software
Practise setting up your own workshop?
- eg. choose a topic from GTN
- check that it runs on Galaxy server of choice
- time it // modify if need be (e.g. cut down data set more?)
- create schedule, eg google doc → publish → tinyurl
Getting good feedback!

Prerequisites

An interest in using Galaxy to teach/train people

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-ttt

Speakers

Saskia Hiltemann

Erasmus MC

Metagenomics, Training materials, board games, CTF & security

Helena Rasche

Simon Gladman

University of Melbourne

Bérénice Batut

Post-doc, University of Freiburg

Anna Syme

Bioinformatician, Royal Botanical Gardens, Melbourne, Australia

Wednesday July 3, 2019 13:20 - 14:50 CEST
Spain

A. Training, Introduction / General

13:20 CEST

Visualization of HTS Data in Galaxy

Visualization of NGS data from various methods (Hi-C, WGBS, RNA, ChIP...). This workshop will focus on visualization of large datasets in Galaxy, focusing on high-throughput sequencing (HTS) data and the resulting downstream, aggregated data. Participants will visualise alignments, variation, expression levels, and annotations. The workshop will use widely available visualization tools.

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-htsviz

Wednesday July 3, 2019 13:20 - 14:50 CEST
Italy

A. Training, Introduction / General

15:49 CEST

Session 11: Training

Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

Wednesday July 3, 2019 15:49 - 17:20 CEST
Konzerthaus

A. Training

15:50 CEST

Beyond the Intro: Further Adventures in Using Galaxy

→ Slides

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/gcc2019-using-galaxy

SLIDES http://bit.do/gcc2019-2nd-further

This workshop continues where the Introduction to Galaxy session ends. Additional features of Galaxy will be introduced and several topics introduced in that first session will be explored in more detail. Topics covered will include:

Managing and backing up your account's Objects: Histories, Datasets, Workflows
Moving your work between Galaxy servers: Publish versus Share, Archive Creation, Export/Import
Datasets and Tools: Why format matters, Interpretting metadata, Troubleshooting
Get Data tools plus loading data: Browser, URL, Pasted Text, FTP, Data Libraries
Creating a Custom Genome, promoting it to a Custom Build, then DOING STUFF with it
Get a Galaxy Help Account and explore Galaxy's Learning and Support resources

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-using-galaxy

Speakers

Mo Heydarian

Galaxy Project, Johns Hopkins University

Jennifer Hillman-Jackson

Galaxy Project, Penn State University

Application Science Support Training at GalaxyProject.org

Wednesday July 3, 2019 15:50 - 17:20 CEST
Italy

A. Training, Introduction / General

15:50 CEST

Making your open source project awesome

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/open-source-awesome

Many journals require that scientific / research code to be open source in order to be published, but simply sharing source code alone isn’t usually enough to draw in new users and contributors. This session will discuss how researchers and coders can make their open source code repositories inclusive and welcoming to contributors.

This workshop will be led by members of the InterMine and Galaxy teams (and hopefully other equally awesome projects).

Prerequisites

A laptop with wifi
Interest in open source code

Speakers

Bérénice Batut

Post-doc, University of Freiburg

Yo Yehudi

Software Developer, University of Cambridge & Open Life Science

Integrated genomic data (InterMine)

Wednesday July 3, 2019 15:50 - 17:20 CEST
Spain

A. Training, Diverse Communities

15:50 CEST

Running Galaxy on Kubernetes

Do technologies like Docker, Kubernetes, and Helm sound interesting? How about standardized, production-grade deployment of Galaxy with a single command, or no-downtime configuration changes? In this training we will take a look at the basics of Helm and Kubernetes, a Helm Chart for Galaxy, delve into how to set and change Galaxy deployment configurations, how to interface Galaxy jobs with Kubernetes, etc.

Prerequisites

An understanding of Galaxy deployment requirements, comfortable on the command line, ideally, an understanding of container principles.

Speakers

Pablo Moreno

EMBL-EBI European Bioinformatics Institute

That Other Person

Software Engineer, Galaxy Project, Johns Hopkins University

Enis Afgan

Research Scientist, Johns Hopkins University (JHU)

A long-standing member of the Galaxy community, spanning roles from system deployment to leadership.

Nuwan Goonasekera

University of Melbourne

Alexandru Mahmoud

Galaxy Team, Johns Hopkins University

Wednesday July 3, 2019 15:50 - 17:20 CEST
Greece

A. Training, Admin / Dev

15:50 CEST

Single cell RNA-seq analysis II

Mapping of single cell data, cluster analysis, diff. gene expression, workflows for standard platforms (10x, CELSeq2...)

This session focuses on the downstream analysis, clustering, and classification of a downstream matrix

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-singlecell

Speakers

Alex Ostrovsky

Johns Hopkins University

Mehmet Tekman

Post Doc, University of Freiburg

Single-Cell, Developing Wrappers with Emacs

Wednesday July 3, 2019 15:50 - 17:20 CEST
Germany

A. Training, Transciptomics / Genome Variation

15:50 CEST

Visualisation development in Galaxy

In this age of high-throughput analysis and big data, visualisations have become an invaluable resource for the presentation and exploration of these often high-dimensional, complex, and large datasets.

While many tools in Galaxy produce static visual outputs (graphs, trees, etc), often some more interactivity is desired to aid in the exploration of these datasets. To support this need, Galaxy offers a range of visualisation options, such as Trackster for browsing genomic data and Charts for the interactive visualisation of tabular data and other datatypes.

In this workshop participants will learn how to develop such visualisations in Galaxy, more specifically:

Develop a module within the Charts visualisation plugin using Javascript
Develop a simple visualisation plugin from scratch

Prerequisites

Basic understanding of Galaxy from a developer point of view
Some familiarity with Javascript
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

Speakers

Anup Kumar

PhD candidate, University of Freiburg

Aysam Guerler

Galaxy Project, Johns Hopkins University

Johns Hopkins University

Jeremy Goecks

Associate Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University

Wednesday July 3, 2019 15:50 - 17:20 CEST
France

A. Training, Admin / Dev

13:20 CEST

15: Training Session

Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

Thursday July 4, 2019 13:20 - 14:50 CEST
Konzerthaus

A. Training

13:20 CEST

Assembly, annotation and analysis of bacterial genomes

Assembly and annotation of bacterial genomes

Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-assembly

Speakers

Delphine Lariviere

Penn State University

Post-doc in the Galaxy Team (Nekrutenko Lab). Works on bacterial genomics, assembly, RNA Seq, TnSeq. Also interested in evolution, metagenomics, epigenetics and visualisation.

Anna Syme

Bioinformatician, Royal Botanical Gardens, Melbourne, Australia

Thursday July 4, 2019 13:20 - 14:50 CEST
Italy

A. Training, Metagenomics / Assembly

13:20 CEST

CVMFS and Pulsar

Learn to use CVMFS for easy access to terabytes of reference data in Galaxy. Then find out how to send jobs to the ends of the universe with Pulsar!

Prerequisites

Basic understanding of Galaxy from a developer point of view.
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

Speakers

Simon Gladman

University of Melbourne

Nate Coraor

System Administrator, Galaxy Project, Penn State University

Gianmauro Cuccuru

University of Freiburg

Helena Rasche

Thursday July 4, 2019 13:20 - 14:50 CEST
Greece

A. Training, Admin / Dev

13:20 CEST

Import, handle, visualize and analyze biodiversity data in Galaxy

This Ecology-focused session will introduce using Galaxy to import (from external sources as GBIF, iNaturalist, Atlas of Living Australia or Zenodo repositories), handle (filter, rename fields, search/replace text patterns), visualize (stacked histograms) and analyze (calculate species abundance, phenology and trends) biodiversity data.

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-biodiversity

Speakers

Yvan Le Bras

Research engineer, French National Museum of Natural History

Simon Bénateau

Paris, French National Museum of Natural History

Thursday July 4, 2019 13:20 - 14:50 CEST
Spain

A. Training, Diverse Communities

13:20 CEST

Machine Learning with Galaxy - Predict age from DNA-methylation dataset

What is machine learning?
Why is it useful?
What are its different approaches?
How can we predict age from DNA-methylation dataset using Machine Learning?

Learning objectives

Provide the basics of machine learning and its variants
Learn how to do classification using the training and test data
Learn how to use Galaxy's machine learning tools

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-machine-learning

Speakers

Alireza Khanteymoori

Postdoc Researcher, University of Freiburg

Anup Kumar

PhD candidate, University of Freiburg

Age prediction Training presentation pdf

Thursday July 4, 2019 13:20 - 14:50 CEST
Germany

A. Training, Diverse Communities

13:20 CEST

Metabolomics data analysis I

Metabolomics data analysis is a complex, multistep process, which is constantly evolving with the development of new analytical technologies, mathematical methods, and bioinformatics tools and databases. The Workflow4Metabolomics (W4M) project aims to develop full LC/MS, GC/MS, FIA/MS and NMR pipelines using Galaxy framework for data analysis including preprocessing, normalization, quality control, statistical analysis and annotation steps.

This workshop will introduce W4M and how to use it for metabolomics data analysis.
This is part I of a two part training.

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-metabolomics

Speakers

Ralf Weber

University of Birmingham

Gildas Le Corguillé

CNRS-SU - Station Biologique de Roscoff - ABiMS

Mélanie Petera

Thomas N. Lawson

Post doc, University of Birmingham

Thursday July 4, 2019 13:20 - 14:50 CEST
France

A. Training, Proteomics / Metabolomics

13:20 CEST

Proteomic data analysis with Galaxy

→ Slides

Mass spectrometry is the state-of-the-art technique to analyze the proteome of complex samples. This training covers protein identification and quantification based on stable isotopes. For the training dataset, HEK cells were grown in either light or heavy SILAC (Stable Isotope Labeling with amino acids in cell culture) medium, lysed and mixed together in a certain ratio. The quantification step at the end of the training will reveal in which ratio the cells were mixed.

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-proteomics

Speakers

Matthias Fahrner

PhD student, Institute for Surgical Pathology, Medical Center – University of Freiburg

Maren Stillger

University of Freiburg

Melanie Föll

PostDoc, Northeastern University Boston

GCC Proteomics I pdf

Thursday July 4, 2019 13:20 - 14:50 CEST
Belgium

A. Training, Proteomics / Metabolomics

15:50 CEST

17: Training Session

Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

Thursday July 4, 2019 15:50 - 17:20 CEST
Konzerthaus

A. Training

15:50 CEST

ELIXIR Galaxy AAI: Authentication and Authorisation Infrastructure

→ Slides

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/galaxy-aai

This hands-on workshop is targeting Galaxy admins that would like to connect their Galaxy server to Elixir AAI, so that their end-users can use their Elixir AAI identity to login and maintain their data. This is a new feature of the newly released Galaxy ver. 19.05 and you can test it live at https://usegalaxy.eu/login.
Prerequisites:

Know how to run your own Galaxy server
Have your server available remotely online for testing (or alternatively on your laptop). NB. ver 19.05 (or later, i.e. master)

What you will learn:

Background information on registering your Galaxy server as a Service Provider to the Elixir AAI framework.
Hands-on
- Live registration of your Galaxy server to Elixir AAI test environment.
- Configuring your Galaxy server to use your new client credentials to communicate properly with Elixir AAI services
- Test login!
How to complete the registration process and promote your test client to a production client once you are done with your testing.

Organisers and organization:

Elixir Galaxy Community and the Elixir AAI team
The workshop will be organized as a virtual collaboration across multiple sites

Speakers

Kjetil Klepper

Senior Engineer, Norwegian University of Science and Technology (NTNU)

ELIXIR AAI introduction Galaxy Community Conference 2019 pdf

Thursday July 4, 2019 15:50 - 17:20 CEST
Italy

A. Training

15:50 CEST

Genomic assembly and data analysis in Galaxy with Nanopore ONT long read sequencing

The session would cover an introduction long read sequencing with technologies like Oxford Nanopore. Followed by presenting tools in Galaxy to

description of best practices to perform genome assembly from long reads or hybrid long-short reads,
determine and plot the structure of genome
application use-cases such as determining antimicrobial resistance genes from the data

Prerequisites

Basic understanding of Genomics
Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-nanopore

Speakers

Willem de Koning

Saskia Hiltemann

Erasmus MC

Metagenomics, Training materials, board games, CTF & security

Milad Miladi

Thursday July 4, 2019 15:50 - 17:20 CEST
Greece

A. Training, Metagenomics / Assembly

15:50 CEST

Handling integrated biological data using Python, Jupyter, and InterMine

This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.

https://gitter.im/galaxyproject/galaxy-intermine

This tutorial will guide you through loading and analyzing integrated biological data (generally genomic or proteomic data) using InterMine, either via UI or via an API in Python. Topics covered will include automatically generating code to perform queries, customising the code to meet your needs, and automated analysis of sets, e.g gene sets, including enrichment statistics. Skills gained can be re-used in any of the dozens of InterMines available, covering a broad range of organisms and dedicated purposes, from model organisms to plants, drug targets, and mitochondrial DNA.
Users will also be shown how to import and export their gene and protein lists to and from Galaxy to link Galaxy pipelines with InterMine analyses.

Prerequisites

Basic Python skills are advantageous but not required.
A laptop with wifi. Python optional as we can use Jupyter notebooks to run analyses.

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-intermine

Speakers

Kevin Reierskog

Yo Yehudi

Software Developer, University of Cambridge & Open Life Science

Integrated genomic data (InterMine)

Thursday July 4, 2019 15:50 - 17:20 CEST
Germany

A. Training, Diverse Communities

15:50 CEST

MALDI imaging of peptides data analysis

→ Slides

MALDI imaging measures the spatial distribution of hundreds of analytes (peptides, proteins, metabolites or chemical compounds) in a tissue section. The technique is increasingly used in biological, translational and clinical settings as it combines molecular and morphological information. The training will cover quality control, preprocessing and visualizations of MALDI imaging data.

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-maldi

Speakers

Matthias Fahrner

PhD student, Institute for Surgical Pathology, Medical Center – University of Freiburg

Maren Stillger

University of Freiburg

Melanie Föll

PostDoc, Northeastern University Boston

GCC proteomics II pdf

Thursday July 4, 2019 15:50 - 17:20 CEST
Belgium

A. Training, Proteomics / Metabolomics

15:50 CEST

Metabolomics data analysis II

Metabolomics data analysis is a complex, multistep process, which is constantly evolving with the development of new analytical technologies, mathematical methods, and bioinformatics tools and databases. The Workflow4Metabolomics (W4M) project aims to develop full LC/MS, GC/MS, FIA/MS and NMR pipelines using Galaxy framework for data analysis including preprocessing, normalization, quality control, statistical analysis and annotation steps.

This workshop will introduce W4M and how to use it for metabolomics data analysis.

This is part II of a two part training.

Prerequisites

Introduction to Galaxy or equivalent experience
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-metabolomics

Speakers

15:50 CEST

Population genomics with RADseq

Use of RAD-seq, Genotyping by sequencing and similar data for analysis of populations, effects of selection, phylogeography studies.
Prerequisites

Introduction to Galaxy or equivalent experience
Quality Contol of HTS Data or prior exposure to HTS data
A wi-fi enabled laptop with a modern web browser. Google Chrome, Firefox and Safari will work best

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-radseq

Speakers