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GCC2019 has ended
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!

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Monday, July 1
 

09:00

Beer Decoded, Here and Now!
The Street Science Community will demonstrate how to extract the DNA of beer.  We will demonstrate

  • sample preparation, 
  • an introduction to the Nanopore technology, 
  • sample loading and taxonomy classification of ONT metagenomic data in Galaxy.

By the end of the day we'll know a whole lot more about what we are drinking.

Want to actually get your hands dirty?  The Nanopore Loading Zone will be open during all breaks today, and you can load samples onto a MinION.

Monday July 1, 2019 09:00 - 18:00
Italy

09:00

Nanopore Loading Zone!
Want to learn about the portable MinION sequencers to sequence your samples in real-time? This is the place. Experienced MinION users will be on-hand to teach how to load samples* from anywhere in the world.

Biologists - see and try this new generation of sequencing.
Computer Scientists - learn to use a pipette!

The Nanopore Loading Zone will be open during all breaks today.  Please stop on by.

* Want to actually sequence something? See the Beer Decoded demos.

Monday July 1, 2019 09:00 - 18:00
Italy

09:00

Conference Desk Open
The conference desk will be open all day for conference checkin and questions.

Monday July 1, 2019 09:00 - 18:00
Konzerthaus

10:00

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
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University
avatar for Enis Afgan

Enis Afgan

Galaxy Project, Johns Hopkins University
Everything 'Galaxy on the Cloud' related!
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe


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

10:00

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
avatar for Mo Heydarian

Mo Heydarian

Galaxy Project, Johns Hopkins University
avatar for Jennifer Hillman-Jackson

Jennifer Hillman-Jackson

Galaxy Project, Penn State University



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

12:00

13:00

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
avatar for Mo Heydarian

Mo Heydarian

Galaxy Project, Johns Hopkins University
avatar for Jennifer Hillman-Jackson

Jennifer Hillman-Jackson

Galaxy Project, Penn State University



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

13:00

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
avatar for Enis Afgan

Enis Afgan

Galaxy Project, Johns Hopkins University
Everything 'Galaxy on the Cloud' related!
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe


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

15:00

15:30

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

Speakers
avatar for Daniel Blankenberg

Daniel Blankenberg

Assistant Professor, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris
avatar for Mo Heydarian

Mo Heydarian

Galaxy Project, Johns Hopkins University
avatar for Jennifer Hillman-Jackson

Jennifer Hillman-Jackson

Galaxy Project, Penn State University



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

15:30

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
avatar for Enis Afgan

Enis Afgan

Galaxy Project, Johns Hopkins University
Everything 'Galaxy on the Cloud' related!
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe


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

18:00

Birds-of-a-Feather (BoFs), with Your Dinner!
Birds-of-a-feather are informal gatherings or participants with a shared interest. Anyone can organize a BoF session.

BoFs with Your Dinner are held offsite, in a nearby restaurant or other location, that the BoF organizer is responsible for choosing.  

BoFs offered during this flocking:


Interested?
Sign in / Create an account, and add yourself as a participant to BoF you plan on attending

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...



Monday July 1, 2019 18:00 - 20:00
Offsite

18:00

BOF: Single Cell
General discussion about Single Cell RNA tools or analyses

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Speakers
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, Freiburg Galaxy Team
Single-Cell, General Galaxy Queries, and the weather



Monday July 1, 2019 18:00 - 20:00
Offsite
  • about Single-Cell, General Galaxy Queries, and the weather

18:00

Genome Annotation BoF
This BoF is for users and developers of tools and workflows for genome annotation.
What do you need?
What are you working on?
Meet the Galaxy Genome Annotation Project!


Interested?
Sign in / Create an account, and add yourself as a participant to BoF you plan on attending

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...



Speakers
avatar for Nathan Dunn

Nathan Dunn

Software Developer, UC Berkeley
I work on the Apollo project, but also have worked on various other projects such as the Monarch Initiative, the (cross-species ontology relations between phenotypes and genomics), the Alliance of Genome resources (major mods curating data), the Gene Ontology, and the Xena Variant... Read More →
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe



Monday July 1, 2019 18:00 - 20:00
Offsite

18:00

The Computational Chemistry BoF
This BoF is for everyone working in computational chemistry, cheminformatics and molecular dynamics and interested in implementations of tools, workflows and training in Galaxy. We will discuss our current projects and possible opportunities for collaboration. Anyone from related communities, such as metabolomics, is of course also welcome to attend.

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Speakers
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg
CB

Christopher Barnett

Lecturer, University of Cape Town
I'm a computational and theoretical chemist interested in glycobiology, data analytics and visualisation.



Monday July 1, 2019 18:00 - 20:00
Offsite
 
Tuesday, July 2
 

08:00

Conference Desk Open
The conference desk will be open all day for conference checkin and questions.

Tuesday July 2, 2019 08:00 - 19:30
Konzerthaus

08:59

Session 1: Opening Plenary
The opening session of GCC2019.

Welcome to Freiburg.

Moderators
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg

Tuesday July 2, 2019 08:59 - 10:30
Greece

09:00

Welcome
Welcome and conference logistics.

Speakers
avatar for Anika Erxleben

Anika Erxleben

PostDoc, University of Freiburg
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg


Tuesday July 2, 2019 09:00 - 09:10
Greece

09:10

Invited Talk: Evolution of X chromosome recognition during Drosophila Dosage Compensation
→ Abstract

Claudia Isabelle Keller Valsecchi 1,*, M. Felicia Basilicata 1,*, Plamen Georgiev 1, Aline Gaub1, Janine Seyfferth1, Giuseppe Semplicio1, Herbert Holz1, Pouria Dasmeh2, Asifa Akhtar1

  1. Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany
  2. Institute for Data Valorization (IVADO) and Department of Biochemistry, University of Montreal, Canada
* equal contribution

Speakers
CI

Claudia Isabelle Keller Valsecchi

Max-Planck Institute of Immunobiology and Epigenetics
Reconstitution of the Dosage Compensation ComplexKeller1, C. I., Hallacli1, E., Akhtar1, A.1Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germanykeller@ie-freiburg.mpg.deGenetic information can be epigenetically modified independently of the DNA sequence... Read More →



Tuesday July 2, 2019 09:10 - 09:40
Greece

09:40

Galaxy Australia – inside the national vision of a data commons
Abstract, Slides

Gareth Price 1*, Derek Benson 2#, Simon Gladman 3#, Igor Makunin 2, Anna Syme 4, Grahame Bowland 5, Helen van de Pol 3, Christina Hall 3, Nuwan Goonasekera 3, Nigel Ward 6, Jeffrey H Christiansen 2,6 and Andrew Lonie 3

  1. Queensland Facility for Advanced Bioinformatics, Queensland Cyber Infrastructure Foundation, 306 Carmody Rd, St Lucia, Queensland 4067, Australia,
  2. Research Computing Centre, Level 5, Axon Building, The University of Queensland, St Lucia Queensland 4072, Australia
  3. Melbourne Bioinformatics, University of Melbourne, 187 Grattan Street, Victoria 3010, Australia
  4. Royal Botanic Gardens Private Bag 2000, Birdwood Avenue, South Yarra, Victoria 3141, Australia
  5. Centre for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
  6. Queensland Cyber Infrastructure Foundation, Level 5, Axon Building, The University of Queensland, St Lucia QLD 4072, Australia
* To whom correspondence should be addressed.
# These Authors contributed equally and are listed alphabetically.

Speakers
avatar for Gareth Price

Gareth Price

Head of Computational Biology, Queensland Facility for Advanced Bioinformatics
Work: Gareth is Head of the Computational Biology team at QFAB, joining in early 2017 after nearly 15 years as a genomics scientist. He has been involved in experimental design, data QC, analysis and interpretation from early printed microarrays through to multiple NGS platforms... Read More →



Tuesday July 2, 2019 09:40 - 10:00
Greece

10:00

A Machine Learning Tool Suite for Galaxy
Abstract, Slides

Qiang Gu 1, Anup Kumar 2, Björn Grüning 2, Jeremy Goecks 1

  1. Department of Biomedical Engineering, Oregon Health and Science University
  2. Department of Computer Science, University of Freiburg

Speakers
avatar for Jeremy Goecks

Jeremy Goecks

Assistant Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University (OHSU)



Tuesday July 2, 2019 10:00 - 10:20
Greece

10:20

An Update on Galaxy Workflows: More Accessible, Expressive, Robust, and Scalable
→ Abstract, Slides

Marius van den Beek 1, John Chilton 2, the Galaxy Team

  1. Institut Curie, 26 rue d’Ulm, F-75248 Paris, France.
  2. Department of Biochemistry and Molecular Biology, Penn State University, University Park PA USA.

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris



Tuesday July 2, 2019 10:20 - 10:40
Greece

10:30

10:59

Session 2: Administration & Development
Talks (invited, accepted and lightning) about Galaxy administration and development.

Moderators
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe

Tuesday July 2, 2019 10:59 - 12:00
Greece

10:59

Session 2: Outside the Genome & Community Track
Talks (invited, accepted and lightning) about about applications of Galaxy in novel domains, and about community resources.

Moderators
avatar for Yvan Le Bras

Yvan Le Bras

Research engineer, French National Museum of Natural History

Tuesday July 2, 2019 10:59 - 12:00
Germany

11:00

GalaxyCloudRunner: Streamlined Cloud Bursting for Galaxy
Abstract, Slides

Nuwan Goonasekera 1 , Alexandru Mahmoud 2 , Enis Afgan 2

  1. University of Melbourne, Melbourne, VIC, AUS
  2. Johns Hopkins University, Baltimore, MD, USA

Speakers
avatar for Nuwan Goonasekera

Nuwan Goonasekera

Melbourne Bioinformatics / University of Melbourne



Tuesday July 2, 2019 11:00 - 11:07
Greece

11:00

Galaxy Computational Chemistry
→ Abstract, Slides

Tharindu Senapathi 1, Simon Bray 2, Christopher B Barnett 1, Björn Grüning 2,3, Kevin J Naidoo 1

  1. Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch, South Africa
  2. Department of Computer Science, University of Freiburg, Freiburg, Germany
  3. Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany

Speakers
CB

Christopher Barnett

Lecturer, University of Cape Town
I'm a computational and theoretical chemist interested in glycobiology, data analytics and visualisation.



Tuesday July 2, 2019 11:00 - 11:20
Germany

11:07

Laniakea: A Galaxy-on-demand Provider Platform Through Cloud Technologies
Abstract, Slides

Tangaro Marco Antonio 1, Donvito Giacinto 2, Antonacci Marica 2, Chiara Matteo 3, Mandreoli Pietro 3, Pesole Graziano 1,4, Zambelli Federico 1,3

  1. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies - National Research Council (IBIOM-CNR), Bari, Italy
  2. National Institute for Nuclear Physics, Bari Section, Italy
  3. Dept. of Biosciences, University of Milan, Italy
  4. Dept. of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari “Aldo Moro”, Italy



Tuesday July 2, 2019 11:07 - 11:27
Greece

11:20

Climate Analysis with Galaxy
→ Abstract, Slides

Anne Fouilloux 1, Kirstin Krüger 1, Jean Iaquinta 1

  1. Department of Geosciences, University of Oslo, Norway

Speakers


Tuesday July 2, 2019 11:20 - 11:40
Germany

11:27

Enabling Single Sign-On for Multiple Galaxy Instances
Abstract, Slides

Enis Afgan 1, Marcus Christie 2 , Vahid Jalili 3 , Suresh Marru 2 , Marlon Pierce 2

  1. Johns Hopkins University, Baltimore, MD, USA
  2. Indiana University, Bloomington, IN, USA
  3. Oregon Health and Sciences University, Portland, OR, USA

Speakers
avatar for Enis Afgan

Enis Afgan

Galaxy Project, Johns Hopkins University
Everything 'Galaxy on the Cloud' related!



Tuesday July 2, 2019 11:27 - 11:34
Greece

11:34

How – And How not – to manage successful local Galaxies deployments
→ Abstract, Slides

Philip Mabon 1, Matthew Spelchak 1, Shane Thiessen 1

  1. Public Health Agency of Canada, Winnipeg, MB

Speakers
avatar for Philip Mabon

Philip Mabon

Senior Bioinformatician, Public Health Agency of Canada



Tuesday July 2, 2019 11:34 - 11:54
Greece

11:40

Galaxy Image Analysis: Web-based microscopy image analysis and cellular phenotyping
→ Abstract, Slides

Thomas Wollmann and Karl Rohr

  1. Heidelberg University, BioQuant, and IPMB, Biomedical Computer Vision Group, Heidelberg, Germany
  2. Heidelberg Center for Human Bioinformatics (HD-HuB), Heidelberg, Germany

Speakers


Tuesday July 2, 2019 11:40 - 12:00
Germany

11:54

Building a Pulsar Network across Europe
→ Abstract, Slides

Gianmauro Cuccuru 1, Helena Rasche 1 , Björn Grüning 1, Marco Tangaro 2 , Miroslav Ruda 3, Maximilian Hanussek 4

  1. Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany
  2. Italian National Research Council, Bari, Italy
  3. CESNET, Prague, Czech Republic
  4. University of Tübingen, Tübingen, Germany

Speakers
avatar for Gianmauro Cuccuru

Gianmauro Cuccuru

University of Freiburg



Tuesday July 2, 2019 11:54 - 12:01
Greece

12:00

12:15

Arts & Crafts
GCC sure can be overwhelming sometimes! This BoF is a quiet place to do some stress-free, science related, arts and crafts.

Interested?
Sign in / Create an account, and add yourself as a participant (or just show up)

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Speakers
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe


Tuesday July 2, 2019 12:15 - 13:20
Czechia

12:15

Birds-of-a-Feather (BoFs), with Lunch
Birds-of-a-feather are informal gatherings or participants with a shared interest. Anyone can organize a BoF session.

BoFs with Lunch are held during the lunch hour.  A projector and screen are available during these BoFs.

BoFs offered during this flocking:


Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...



Tuesday July 2, 2019 12:15 - 13:20
Konzerthaus

12:15

BOF: Galaxy Workflow Discovery (IWC)
People should be able to discover galaxy via the scientific workflow that they are looking for.  Let's build a good place for these and generate a few test case workflows. (Ideas: Differential Expression, Variant calling, DNA-methylation, Metagenomics).

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Bradley W. Langhorst

Bradley W. Langhorst

New England Biolabs

Tuesday July 2, 2019 12:15 - 13:20
Spain

12:15

BoF: Remote computation with Pulsar
This BoF is for everyone working with or interested to work with a Pulsar installation. We will discuss our current projects and possible opportunities for collaboration.

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Gianmauro Cuccuru

Gianmauro Cuccuru

University of Freiburg


Tuesday July 2, 2019 12:15 - 13:20
France

12:15

BoF: Using Galaxy in automated production setups
While Galaxy excels at being a workflow for the biologist with no major computational knowledge, recent advances in the past 3-4 years allow its use now as a system for handling production pipelines in larger bioinformatics setups (large data providers, core facilities, etc). I would like to bring together the people that see Galaxy as a reasonable alternative to more cli oriented workflow systems in the setting of production bioinformatics, that would have an interest in using Galaxy on these environments or that are already doing it. At the EBI we piloted recently tertiary analysis single cells pipelines from Galaxy being used in our production pipelines for the Single Cell Expression Atlas. We clearly had to go through some hurdles, but we think we have now something that is relatively generic. We had to add support on the client side layer to be able to allow errors and other border conditions and elements at the server side for things like automatic resubmissions on out of memory termination, among others. It would be great to share and hear what we have all learned in our experiences in this sort of setups and what other constraints we should be aware of when trying to do this.

Interested?
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Interested in proposing another idea for a BoF?
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Moderators
avatar for Pablo Moreno

Pablo Moreno

EMBL-EBI

Tuesday July 2, 2019 12:15 - 13:20
Italy

13:19

Session 3: Training
Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

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

13:20

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
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security


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

13:20

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

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

Speakers
avatar for Devon Ryan

Devon Ryan

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



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

13:20

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

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

Speakers
avatar for Krzysztof Poterlowicz

Krzysztof Poterlowicz

University of Bradford


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

13:20

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:
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

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute


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

13:20

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
Germany

13:20

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

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

Speakers
avatar for Wolfgang Maier

Wolfgang Maier

Member of the Galaxy Europe team, University of Freiburg
University of Freiburg


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

14:50

Poster 01 A: Alternative Splicing Analysis: The Silencing of the Human Colon Oxidase Complex
Abstract, Poster

Beáta Scholtz 1 , Anna Orient 2,3, Miklós Geiszt 2,3

  1. Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
  2. Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
  3. “Momentum” Peroxidase Enzyme Research Group of the Semmelweis University

Speakers
BS

Beáta Scholtz

associate professor, University of Debrecen, Faculty of Medicine, Genomics Core



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 04 A: Gene Expression Analysis of In vitro Anti-filarial Activity of Natural and Synthetic Sesquiterpene Lactones from the Plant Neurolaena lobata
→ Abstract, Poster

Lizzette Perez-Perez 1, Jessica R. Grant 1, Susan Haynes 1, Kevin M. Shea 2, Steven A. Williams 1

  1. Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
  2. Department of Chemistry, Smith College, Northampton, Massachusetts, United States of America

Speakers
LP

Lizzette Perez-Perez

Graduate Student, Smith College



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 07 A: Knockdown Effects of MAGOHB on Alternative Splicing Via RNA-Seq Analysis
→ Abstract, Poster

Glory Basumata 1, Kusum K. Singh 2

  1. Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati, Assam
  2. Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati, Assam


Speakers
avatar for Glory Basumata

Glory Basumata

Graduate Student, Indian Institute of Technology Guwahati
In the RNA Binding Protein Laboratory, IIT- Guwahati I mainly focus on RNA-Seq Analysis. [Travel Fellowship Recipient for GCC2019)



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

14:50

Poster 13 A: Evaluation of tools and workflows for database construction for environmental metaproteomics
Virginie Jouffret, Olivier Pible, Yannick Cogne, Sophie Ayrault and Jean Armengaud

Speakers
avatar for Virginie Jouffret

Virginie Jouffret

PhD student, CEA



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 16 A: Predicting Gene Expression from Histone Modifications and Chronological Age by RNA-Seq Data using Galaxy Machine Learning Tools
→ AbstractPoster (doi: 10.7490/f1000research.1117045.1)

Alireza Khanteymoori and Anup Kumar

Bioinformatics Lab, Albert-Ludwigs-Universität Freiburg, Germany

Speakers
avatar for Alireza Khanteymoori

Alireza Khanteymoori

Postdoc Researcher, University of Freiburg



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 19 A: EpiGeEC allows fast comparison of user datasets with thousands of public epigenomic datasets through Galaxy
Jonathan Laperle, Simon Hébert-Deschamps, Joanny Raby, David Bujold, David Morais, Michel Barrette, Guillaume Bourque and Pierre-Étienne Jacques

Summary

The Epigenomic Efficient Correlator (EpiGeEC) tool, aimed at efficiently performing pairwise correlate of thousands of epigenomic datasets, has been used over the last year to pre-calculate correlation matrices that are incorporated to the IHEC Data Portal (http://epigenomesportal.ca/ihec/) (Bujjold et al.). GeEC was also proven useful for some members of IHEC (Breeze et al.) to demonstrate that even if the experiemental procedures are not necessarily consistent through all projejcts, the generated datasets are still overall highly comparable since they tend to cluster based on the assay type and sample cell type, rather than on the producing consortium. Moreover, the correlation data were used to identify potentially mislabeled or problematic datasets, as part of a quality control pipeline implemented in the IHEC Data Portal.

In addition to visualizing the pre-compued correlation scores from the Data Portal, users can now also compare their own epigenomic datasets to IHEC ones using a public version of EpiGeEC recently launched. The could be useful, for instance, to help in the characterization of datasets, or as a quality control. The various features of EpiGeEC, integrated into the Galaxy framework of the Genetics and genomics Analysis Platform (GenAP, genap.ca) project, include the support of any genomic file formats (bigWig, WIG, bedGraph, BAM), the possibility to compute correlations at different metrics (e.g. Pearson Spearman), on different subsets of regions (e.g. genes, TSS, user-defined) or the complete genome, and the clustering algorithms to display the results as an annotated heatmap and/or dendrogram. We also provide a user-friendly interface facilitating the selection of the desired datasets, and we plan to offer datasets from model organisms generated by international consortia such as modENCODE as well as data downloaded from GEO/SRA and uniformly processed. We will present the design and implementation of EpiGeEC as well as a performance comparison with other tools and some of the key results obtained so far.


Speakers


Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 22 A: Laniakea: A Galaxy-on-demand Provider Platform Through Cloud Technologies
Abstract, Poster

Marco Antonio Tangaro 1, Giacinto Donvito 2, Marica Antonacci 2, Pietro Mandreoli 3, Matteo Chiara 3, Graziano Pesole 1,4 and Federico Zambelli 1,3

  1. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies - National Research Council (IBIOM-CNR), Bari, Italy
  2. National Institute for Nuclear Physics, Bari Section, Italy
  3. Dept. of Biosciences, University of Milan, Italy
  4. Dept. of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari “Aldo Moro”, Italy



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 25 A: Building a Galaxy Trusted Server to Ensure Privacy and Ownership in Genomic Research
Abstract, Poster

Guokun Zhang 1,2, Aarif Mohamed Nazeer Batcha 1,2,  Nikolaus von Bomhard 1,  Ulrich Mansmann 1,2

  1. Department of Medical Informatics, Biometry and Epidemiology (IBE), University of Munich (LMU), Germany
  2. Medical Data Integration Center (MeDIC), Medical center of the university of Munich, Germany

Speakers
GZ

Guokun Zhang

Scientific assistant, Department of Medical Informatics, Biometry and Epidemiology, University of Munich
Department of Medical Informatics, Biometry and Epidemiology, University of Munich (IBE, LMU)



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 28 A: InteractoMIX integration in Galaxy
Abstract, Poster

Patricia Mirela Bota 1, Joaquim Aguirre-Plans 2, Baldo Oliva 2 and Narcis Fernandez-Fuentes 1

  1. UVic: Universitat de Vic - Universitat Central de Catalunya
  2. Research Programme on Biomedical Informatics, the Hospital del Mar Medical Research Institute and Pompeu Fabra University



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 31 A: Development and implementation of a Galaxy instance geared towards microbiological applications within an applied public health setting
→ AbstractPoster

Julien Van Braekel 1, Bert Bogaerts 1, Raf Winand 1, Qiang Fu 1, Sigrid C. J.De Keersmaecker 1, Nancy H. Roosens 1,Kevin Vanneste 1

  1. Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium


Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 34 A: A Newly Opened Galaxy Platform at Clermont Auvergne University
→ AbstractPoster

Nadia Goué 1,3, David Grimbichler 1,3, Pierre Peyret 2,3, Antoine Mahul 1,3

  1. Mésocentre Clermont Auvergne, Université Clermont Auvergne, 7 Avenue Blaise Pascal, 63 178 Aubière
  2. UMR454 MEDIS Microbiologie Environnement Digestif Santé, INRA Site de Theix 63 122 Saint-Genès-Champanelle, CBRV 26 Place Henri Dunant 63 001 Clermont-Ferrand
  3. Auvergne Bioinformatics platform, CBRV Faculté de Médecine & Pharmacie 28 Place Henri Dunant 63001 Clermont-Ferrand INRA Theix 63122 Saint-Genès-Champanelle

Speakers
avatar for Nadia Goué

Nadia Goué

Bioinformatics Engineer, Clermont Auvergne University
Working at the UCA Mesocenter. Recipient of the GCC2019 Fellowship.



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 37 A: Galaxy Genome Annotation Project: Easier Genome Annotation Using Galaxy and GMOD Tools
Abstract, Poster (doi: 10.7490/f1000research.1116992.1)

Anthony Bretaudeau 1, Helena Rasche 2, Matéo Boudet 3, Loraine Brillet-Guéguen 4,5, Simon Gladman 6, Torsten Seemann 6 , Nathan Dunn 7, Björn Grüning 2

  1. INRA, UMR IGEPP, BIPAA/GenOuest, Campus Beaulieu, Rennes, France
  2. de.NBI, Albert Ludwigs Universität, Freiburg, Baden-Württemberg, Germany
  3. Plate-forme GenOuest, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
  4. Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique deRoscoff (SBR), 29680 Roscoff, France
  5. CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680, Roscoff, France
  6. Melbourne Bioinformatics, University of Melbourne, Australia
  7. Lawrence Berkeley National Lab, Berkeley, CA, USA

Speakers
avatar for Anthony Bretaudeau

Anthony Bretaudeau

BIPAA/GenOuest



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 40 A: Aequatus.js: a plugin to visualise gene trees in Galaxy
→ AbstractPoster

Anil S. Thanki 1, Nicola Soranzo 1, Wilfried Haerty 1, Robert P. Davey 1

  1. Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK

Speakers
avatar for Anil S. Thanki

Anil S. Thanki

Scientific Programmer, Earlham Institute



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 43 A: Galaxy and Training: 2019 updates from the Galaxy Training Network
AbstractPoster (doi: 10.7490/f1000research.1117108.1)

Bérénice Batut 1, Saskia Hiltemann 2, Helena Rasche 1, Subina Mehta 3, Pratik Jagtap 3, Praveen Kumar 3, Timothy Griffin 3, Dave Clements 4, over 100 other GTN contributors 5, Björn Grüning 1

  1. University of Freiburg, Freiburg, Germany
  2. Erasmus Medical Center, The Hague, Netherlands
  3. Galaxy-P Project, University of Minnesota, United States
  4. Galaxy Project, Johns Hopkins University, United States
  5. https://training.galaxyproject.org/training-material/hall-of-fame

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 46 A: Galaxy-E project: 2019 news
Yvan Le Bras, Alan Amosse, Simon Benateau and Benjamin Yguel

Speakers
avatar for Yvan Le Bras

Yvan Le Bras

Research engineer, French National Museum of Natural History



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

14:50

Poster 52 A: Poster: Science Data Center BioDATEN in relation to the Galaxy Community
Dirk von Suchodoletz, Jens Krüger, Jonathan Bauer and Björn Grüning

Speakers
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg



Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

14:50

Session 4: Posters, Demos, and Sponsors
Posters and demos will be presented on all three days, concurrently with the sponsor exhibits.

Tuesday July 2, 2019 14:50 - 15:50
Konzerthaus

15:00

Demo 01 A: Galaxy Computational Chemistry
Tharindu Senapathi, Simon Bray, Christopher Barnett, Björn Grüning and Kevin Naidoo

Speakers
CB

Christopher Barnett

Lecturer, University of Cape Town
I'm a computational and theoretical chemist interested in glycobiology, data analytics and visualisation.



Tuesday July 2, 2019 15:00 - 15:20
Spain

15:00

Demo 03 A: Analysing and organising large-scale metabolome annotation studies with Django, ISA and Galaxy
Thomas N. Lawson, Martin R. Jones, Mark R. Viant and Ralf J. M. Weber

Speakers
TN

Thomas N. Lawson

Post doc, University of Birmingham



Tuesday July 2, 2019 15:00 - 15:20
France

15:25

Demo 02 A: Climate Analysis with Galaxy
Abstract, Poster (doi: 10.7490/f1000research.1116911.1)

Anne Fouilloux 1, Jean Iaquinta 1 and Kirstin Krüger 1

  1. Department of Geosciences, University of Oslo, Norway

Speakers


Tuesday July 2, 2019 15:25 - 15:45
Spain

15:25

Demo 04 A: GalaxyCloudRunner: Streamlined Cloud Bursting for Galaxy
Nuwan Goonasekera, Alexandru Mahmoud and Enis Afgan

Speakers
avatar for Nuwan Goonasekera

Nuwan Goonasekera

Melbourne Bioinformatics / University of Melbourne



Tuesday July 2, 2019 15:25 - 15:45
France

15:49

Session 5: Training
Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

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

15:50

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

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

Speakers
JW

Joachim Wolff

Albert-Ludwigs-University Freiburg


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

15:50

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
avatar for Alireza Khanteymoori

Alireza Khanteymoori

Postdoc Researcher, University of Freiburg
avatar for Jeremy Goecks

Jeremy Goecks

Assistant Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University (OHSU)
avatar for Anup Kumar

Anup Kumar

PhD candidate, University of Freiburg



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

15:50

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
avatar for Tim Griffin

Tim Griffin

Professor, University of Minnesota
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →
avatar for Ray Sajulga

Ray Sajulga

University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota


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

15:50

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
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute


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

15:50

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

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

Speakers
avatar for Wolfgang Maier

Wolfgang Maier

Member of the Galaxy Europe team, University of Freiburg
University of Freiburg


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

17:20

17:29

Session 6: Epigenetics Track & Late Breaking Lightning Talks
Presentations focused on epigenetic applications of Galaxy, followed by late breaking lightning talks on a range of topics.

Moderators
avatar for Devon Ryan

Devon Ryan

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

Tuesday July 2, 2019 17:29 - 18:30
Greece

17:29

Session 6: Outside the Genome & Community Track
Talks on 1) novel applications of Galaxy, and 2) Community resources.

See the list of presentations in this session.


Moderators
Tuesday July 2, 2019 17:29 - 18:30
Germany

17:30

HiCExplorer 3: A toolbox for Hi-C data analysis
→ Abstract, Slides

Joachim Wolff 1 , Leily Rabbani 2 , Gautier Richard 2 , Thomas Manke 2 , Asifa Akhtar 2 , Rolf Backofen 1 , Fidel Ramirez 3 , Björn Grüning 1

  1. Bioinformatics Lab, Albert-Ludwigs-Universität Freiburg im Breisgau, Germany
  2. Max-Planck-Institut für Immunbiologie und Epigenetik, Freiburg im Breisgau, Germany
  3. Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany

Speakers
JW

Joachim Wolff

Albert-Ludwigs-University Freiburg



Tuesday July 2, 2019 17:30 - 17:50
Greece

17:30

Using Galaxy for Creation and Execution of Text Mining Workflows in the OpenMinTeD platform
→ Abstract, Slides

Dimitrios Galanis 1, Penny Labropoulou 1, Stelios Piperidis 1, Androniki Pavlidou 1, Antonis Lempesis 1 , Natalia Manola 1

  1. Athena Research and Innovation Center in Information, Communication and Knowledge Technologies



Tuesday July 2, 2019 17:30 - 17:50
Germany

17:50

Histone Deacetylases 1/2 In Microglia Function During Development And Neurodegeneration
Abstract, Slides

M. Datta 2, O. Staszewski 1, E. Raschi 3, M. Frosch 1, N. Hagemeyer 1, T. L. Tay 8,9, T. Blank 1, M. Kreutzfeld 4, D. Merkler 4, S. Ziegler-Waldkirch 5, P. Matthias 6, M. Meyer-Lühmann 5, M. Prinz 1,7

  1. Faculty of Medicine, University of Freiburg, Institute of Neuropathology, Freiburg, Baden-Württemberg, Germany
  2. Faculty of Medicine, Ulm University, Institue for Immunology, Ulm, Baden-Württemberg, Germany
  3. School of Medicine, Alma Mater Studiorum University of Bologna, Department of Experimental, Diagnostic and Speciality Medicine, Bologna, Italy
  4. Geneva Faculty of Medicine, Department of Pathology and Immunology, Geneva, Genève, Switzerland
  5. Faculty of Medicine, University of Freiburg, Department of Neurology, Freiburg, Baden-Württemberg, Germany
  6. Friedrich Miescher Institute for Biomedical Research, Basel, Basel-Stadt, Switzerland
  7. University of Freiburg, BIOSS Centre for Biological Signalling Studies, Freiburg, Baden-Württemberg, Germany
  8. University of Freiburg, BrainLinks-BrainTools Center, Freiburg, Baden-Württemberg, Germany
  9. Faculty of Biology, University of Freiburg, Freiburg, Baden-Württemberg, Germany



Tuesday July 2, 2019 17:50 - 17:57
Greece

17:50

To Better Benefit from Shared Tasks in Biomedical Text Mining
→ Abstract, Slides

Mouhamadou Ba 1, Arnaud Ferre 1,2, Richard Eckart de Castilho 3, Robert Bossy 1, Louise Deléger 1, Claire Nédellec 1

  1. Bibliome, MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
  2. ILES, LIMSI, CNRS, Université Paris-Saclay, 91405 Orsay, France
  3. UKP Lab, Department of Computer, Science Technische Universität Darmstadt

Speakers
avatar for Mouhamadou Ba

Mouhamadou Ba

MaIAGE, INRA
INRA



Tuesday July 2, 2019 17:50 - 17:57
Germany

17:57

Analysis and visualization of the human cardiac myocyte epigenome using Galaxy
→ Abstract, Slides

Gilsbach R. 1, Schwaderer M. 1, Grüning B.A., 2, Hein L. 1

  1. Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Germany
  2. Department of Computer Science, University of Freiburg, Germany

Speakers


Tuesday July 2, 2019 17:57 - 18:17
Greece

17:57

The LAPPS Grid/Galaxy Platform for Mining Scientific Publications
→ Abstract, Slides

Nancy Ide 1 , Keith Suderman 1, Alexandru Mahmoud 2

  1. Vassar College, Poughkeepsie, NY USA
  2. Johns Hopkins University, Baltimore, MD, USA

Speakers
avatar for Alexandru Mahmoud

Alexandru Mahmoud

Galaxy Team, Johns Hopkins University



Tuesday July 2, 2019 17:57 - 18:17
Germany

18:17

Training Infrastructure as a Service
Slides

Helena Rasche 1
  1. University of Freiburg

Speakers
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe



Tuesday July 2, 2019 18:17 - 18:24
Greece

18:17

Infrastructure for Healthier Living: Galaxy at Quadram Institute Bioscience
→ Abstract, Slides

Thanh Le Viet 1, Nabil-Fareed Alikhan 1, Purnima Pachori 1, Andrew J. Page 1

  1. Quadram Institute Bioscience, Norwich Research Park, Colney Lane, Norwich, NR4 7UQ, UK

Speakers


Tuesday July 2, 2019 18:17 - 18:24
Germany

18:17

Late Breaking Lightning Talks
Late breaking lightning talks.  The call for these will go out shortly before GCC2019.

Tuesday July 2, 2019 18:17 - 18:31
Greece

18:24

19:00

Galaxy Runners: Tuesday Edition
Do you like running? We will take you on a small 6km round through Freiburg and along the Dreisam. We will meet at 19:00 in front of the Konzerthaus.
Like to run more? At Thursday, there will be a 12km round offered.

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Florian Eggenhofer

Florian Eggenhofer

Postdoc, University of Freiburg (ALU)
University of Freiburg (ALU)
avatar for Anika Erxleben

Anika Erxleben

PostDoc, University of Freiburg

Tuesday July 2, 2019 19:00 - 20:00
Offsite

19:00

Birds-of-a-Feather (BoFs), with Your Dinner!
Birds-of-a-feather are informal gatherings or participants with a shared interest. Anyone can organize a BoF session.

BoFs with Your Dinner are held offsite, in a nearby restaurant or other location, that the BoF organizer is responsible for choosing.  There will not be any A/V support during these BoFs.

BoFs offered during this flocking:


Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...



Tuesday July 2, 2019 19:00 - 21:00
Offsite

19:00

The Freiburg City Tour BoF!
Limited Capacity full

This BoF will offer a guided Freiburg City tour. It will last for ~1h and 30min and is open for 30 people.  Please meet in front of the Konzerthaus.

There is a second Freiburg City Tour BoF on Thursday evening.

Interested?
Sign in / Create an account, and add yourself as a participant.  Space is limited.
Please note that adding your name here is considered a firm commitment to attend.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Tuesday July 2, 2019 19:00 - 21:00
Offsite

19:00

The Galaxy Training Network BoF!
Discussions around Galaxy related training and the Galaxy Training Network community:

  • training material (recent and future developments)
  • events and form of training
  • community building (instructors, contributors, users, mentoring)

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Speakers
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe


Tuesday July 2, 2019 19:00 - 21:00
Offsite
 
Wednesday, July 3
 

08:00

Conference Desk Open
The conference desk will be open all day for conference checkin and questions.

Wednesday July 3, 2019 08:00 - 19:15
Konzerthaus

08:59

Session 7: Administration & Development Track
Talks (invited, accepted and lightning) about Galaxy Administration and development.

Speakers
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne


Wednesday July 3, 2019 08:59 - 10:30
Greece

08:59

Session 7: Transcriptomics & Genomics Track
Talks (invited, accepted and lightning) about Transcriptomics and Genomics research with Galaxy.

Moderators
avatar for Anna Syme

Anna Syme

Bioinformatician, Royal Botanic Gardens Melbourne
Plant genomes! 

Wednesday July 3, 2019 08:59 - 10:30
Germany

09:00

Containerizing Galaxy server as a Singularity application on HPC clusters for GenAP
→ Abstract, Slides

Michel Barrette 1, David A. L. Morais 1, Jonathan Laperle 1, Carol Gauthier 1, David Bujold 2, Kuang Chung Chen 2, Bryan Caron 2, Alain Veilleux 1, Guillaume Bourque 2, Pierre-Etienne Jacques 1

  1. Université de Sherbrooke, Sherbrooke, Quebec, Canada
  2. McGill University, Montreal, Quebec, Canada

Speakers


Wednesday July 3, 2019 09:00 - 09:20
Greece

09:00

Invited Talk: Pou5f3, SoxB1 and Nanog control the Zygotic Genome Activation in Zebrafish by Chromatin Remodeling
→ Abstract, Slides

Marina Veil 1 , Lev Y. Yampolsky 2,3 , Björn Grüning 4,5 , and Daria Onichtchouk 1,6,7

  1. Department of Developmental Biology, Institute of Biology I, Faculty of Biology, Albert Ludwigs University of Freiburg, 79104, Freiburg, Germany
  2. Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee 37614-1710, USA
  3. Zoological Institute, Basel University, Basel, CH-4051 Switzerland;
  4. Department of Computer Science, Albert Ludwigs University of Freiburg, 79110, Freiburg, Germany
  5. Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104, Freiburg, Germany
  6. Signalling Research centers BIOSS and CIBSS, 79104, Freiburg, Germany
  7. Institute of Developmental Biology RAS, 119991 Moscow, Russia

Speakers


Wednesday July 3, 2019 09:00 - 09:30
Germany

09:20

Galaxy on Kubernetes: where we are and future challenges
→ Abstract, Slides

Pablo Moreno 1, Luca Pireddu 2 , Marius van den Beek 3 , Ennis Afgan 4 , Nuwan Goonasekera 5 , Bjoern Gruening 6 , Yasset Perez-Riverol 1 , Irene Papatheodorou 1

  1. European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
  2. Distributed Computing Group, CRS4, Italy
  3. Institut Curie, PSL Research University, Paris, France
  4. Johns Hopkins University, Department of Biology, USA
  5. Melbourne Bioinformatics & EMBL Australia Bioinformatics Resource, U. of Melbourne, Australia
  6. University of Freiburg, Department of Computer Science, Freiburg, Germany

Speakers
avatar for Pablo Moreno

Pablo Moreno

EMBL-EBI



Wednesday July 3, 2019 09:20 - 09:40
Greece

09:30

Single-cell RNA Analysis in Galaxy on 10X Datasets
Abstract, Slides

  • Mehmet Tekman, Bioinformatics Lab, Albert-Ludwigs-Universität Freiburg im Breisgau, Germany
  • Bérénice Batut, Bioinformatics Lab, Albert-Ludwigs-Universität Freiburg im Breisgau, Germany
  • Björn Grüning, Bioinformatics Lab, Albert-Ludwigs-Universität Freiburg im Breisgau, Germany

Speakers
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, Freiburg Galaxy Team
Single-Cell, General Galaxy Queries, and the weather



Wednesday July 3, 2019 09:30 - 09:50
Germany

09:40

A Minimal Docker Image for Galaxy
→ Abstract, Slides

Sergey Golitsynskiy 1 , Nuwan Goonasekera 2 , Alexandru Mahmoud 1 , Enis Afgan 1

  1. Johns Hopkins University, Baltimore, MD, USA
  2. University of Melbourne, Melbourne, VIC, AUS

Speakers
avatar for Sergey Golitsynskiy

Sergey Golitsynskiy

software engineer, Johns Hopkins University



Wednesday July 3, 2019 09:40 - 09:47
Greece

09:47

CVMFS-CSI for Galaxy: Efficient Access to Read-only Data in Kubernetes
→ Abstract, Slides 

Alexandru Mahmoud 1 , Nuwan Goonasekera 2 , Sergey Golitsynskiy 1 , Enis Afgan 1

  1. Johns Hopkins University, Baltimore, MD, USA
  2. University of Melbourne, Melbourne, VIC, AUS

Speakers
avatar for Alexandru Mahmoud

Alexandru Mahmoud

Galaxy Team, Johns Hopkins University



Wednesday July 3, 2019 09:47 - 09:54
Greece

09:50

Biology-driven classification of Single-Cells RNAseq data in Galaxy
→ AbstractSlides (doi: 10.7490/f1000research.1116983.1)

Léa BELLENGER 1 , Mirca S. SAURTY 2 , Ghislaine MORVAN-DUBOIS 2 , Hervé CHNEIWEISS 2 , Marie-Pierre JUNIER 2 , Naïra NAOUAR 1 , Christophe ANTONIEWSKI 1

  1. ARTbio bioinformatic platform, Institut de Biologie Paris Seine, Sorbonne-université, 7 Quai St Bernard, 75005, Paris, France
  2. UMR 8246 - Neuroscience and Glial plasticity, Institut de Biologie Paris Seine, Sorbonne-université, 7 Quai St Bernard, 75005, Paris, France

Speakers
avatar for Christophe Antoniewski

Christophe Antoniewski

Head of ARTbio bioinformatics, CNRS - Institut de Biologie Paris Seine
Institut de Biologie Paris-Seine (IBPS)



Wednesday July 3, 2019 09:50 - 10:10
Germany

09:54

gxadmin: usegalaxy.* administration wisdom
→ Abstract, Slides

Helena Rasche 1, Nate Coraor 2, Simon Gladman 3

  1. Galaxy Europe, University of Freiburg, Freiburg, Germany
  2. Galaxy Project, Penn State University, University Park, Pennsylvania, United States
  3. Galaxy Australia, Melbourne Bioinformatics, University of Melbourne, Parkville, Australia

Speakers
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe



Wednesday July 3, 2019 09:54 - 10:14
Greece

10:10

Improving Transcriptome Analysis with Molecular Indices and Galaxy
→ AbstractSlides 

Gautam Naishadham 1, Deyra N. Rodriguez 1, Keerthana Krishnan 1, Bradley W. Langhorst 1

  1. New England Biolabs

Speakers
avatar for Bradley W. Langhorst

Bradley W. Langhorst

New England Biolabs



Wednesday July 3, 2019 10:10 - 10:17
Germany

10:14

Galaxy container for Hinxton Single Cell Interactive Analysis Portal (HiSciAP)
→ Abstract, Slides 

Pablo Moreno 1*, Ni Huang 2*, Suhaib Mohammed 1, Jonathan Manning 1, Carlos Talavera-López 2, Kerstin Meyer 2, Irene Papatheodorou 1
  1. European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
  2. Wellcome Trust Sanger Institute, Hinxton, UK
* Joint first author

Speakers
avatar for Jonathan Manning

Jonathan Manning

Senior Bioinformatician, EMBL-EBI
I am a senior bioinformatician in the Gene Expression group at the EBI, which runs resources such as Single Cell Expression Atlas. We're interested in finding the best ways to run production-quality workflows using resources such as Bioconda, Galaxy and (whisper it) Nextflow



Wednesday July 3, 2019 10:14 - 10:34
Greece

10:17

Transposon Insertion Sequencing Analysis in Galaxy
→ Abstract, Slides 

Delphine Larivière 1,3 , Prabhani Kuruppumullage Don 2 , Laura Wickham 1 , Francesca Chiaromonte 2 , Kenneth Keiler 1 , Anton Nekrutenko 1,3

  1. Biochemistry and Molecular Biology Department, Eberly College of Science, The Pennsylvania State University, University Park, Pennsylvania, USA.
  2. Department of Statistics, Eberly College of Science, The Pennsylvania State University, University Park, Pennsylvania, USA.
  3. Galaxy Project , https://galaxyproject.org/

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

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



Wednesday July 3, 2019 10:17 - 10:37
Germany

10:30

10:59

Session 8: Administration & Development Track
Talks (invited, accepted and lightning) about Galaxy Administration and development.

Moderators
Wednesday July 3, 2019 10:59 - 12:00
Greece

10:59

Session 8: Transcriptomics & Genomics Track
Talks (invited, accepted and lightning) about transcriptomics and genomics research with Galaxy.

Moderators
avatar for Anshu Bhardwaj

Anshu Bhardwaj

Long term Fellow, Senior Scientist, Interdisciplinary Research Center (CRI) and CSIR-Institute of Microbial Technology
I did Masters in Biotech followed by Ph.D. in Life Sciences (Comp bio) at Centre for Cellular & Molecular Biology, Hyderabad, India, in 2008. I then served as one of the founding PIs for Open Source Drug Discovery Project where I conceived & developed protocols for crowdsourcing drug... Read More →

Wednesday July 3, 2019 10:59 - 12:00
Germany

11:00

Working Effectively with Remote Data in Galaxy - A Progress Report
→ Abstract, Slides 

John Chilton 1 , the Galaxy Team

  1. Department of Biochemistry and Molecular Biology, Penn State University, University Park PA, USA

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University



Wednesday July 3, 2019 11:00 - 11:07
Greece

11:00

Aequatus.js: a plugin to visualise gene trees in Galaxy
→ AbstractSlides (doi:10.7490/f1000research.1117044.1)

Anil S. Thanki 1
, Nicola Soranzo 1 , Wilfried Haerty 1 , Robert P. Davey 1

  1. Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK

Speakers
avatar for Anil S. Thanki

Anil S. Thanki

Scientific Programmer, Earlham Institute



Wednesday July 3, 2019 11:00 - 11:20
Germany

11:07

Testing and Visualizing the State of Galaxy Tools and Workflows
→ Abstract, Slides 

** Helena Rasche 1 , Nate Coraor 2 , Marius van den Beek 3 , Björn Grüning 1 , John Chilton 2, Martin Čech 2 , and the Galaxy Team

  1. Bioinformatics Group, University of Freiburg, Freiburg, Germany
  2. Department of Biochemistry and Molecular Biology, Pennsylvania State University, USA
  3. Institut Curie, 26 rue d’Ulm, F-75248 Paris, France
** All authors are listed in random order

Speakers
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University



Wednesday July 3, 2019 11:07 - 11:27
Greece

11:20

Visual Refinement of Genome Annotations with Apollo in a Community Environment
→ AbstractSlides (doi: 10.7490/f1000research.1116981.1)

Nathan Dunn 1,2
, Deepak Unni 1 , Colin Diesh 2 , Helena Rasche 3 , Anthony Bretaudeau 4 , Nomi Harris 1 , Ian Holmes 2

  1. Lawrence Berkeley National Lab
  2. University of Californa Berkeley
  3. University of Freiburg
  4. INRA, BIPAA/GenOuest, France

Speakers
avatar for Nathan Dunn

Nathan Dunn

Software Developer, UC Berkeley
I work on the Apollo project, but also have worked on various other projects such as the Monarch Initiative, the (cross-species ontology relations between phenotypes and genomics), the Alliance of Genome resources (major mods curating data), the Gene Ontology, and the Xena Variant... Read More →



Wednesday July 3, 2019 11:20 - 11:27
Germany

11:27

Setting up a Galaxy Platform in a HPC Infrastructure for Genomics Implementation into Diagnosis Routines for a Health Reference Center
Abstract, Slides

Miguel Juliá 1, Sara Monzón Fernández 1, Luis Chapado 1, Ángel Zaballos 2 and Isabel Cuesta 1

  1. Bioinformatics Unit (BU-ISCIII), Core facility, Health Institute Carlos III (ISCIII)
  2. Genomics Unit, Core facility, Health Institute Carlos III (ISCIII)

Speakers
avatar for Miguel Juliá

Miguel Juliá

Bioinformatics technician, ISCIII



Wednesday July 3, 2019 11:27 - 11:34
Greece

11:27

Architectural and Systems Improvements to G-OnRamp, a Collaborative Eukaryotic Genome Annotation Platform
→ Abstract, Slides 

Luke Sargent 1
, Yating Liu 2, Wilson Leung 2, Sarah C.R. Elgin 2, Jeremy Goecks 1

  1. Oregon Health & Science University
  2. Washington University in St. Louis

Speakers
avatar for Luke Sargent

Luke Sargent

Oregon Health and Science University (OHSU)
Hello, I am a developer on the G-OnRamp project (g-onramp.org). I am happy to talk about all manifestations of the logical majesty of the Machine Spirit.



Wednesday July 3, 2019 11:27 - 11:34
Germany

11:34

RealTimeTools: Integrating, Customizing, and Accessing UI-based Tools in Galaxy
→ Abstract, Slides 

Daniel Blankenberg 1,2,3,4


  1. Assistant Staff, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic
  2. Assistant Professor, Molecular Medicine, Cleveland Clinic Lerner College of Medicine
  3. Blankenberg Lab: blankenberglab.org
  4. Galaxy Team: galaxyproject.org

Speakers
avatar for Daniel Blankenberg

Daniel Blankenberg

Assistant Professor, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University



Wednesday July 3, 2019 11:34 - 11:54
Greece

11:34

ChiRA: an integrated framework for Chimeric Read Annotation
→ Abstract, Slides 

Pavankumar Videm 1
, Steffen Heyne 2, Rolf Backofen 1,3

  1. Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany
  2. Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
  3. Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Schänzlestr. 18, Freiburg 79104, Germany

Speakers


Wednesday July 3, 2019 11:34 - 11:54
Germany

11:54

Creating a Universe of Galaxies: The UseGalaxy.* Project
→ Abstract, Slides 

Nate Coraor 1
, Simon Gladman 2, Helena Rasche 3

  1. Galaxy Project, Penn State University, University Park, Pennsylvania, United States
  2. Galaxy Project Australia, Melbourne Bioinformatics, University of Melbourne, Parkville, Australia
  3. Galaxy Project Europe, University of Freiburg, Freiburg, Germany

Speakers
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University



Wednesday July 3, 2019 11:54 - 12:01
Greece

11:54

Training experience on “Data analysis and interpretation for clinical genomics” using Galaxy
→ Abstract, Slides 

Gianmauro Cuccuru 1,2
, Paolo Uva 2, Alessandro Bruselles 3, Giuseppe Marangi 4, Tommaso Pippucci 5 on behalf of the Italian Society of Human Genetics (SIGU)

  1. Albert Ludwigs University, Freiburg, Germany
  2. Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna (CRS4), Pula, Cagliari, Italy
  3. Istituto Superiore di Sanità, Rome, Italy
  4. Institute of Genomic Medicine, Fondazione Policlinico Universitario
  5. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Roma, Italy
  6. Sant’Orsola-Malpighi University Hospital, Bologna, Italy

Speakers
avatar for Gianmauro Cuccuru

Gianmauro Cuccuru

University of Freiburg



Wednesday July 3, 2019 11:54 - 12:01
Germany

12:00

12:15

Arts & Crafts
GCC sure can be overwhelming sometimes! This BoF is a quiet place to do some stress-free, science related, arts and crafts.

Interested?
Sign in / Create an account, and add yourself as a participant (or just show up!).

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Speakers
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe


Wednesday July 3, 2019 12:15 - 13:20
Czechia

12:15

Birds-of-a-Feather (BoFs), with Lunch
Birds-of-a-feather are informal gatherings or participants with a shared interest. Anyone can organize a BoF session.

BoFs with lunch offer a projector and screen, if desired.

BoFs offered during this flocking:

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...



Wednesday July 3, 2019 12:15 - 13:20
Konzerthaus

12:15

BoF: Galactic Visualisation!
Visualisation is absolutely key to scientific insight.  This BoF is about visualisations in Galaxy: How it works, best practices, what have we got, where are we going* ....

Interested? Show up! (Better yet, signup! That way we will get a bigger room.)

* A new format has been adapted but we need documentation/tutorials!

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe
avatar for Anil S. Thanki

Anil S. Thanki

Scientific Programmer, Earlham Institute

Wednesday July 3, 2019 12:15 - 13:20
Italy

12:15

BoF: Multi-omics
Discussion about Galaxy tools and workflows in area of proteomics, proteogenomics and metaproteomics.

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Tim Griffin

Tim Griffin

Professor, University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota


Wednesday July 3, 2019 12:15 - 13:20
France

12:15

EOSC-Life roadmap BOF
Discuss aspects of the EOSC-Life roadmap relevant to the computational biology community. It's for anyone interested in the future of the European Open Science Cloud.

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
JH

Jean-Karim Heriche

EMBL
Bioimage informatics, computational biology


Wednesday July 3, 2019 12:15 - 13:20
Spain

13:19

Session 9: Training
Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

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

13:20

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
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University


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

13:20

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



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
avatar for Alex Ostrovsky

Alex Ostrovsky

Johns Hopkins University
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, Freiburg Galaxy Team
Single-Cell, General Galaxy Queries, and the weather


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

13:20

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

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

Speakers
avatar for Florian Eggenhofer

Florian Eggenhofer

Postdoc, University of Freiburg (ALU)
University of Freiburg (ALU)


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

13:20

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
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →
avatar for Anna Syme

Anna Syme

Bioinformatician, Royal Botanic Gardens Melbourne
Plant genomes! 


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

13:20

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

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

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

14:50

Poster 14 B: Modulation of Nav1.5 mechanosensitivity by β1 and β3 subunits
→ AbstractPoster

Michele Maroni, Esther Eberhardt, Jannis Koerner, Angelika Lampert and Beate Winner

Michele Maroni 1,, Jannis Koerner 2 , Juergen Schuettler 3 , Angelika Lampert 2 , Beate Winner 1 and Esther Eberhardt 1,3

  1. Department for Stem Cell Biology, Universitätsklinikum Erlangen. 
  2. Institute of Physiology, RWTH Aachen University. 
  3. Department for Anesthesiology, Universitätsklinikum Erlangen.

Speakers


Wednesday July 3, 2019 14:50 - 14:50
Konzerthaus

14:50

Poster 02 B: Galaxy container for Hinxton Single Cell Interactive Analysis Portal (HiSciAP)
→ Abstract, Poster

Pablo Moreno, Ni Huang, Suhaib Mohammed, Jonathan Manning, Carlos Talavera-López, Kerstin Meyer and Irene Papatheodorou

Speakers
avatar for Jonathan Manning

Jonathan Manning

Senior Bioinformatician, EMBL-EBI
I am a senior bioinformatician in the Gene Expression group at the EBI, which runs resources such as Single Cell Expression Atlas. We're interested in finding the best ways to run production-quality workflows using resources such as Bioconda, Galaxy and (whisper it) Nextflow



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 05 B: Improving Transcriptome Analysis with Molecular Indices and Galaxy
→ AbstractPoster

Gautam Naishadham 1, Deyra N. Rodriguez 1, Keerthana Krishnan 1, Bradley W. Langhorst 1

  1. New England Biolabs

Speakers
avatar for Bradley W. Langhorst

Bradley W. Langhorst

New England Biolabs



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 08 B: Transposon Insertion Sequencing Analysis in Galaxy
Delphine Lariviere, Prabhani Kuruppumullage Don, Laura Wickham, Francesca Chiaromonte, Kenneth Keiler and Anton Nekrutenko

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

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



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 11 B: LC-MS/MS tool and interactive visualizations integration on Galaxy Workflow4Metabolomics infrastructure
Abstract, Poster

Romain Dallet, Gildas Le Corguillé, Julien Saint-Vanne, Yann Guitton and Erwan Corre

Speakers
RD

Romain Dallet

ABiMS, IFB Core - FR2424 - CNRS - Station Biologique de Roscoff, France



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 17 B: Analysis and visualization of the human cardiac myocyte epigenome using Galaxy
→ Abstract, Poster

Ralf Gilsbach1, Martin Schwaderer 1, Björn A. Grüning 2 and Lutz Hein 1

  1. Institute of Experimental and Clinical Pharmacology and Toxicology, BIOSS Centre for Biological Signaling Studies, University of Freiburg, Germany
  2. Department of Computer Science, University of Freiburg, Germany

Speakers


Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 20 B: Testing and Visualizing the State of Galaxy Tools and Workflows
Helena Rasche, Nate Coraor, Marius van den Beek, Björn Grüning, John Chilton, Martin Čech and Galaxy Team

Speakers
avatar for Martin Čech

Martin Čech

Dev, Galaxy Project, Penn State University
Galaxy Project, Penn State University



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 23 B: Galaxy on Kubernetes: where we are and future challenges
Pablo Moreno, Luca Pireddu, Marius van den Beek, Ennis Afgan, Nuwan Goonasekera, Bjoern Gruening, Yasset Perez-Riverol and Irene Papatheodorou

Speakers
avatar for Pablo Moreno

Pablo Moreno

EMBL-EBI



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 26 B: RealTimeTools: Integrating, Customizing, and Accessing UI-based Tools in Galaxy
Daniel Blankenberg

Speakers
avatar for Daniel Blankenberg

Daniel Blankenberg

Assistant Professor, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 29 B: ARIAWeb: a new web service for automated NMR structure calculation with ARIA
Fabien Mareuil, Fabrice Allain, Herve Menager, Michael Nilges and Benjamin Bardiaux

Speakers
FM

Fabien Mareuil

Research Engineer, Institut Pasteur



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 32 B: The IRIDA Platform for Microbial Genomics
AbstractPoster

Aaron Petkau 1, Thomas Matthews 1, Franklin Bristow 2, Josh Adam 1, Jeff Thiessen 1, Sukhdeep Sidhu 1, Peter Kruczkiewicz 1, Emma Griffiths 3, Damion Dooley 4, Dan Fornika 4, Geoff Winsor 3, Amogelang R. Raphenya 5, Morag Graham 1,2, The IRIDA consortium, Eduardo Taboada 1, Andrew G. McArthur 5, Robert Beiko 6, William Hsiao 4, Fiona Brinkman 3, Gary Van Domselaar 1,2

  1. Public Health Agency of Canada, Winnipeg, Canada
  2. University of Manitoba, Winnipeg, Canada
  3. Simon Fraser University, Burnaby, Canada
  4. BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
  5. McMaster University, Hamilton,Canada6.Dalhousie University, Halifax, Canada

Speakers
avatar for Aaron Petkau

Aaron Petkau

Bioinformatician, Public Health Agency of Canada



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 35 B: NanoGalaxy: A Galaxy toolkit and workflows for long-read sequencing
Abstract, Poster

Willem de Koning, Milad Miladi, Saskia Hiltemann and Bjoern Gruening

Speakers


Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 38 B: Visual Refinement of Genome Annotations with Apollo in a Community Environment
Nathan Dunn, Deepak Unni, Colin Diesh, Helena Rasche, Anthony Bretaudeau, Nomi Harris and Ian Holmes

Speakers
avatar for Nathan Dunn

Nathan Dunn

Software Developer, UC Berkeley
I work on the Apollo project, but also have worked on various other projects such as the Monarch Initiative, the (cross-species ontology relations between phenotypes and genomics), the Alliance of Genome resources (major mods curating data), the Gene Ontology, and the Xena Variant... Read More →



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 41 B: Training experience on “Data analysis and interpretation for clinical genomics” using Galaxy
→ Abstract, Poster

Gianmauro Cuccuru 1,2, Paolo Uva 2, Alessandro Bruselles 3, Giuseppe Marangi 4, TommasoPippucci 5 on behalf of the Italian Society of Human Genetics (SIGU)

  1. Albert Ludwigs University, Freiburg, Germany
  2. Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna (CRS4), Pula, Cagliari, Italy
  3. Istituto Superiore di Sanità, Rome, Italy
  4. Institute of Genomic Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, UniversitàCattolica del Sacro Cuore, Roma, Italy
  5. Sant’Orsola-Malpighi University Hospital, Bologna, Italy

Speakers
avatar for Gianmauro Cuccuru

Gianmauro Cuccuru

University of Freiburg



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 44 B: A brief overview on how bilille is using Galaxy for sharing knowledge, computational resources & tools.
→ AbstractPoster

Loïc Couderc 1, Isabelle Guigon 1, Pierre Pericard 1, Samuel Blanck 2, Florence Maurier 3,Guillemette Marot 4, Hélène Touzet 5

  1. bilille, Université de Lille, Institut Pasteur de Lille, 59655 Villeneuve d’Ascq cedex, France
  2. EA2694, Université de Lille, 59045 Lille cedex,  France
  3. Institut Pasteur de Lille, 59019 Lille cedex, France
  4. EA2694, Université de Lille and Inria, 59045 Lille cedex, France
  5. CNRS, CRIStAL, 59655 Villeneuve d’Ascq cedex, France

Speakers


Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 47 B: Climate Analysis with Galaxy
→ Abstract, Poster (doi: 10.7490/f1000research.1116911.1)

Anne Fouilloux 1, Kirstin Krüger 1, Jean Iaquinta 1

  1. Department of Geosciences, University of Oslo, Norway

Speakers


Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 50 B: Using Galaxy for Creation and Execution of Text Mining Workflows in the OpenMinTeD platform
→ Abstract, Poster

Dimitrios Galanis 1, PennyLabropoulou 1, Stelios Piperidis 1, Androniki Pavlidou 1, Antonis Lempesis 1 , Natalia Manola 1

  1. Athena   Research   and   Innovation   Center   in   Information,   Communication   and   Knowledge Technologies



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 53 B: UseGalaxy.eu: Community, Training, Infrastructure, and Users
→ Abstract, Poster

Helena Rasche 1, the European Galaxy Project

  1. Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany

Speakers
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe



Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

14:50

Session 10: Posters, Demos, and Sponsors
Posters and demos will be presented on all three days, concurrently with the sponsor exhibits.

Wednesday July 3, 2019 14:50 - 15:50
Konzerthaus

15:00

Demo 05 B: Combat-tb Workbench, A Customizable Platform For Variant Discovery And Annotation, Phylogeny Construction And Variant Prioritisation
Alan Christoffels, Ziphozakhe Mashologu, Peter Van Heusden and Thoba Lose

Speakers
avatar for Ziphozakhe Mashologu

Ziphozakhe Mashologu

Developer, UWC - South African National Bioinformatics Institute
South African National Bioinformatics Institute (SANBI)



Wednesday July 3, 2019 15:00 - 15:20
Belgium

15:00

Demo 07 B: Knockdown Effects of MAGOHB on Alternative Splicing Via RNA-Seq Analysis
Glory Basumata and Kusum K Singh

Speakers
avatar for Glory Basumata

Glory Basumata

Graduate Student, Indian Institute of Technology Guwahati
In the RNA Binding Protein Laboratory, IIT- Guwahati I mainly focus on RNA-Seq Analysis. [Travel Fellowship Recipient for GCC2019)



Wednesday July 3, 2019 15:00 - 15:20
Spain

15:00

Demo 15 B: CWL in Galaxy, 2019-06 snapshot
John Chilton 1, Hervé Ménager 2 and Michael Crusoe 3

  1. Penn State University
  2. Institut Pasteur
  3. CWL Project / ELIXIR-NL

Build the demo yourself at

https://gitlab.pasteur.fr/hmenager/galaxy-cwl-is-docker/tree/20190703#galaxy-cwl-is-docker

Speakers
avatar for Michael R. Crusoe

Michael R. Crusoe

Project Lead & Co-founder, Common Workflow Language project
Michael R. Crusoe is one of the co-founders of the CWL project and is the CWL Project Lead. His facilitation, technical contributions, and training on behalf of the project draw from his time as the former lead developer of C. Titus Brown's k-h-mer project, his previous career as... Read More →
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Hervé Ménager

Hervé Ménager

Research Engineer, Institut Pasteur
Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur



Wednesday July 3, 2019 15:00 - 15:20
Italy

15:25

Demo 06 B: ProteoRE, a Galaxy-based platform for the annotation and the interpretation of proteomics data in biomedical research
Florence Combes, David Christiany, Lien Nguyen, Virginie Brun, Valentin Loux and Yves Vandenbrouck

Speakers


Wednesday July 3, 2019 15:25 - 15:45
Belgium

15:25

Demo 08 B: Tool Prediction in Galaxy Workflows using Deep Learning
Galaxy workflows are scientific data processing pipelines for performing and
reproducing data analyses. The workflows are complex and difficult to create from a
suite of 2,000+ tools available in Galaxy, especially for new Galaxy users. In order to
make creating workflows easier, faster and less error-prone, a recommendation
system was developed to predict following tools. The predictive system analyses the
complete set of workflows available on Galaxy’s European server using a deep
learning approach to create a tool prediction model.

Workflows are directed acyclic graphs. To create the predictive model, sequences
(paths) of tools are extracted from these graphs and learned by a deep learning
approach ( Gated Recurrent Neural Network ). The hyperparameters of the deep
learning model are optimised using bayesian optimisation. The usage frequency of
tools is integrated in the model so that the tools which have not been used recently do
not appear in the set of possible tools. This is achieved by learning the usage of each
tool over time using a support vector regression model.

An API was developed to predict tools and visualize them using a user interface. It can
be used in the Galaxy workflow editor (It is not yet available publicly. The complete
code is located here ). The API can be also used for multiple user interface
integrations. Using the tool recommendation system, a user does not need to search
for the tools in the tool box to create a workflow. The possible tools are available in
the “recommended tools” modal popup.

Speakers
avatar for Anup Kumar

Anup Kumar

PhD candidate, University of Freiburg



Wednesday July 3, 2019 15:25 - 15:45
Spain

15:49

Session 11: Training
Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

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

15:50

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
avatar for Mo Heydarian

Mo Heydarian

Galaxy Project, Johns Hopkins University
avatar for Jennifer Hillman-Jackson

Jennifer Hillman-Jackson

Galaxy Project, Penn State University


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

15:50

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
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →
avatar for Yo Yehudi

Yo Yehudi

Software Developer, InterMine (University of Cambridge)
Integrated genomic data (InterMine)


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

15:50

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
avatar for Pablo Moreno

Pablo Moreno

EMBL-EBI
avatar for Sergey Golitsynskiy

Sergey Golitsynskiy

software engineer, Johns Hopkins University
avatar for Enis Afgan

Enis Afgan

Galaxy Project, Johns Hopkins University
Everything 'Galaxy on the Cloud' related!
avatar for Nuwan Goonasekera

Nuwan Goonasekera

Melbourne Bioinformatics / University of Melbourne
avatar for Alexandru Mahmoud

Alexandru Mahmoud

Galaxy Team, Johns Hopkins University


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

15:50

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


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

Speakers
avatar for Alex Ostrovsky

Alex Ostrovsky

Johns Hopkins University
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, Freiburg Galaxy Team
Single-Cell, General Galaxy Queries, and the weather


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

15:50

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
avatar for Anup Kumar

Anup Kumar

PhD candidate, University of Freiburg
avatar for Aysam Guerler

Aysam Guerler

Galaxy Project, Johns Hopkins University
Johns Hopkins University
avatar for Jeremy Goecks

Jeremy Goecks

Assistant Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University (OHSU)


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

17:29

Session 12: Plenary
Moderators
Wednesday July 3, 2019 17:29 - 18:30
Greece

17:30

Invited Talk: Galaxy Community Update
Slides

What has happened, and what is coming in the Galaxy Project.

Speakers
avatar for Anton Nekrutenko

Anton Nekrutenko

Galaxy Project, Penn State University
Penn State University
avatar for James Taylor

James Taylor

Professor, Johns Hopkins University
James Taylor is the Ralph S. O'Connor Professor of Biology and professor of computer science at Johns Hopkins University. Until 2014, he was an associate professor in the departments of biology and mathematics and computer science at Emory University. He is one of the original developers... Read More →



Wednesday July 3, 2019 17:30 - 18:00
Greece

18:00

Tool Prediction in Galaxy Workflows using Deep Learning
Abstract, Slides

Anup Kumar and Björn Grüning

  1. Freiburg Galaxy Team, Bioinformatics lab, University of Freiburg, Freiburg, Germany

Speakers
avatar for Anup Kumar

Anup Kumar

PhD candidate, University of Freiburg



Wednesday July 3, 2019 18:00 - 18:07
Greece

18:07

Street Science Community: make science tangible & accessible by bringing it to the “street” with open science workshops
→ Abstract, Slides

Teresa Müller 1, Street Science Community 2 , Bérénice Batut 1

  1. University of Freiburg, Freiburg, Germany
  2. https://streetscience.community

Speakers


Wednesday July 3, 2019 18:07 - 18:27
Greece

19:30

Conference Dinner
The GCC2019 Conference Dinner will be on Wednesday evening at Augustiner im Bankepeter (Schwarzwaldstraße 93, Freiburg), within walking distance (~ 30 minutes) from the conference center.  It is also easily reachable by public transport (tram line 1, direction Littenweiler,
stop Freiburg Maria-Hilf-Kirche) or car. See the B on the map at the end of the printed program or the digital map at https://bit.ly/gcc2019map.

There will be a walking group starting at 18.45 from the conference center.

Beer, Wine, and non-alcoholic drinks are free. Vegetarian and vegan food will be available. For any other dietary restrictions please contact Björn Grüning.

To attend the dinner you need to be registered for the conference dinner. Please ask at the registration desk if you are not sure if you are.




Wednesday July 3, 2019 19:30 - 19:45
Offsite
 
Thursday, July 4
 

08:00

Conference Desk Open
The conference desk will be open all day for conference checkin and questions.

Thursday July 4, 2019 08:00 - 19:15
Konzerthaus

08:59

Session 13:Outside the Genome & Community Track
Talks (invited, accepted and lightning) about diverse applications of Galaxy and community resources.

Moderators
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →

Thursday July 4, 2019 08:59 - 10:30
Germany

08:59

Session 13: Proteomics & Metabolomics & Late Breaking Track
Talks (invited, accepted and lightning) about proteomics and metabolomics research with Galaxy followed by late breaking lightning talks on a variety of topics.

Moderators
avatar for Melanie Föll

Melanie Föll

PhD student, Institute of Surgical Pathology Freiburg

Thursday July 4, 2019 08:59 - 10:30
Greece

09:00

Metaproteomics Powered By Metatranscriptomics: Towards a Multi-omic Functional Microbiome Analysis Within Galaxy
→ Abstract, Slides

Pratik Jagtap 1 , Subina Mehta 1 , Praveen Kumar 1 , Ray Sajulga 1 , Caleb Easterly 1 , Francesco Delogu 2 , Benoit Kunath 2 , Marie Crane 3 , Emma Leith 1 , James Johnson 1 , Thomas McGowan 1 , Bérénice Batut 4 , Phil Pope 2 , Magnus Arntzen 2 , Timothy Griffin 1

  1. University of Minnesota, Minneapolis, MN
  2. Faculty of Chemistry, Biotechnology and Food Science, NMBU, Ås, Norway
  3. Macalester College, Saint Paul, MN
  4. Bioinformatics Group, University of Freiburg, Freiburg, Germany

Speakers
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota



Thursday July 4, 2019 09:00 - 09:20
Greece

09:00

Invited Talk: Data visualisation by citizen science participants: the case of birds and bats monitoring schemes and Galaxy-E
→ Abstract, Slides

Yves Bas 1, Romain Lorrilière 1, Yvan Le Bras 1

  1. French National Museum of Natural History

Speakers
YB

Yves Bas

French National Museum of Natural History
avatar for Romain Lorrillière

Romain Lorrillière

French National Museum of Natural History



Thursday July 4, 2019 09:00 - 09:30
Germany

09:20

Interactive Galaxy Visualizations for Multi-omics Research
→ Abstract, Slides

Ray Sajulga 1, Praveen Kumar 1,2, Caleb Easterly 1, Subina Mehta 1, Thomas McGowan 3, James Johnson 3, Pratik Jagtap 1, Timothy J. Griffin 1

  1. Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, USA
  2. Bioinformatics and Computational Biology, University of Minnesota-Rochester, USA
  3. Minnesota Supercomputing Institute, University of Minnesota-Twin Cities, USA

Speakers
avatar for Ray Sajulga

Ray Sajulga

University of Minnesota



Thursday July 4, 2019 09:20 - 09:27
Greece

09:27

ProteoRE, a Galaxy-based platform for the annotation and the interpretation of proteomics data in biomedical research
→ Abstract, Slides

Florence Combes 1
, David Christiany 1,2, Nguyen Lien 1,2, Virginie Brun 1, Valentin Loux 2, Yves Vandenbrouck 1

  1. Univ Grenoble Alpes, CEA, INSERM, BGE U1038, F-38000, Grenoble, France
  2. Univ. Paris-Saclay, INRA, MAIAGE Unit, F-78352, Jouy-en-Josas, France

Speakers


Thursday July 4, 2019 09:27 - 09:47
Greece

09:30

Galaxy-Bricks a Tool for Data Literacy and Scientific Approach Education in the Context of Citizen Science
→ Abstract, Slides

Simon Bénateau 1
, Sébastien Turpin 1, Yvan Le Bras 2

  1. MNHN, CESCO, UMR 7204, 43 rue Buffon, 75005 Paris
  2. MNHN, PatriNat, UMS 2006, station marine de Concarneau, 29900 Concarneau

Speakers
avatar for Simon Bénateau

Simon Bénateau

Paris, French National Museum of Natural History



Thursday July 4, 2019 09:30 - 09:37
Germany

09:37

CITIZEN SCIENCE PROJECT in ECOLOGY with the GALAXY-E PLATFORM
→ Abstract, Slides

Yguel Benjamin 1
, Amosse Alan 1, Lebras Yvan 2

  1. Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, CP 135, 57 rue Cuvier 75005 Paris, France
  2. UMS 2006 Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle, Station marine de Concarneau, Place de la Croix, 29900 Concarneau.

Speakers


Thursday July 4, 2019 09:37 - 09:44
Germany

09:44

Galaxy-E project: 2019 news
→ Abstract, Slides

Yvan Le Bras 1
, Alan Amossé 1, Simon Bénateau 1, Benjamin Yguel 1

  1. French museum of natural history


Speakers
avatar for Yvan Le Bras

Yvan Le Bras

Research engineer, French National Museum of Natural History



Thursday July 4, 2019 09:44 - 10:04
Germany

09:47

Galaxy Wrapper for MaxQuant
→ Abstract, Slides

Damian Glätzer 1
, Melanie Föll 3, Bettina Warscheid 1,2, Oliver Schilling 3, Friedel Drepper 1,2

  1. Faculty of Biology; Biochemistry and Functional Proteomics - University of Freiburg
  2. Signalling Research Center CIBSS - University of Freiburg
  3. Institute of Surgical Pathology; University Medical Center; Faculty of Medicine - University of Freiburg

Speakers


Thursday July 4, 2019 09:47 - 09:54
Greece

09:54

Application of Halogen Bonding in Molecular and Drug Design Facilitated by a Galaxy Webserver
→ AbstractSlides

M. Zimmermann 1, M. Engelhardt 1, Frank M. Boeckler 1

  1. Lab for Molecular Design & Pharm. Biophysics, Chair of Medicinal Chemistry, Dept. of Pharmacy & Biochemistry, Eberhard Karls University, Tuebingen, Germany

Speakers
avatar for Frank M. Boeckler

Frank M. Boeckler

University Professor, Eberhard Karls Univerisitaet Tuebingen



Thursday July 4, 2019 09:54 - 10:14
Greece

10:04

The ChemicalToolBox - Computational Chemistry in Galaxy
→ Abstract, Slides

Simon Bray
, Björn Grüning Freiburg Galaxy Team, Bioinformatics Group, University of Freiburg

Speakers


Thursday July 4, 2019 10:04 - 10:11
Germany

10:11

Improved Reference Data Management in Galaxy: Towards a Plant Data Analysis Platform
→ Abstract, Slides

Ignacio Eguinoa 1,2, Frederik Coppens 1,2

  1. Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
  2. VIB Center for Plant Systems Biology, 9052 Ghent, Belgium

Speakers


Thursday July 4, 2019 10:11 - 10:18
Germany

10:14

Rootless Galaxy Docker, with Backup, for our Lab Intranet
Slides

Art Eschenlauer 1, Mark Esler 1, Tim Griffin 1, Adrian Hegeman 1

  1. University of Minnesota

Speakers
avatar for Arthur Eschenlauer

Arthur Eschenlauer

Postdoc, University of Minnesota
Poster Abstract: Untargeted metabolomics contrasts metabolome-scale analyses of samples without first identifying individual metabolites. Workflow4Metabolomics (W4m) provides a suite of Galaxy tools for untargeted metabolomics including univariate and multivariate statistical tools... Read More →



Thursday July 4, 2019 10:14 - 10:21
Greece

10:14

Late Breaking Lightning Talks
Late breaking lightning talks.  The call for these will go out shortly before GCC2019.

Thursday July 4, 2019 10:14 - 10:28
Greece

10:18

Use Galaxy, Right Now!
→ Abstract, Slides

Dave Clements 1, Helena Rasche 2, Martin Čech 3, Dannon Baker 1, and the 100s of Galaxy Community Members who support these platforms 4

  1. Galaxy Project, Johns Hopkins University, Baltimore, Maryland, United States
  2. Galaxy Project Europe, University of Freiburg, Freiburg, Germany
  3. Galaxy Project, Penn State University, State College, Pennsylvania, United States
  4. Galaxy Platform Directory, https://galaxyproject.org/use/

Speakers
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe
avatar for Dave Clements

Dave Clements

Training and Outreach Coordinator, Galaxy Project, Johns Hopkins University



Thursday July 4, 2019 10:18 - 10:25
Germany

10:21

10:25

Galaxy Publication Library
→ Abstract, Slides

Dave Clements 1, Dannon Baker 1, and 35,000+ Authors of Galaxy Related Publications 2

  1. Galaxy Project, Johns Hopkins University
  2. Galaxy Publication Library, https://www.zotero.org/groups/1732893/galaxy

Speakers
avatar for Dave Clements

Dave Clements

Training and Outreach Coordinator, Galaxy Project, Johns Hopkins University



Thursday July 4, 2019 10:25 - 10:32
Germany

10:30

10:59

Session 14: Proteomics & Metabolomics
Talks (accepted and lightning) about proteomics and metabolomics applications in Galaxy.

Speakers
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota


Thursday July 4, 2019 10:59 - 12:00
Greece

10:59

Session 14: Variation, Metagenomics & Assembly Track
Talks (invited, accepted and lightning) about variation, metagenomics, and assembly research with Galaxy.

Moderators
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security

Thursday July 4, 2019 10:59 - 12:00
Germany

11:00

Analysing and organising large-scale metabolome annotation studies with Django, ISA and Galaxy
→ Abstract, Slides

Thomas N. Lawson 1, Martin R. Jones 1, Mark R. Viant 1,2, Ralf J. M. Weber 1,2

  1. School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
  2. Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT, UK

Speakers
TN

Thomas N. Lawson

Post doc, University of Birmingham



Thursday July 4, 2019 11:00 - 11:20
Greece

11:00

The IRIDA Platform for Microbial Genomics
→ Abstract, Slides

Aaron Petkau 1, Thomas Matthews 1, Franklin Bristow 2, Josh Adam 1, Jeff Thiessen 1, Sukhdeep Sidhu 1, Peter Kruczkiewicz 1, Emma Griffiths 3, Damion Dooley 4, Dan Fornika 4, Geoff Winsor 3, Amogelang R. Raphenya 5, Morag Graham 1,2, The IRIDA consortium, Eduardo Taboada 1, Andrew G. McArthur 5, Robert Beiko 6, William Hsiao 4, Fiona Brinkman 3, Gary Van Domselaar 1,2

  1. Public Health Agency of Canada, Winnipeg, Canada
  2. University of Manitoba, Winnipeg, Canada
  3. Simon Fraser University, Burnaby, Canada
  4. BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
  5. McMaster University, Hamilton, Canada
  6. Dalhousie University, Halifax, Canada

Speakers
avatar for Aaron Petkau

Aaron Petkau

Bioinformatician, Public Health Agency of Canada



Thursday July 4, 2019 11:00 - 11:20
Germany

11:20

Combat-tb Workbench, A Customizable Platform For Variant Discovery And Annotation, Phylogeny Construction And Variant Prioritisation
→ Abstract, Slides

Ziphozakhe Mashologu , Peter van Heusden, Thoba Lose, Alan Christoffels

  1. South African Medical Research Council Bioinformatics Unit
  2. South African National Bioinformatics Institute
  3. University of the Western Cape.

Speakers
avatar for Ziphozakhe Mashologu

Ziphozakhe Mashologu

Developer, UWC - South African National Bioinformatics Institute
South African National Bioinformatics Institute (SANBI)



Thursday July 4, 2019 11:20 - 11:27
Germany

11:20

Reproducible and accessible analysis of spatially resolved proteomics and metabolomics data
→ Abstract, Slides

Melanie Christine Föll 1,2
, Lennart Moritz 1, Thomas Wollmann 3, Maren Nicole Stillger 1,2,4, Niklas Vockert 3, Martin Werner 1,5,6,7, Peter Bronsert 1,5,6,7, Karl Rohr 3, Björn Andreas Grüning 8, Oliver Schilling 1,5,7

  1. Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a 79106 Freiburg, Germany
  2. Faculty of Biology, University of Freiburg, Schänzlestraße 1 79104 Freiburg, Germany
  3. Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Im Neuenheimer Feld 267 69120 Heidelberg, Germany
  4. Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Straße 17 79104 Freiburg, Germany
  5. Faculty of Medicine - University of Freiburg, Germany
  6. Tumorbank Comprehensive Cancer Center Freiburg, Medical Center – University of Freiburg, Germany
  7. German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany
  8. Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106 79110 Freiburg, Germany

Speakers
avatar for Melanie Föll

Melanie Föll

PhD student, Institute of Surgical Pathology Freiburg



Thursday July 4, 2019 11:20 - 11:40
Greece

11:27

High throughput HIV next generation sequence analysis in Galaxy
Abstract, Slides

Dave Bouvier 2, Stephen Shank 1, Ryan Velazquez 1, Steven Weaver 1, Anton Nekrutenko 2, Sergei L Kosakovsky Pond 1

  1. Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia PA 19122
  2. Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College PA, 16802
Findable, accessible, interoperable, and reusable tools for HIV next generation sequencing analyses have not yet become sufficiently adopted by the field. To lower adoption barriers, we have extended the popular and mature genome analytics platform Galaxy (usegalaxy.org) with a collection of HIV-centric tools. These tools (currently over 40 such tools ​​are available at galaxy.hyphy.org) enable tasks that are common to HIV-1 NGS workflows; quality control, read mapping, error correction, haplotype inference, multiple sequence alignment, phylogeny inference, molecular epidemiology, and selection analyses. Coupled with the plethora of other tools available within the Galaxy framework, this enables rapid development, deployment, sharing, and execution of complex end-to-end analytic workflows.

Speakers
avatar for Dave Bouvier

Dave Bouvier

Computational Scientist, Galaxy Project, Penn State University



Thursday July 4, 2019 11:27 - 11:47
Germany

11:40

Workflow4Metabolomics: an international computing infrastructure for Metabolomics
→ Abstract, Slides

Mélanie Pétéra 1, Romain Dallet 2
, Christophe Duperier 1, Franck Giacomoni 1, Yann Guitton 3, Jean-François Martin 4, Pierrick Roger-Mele 5, Julien Saint-Vanne 3,6, Etienne Thévenot 5, Marie Tremblay-Franco 4, Gildas Le Corguillé 6

  1. INRA, UMR 1019, PFEM, 63122, Saint Genes Champanelle, France
  2. Institut Français de Bioinformatique, CNRS UMS 3601, rue John Von Neumann, 91403 Orsay, France
  3. LUNAM Université, Oniris, Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), Nantes, F-44307, France
  4. Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Univ. Toulouse 3 Paul Sabatier, 31027 Toulouse, France
  5. CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence (LADIS), MetaboHUB, F-91191 Gif-sur-Yvette, France
  6. UPMC, CNRS, FR2424, ABiMS, Station Biologique, 29680, Roscoff, France

Speakers
RD

Romain Dallet

ABiMS, IFB Core - FR2424 - CNRS - Station Biologique de Roscoff, France
avatar for Gildas Le Corguillé

Gildas Le Corguillé

CNRS-UPMC - Station Biologique de Roscoff - ABiMS



Thursday July 4, 2019 11:40 - 12:00
Greece

11:47

NanoGalaxy: A Galaxy toolkit and workflows for long-read sequencing
→ Abstract, Slides

Willem de Koning 1, Milad Miladi 2, Saskia Hiltemann 1, Bjoern Gruening 2

  1. Erasmus MC, University Medical Center Rotterdam
  2. University of Freiburg, Albert-Ludwigs-Universität Freiburg

Speakers


Thursday July 4, 2019 11:47 - 11:54
Germany

11:54

MITOLINK: An integrated Web-based Workflow System to Evaluate Genotype-Phenotype Correlations in Human Mitochondrial Diseases
→ Abstract, Slides

Neeraj K Rajput 1, Vipin Singh 2, Amol Narwade 1, Anshu Bhardwaj 1,3

  1. CSIR-Institute of Microbial Technology, India
  2. IBENS, ENS, Paris, France
  3. Interdisciplinary Research Center (CRI), Paris, France

Speakers
avatar for Anshu Bhardwaj

Anshu Bhardwaj

Long term Fellow, Senior Scientist, Interdisciplinary Research Center (CRI) and CSIR-Institute of Microbial Technology
I did Masters in Biotech followed by Ph.D. in Life Sciences (Comp bio) at Centre for Cellular & Molecular Biology, Hyderabad, India, in 2008. I then served as one of the founding PIs for Open Source Drug Discovery Project where I conceived & developed protocols for crowdsourcing drug... Read More →



Thursday July 4, 2019 11:54 - 12:01
Germany

12:00

12:15

Arts & Crafts
GCC sure can be overwhelming sometimes! This BoF is a quiet place to do some stress-free, science related, arts and crafts.

Interested?
Sign in / Create an account, and add yourself as a participant (or just show up!).

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Speakers
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe


Thursday July 4, 2019 12:15 - 13:20
Czechia

12:15

Birds-of-a-Feather (BoFs), with Lunch
Birds-of-a-feather are informal gatherings or participants with a shared interest. Anyone can organize a BoF session.

BoFs with Lunch are held during the lunch hour.  A projector and screen are available during these BoFs.

BoFs offered during this flocking:

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Thursday July 4, 2019 12:15 - 13:20
Konzerthaus

12:15

BoF: Metabolomics: Tools, Resources, and Needs
The aim of this BoF is to identify resources and needs of the Metabolomics Galaxy community. Primarily we will discuss tools, workflows, the Galaxy Training Network (GTN), and metabolomics Galaxy instances. Hopefully discussion will lead to useful hackathon projects, like adding to the Metabolomics GTN.

Resources identified during this BoF will be made public and added to metabolomics.usegalaxy.eu by the organizers (and anyone else interested in contributing). The purpose of this community driven Galaxy instance is to organize and promote metabolomics resources, including other public metabolomics Galaxiess.

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Arthur Eschenlauer

Arthur Eschenlauer

Postdoc, University of Minnesota
Poster Abstract: Untargeted metabolomics contrasts metabolome-scale analyses of samples without first identifying individual metabolites. Workflow4Metabolomics (W4m) provides a suite of Galaxy tools for untargeted metabolomics including univariate and multivariate statistical tools... Read More →

Thursday July 4, 2019 12:15 - 13:20
Italy

12:15

12:15

Galaxy containers BoF
Interested in containerizing Galaxy for deployment, maintenance, and portability? We'll talk about use cases and approaches to software containerization that are suitable for Galaxy. We are likely to cover topics such as container architecture, extensibility, interoperability, and scalability.

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Enis Afgan

Enis Afgan

Galaxy Project, Johns Hopkins University
Everything 'Galaxy on the Cloud' related!
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris
avatar for Nuwan Goonasekera

Nuwan Goonasekera

Melbourne Bioinformatics / University of Melbourne
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg
avatar for Pablo Moreno

Pablo Moreno

EMBL-EBI


Thursday July 4, 2019 12:15 - 13:20
France

13:20

15: Training Session
Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

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

13:20

Assembly, annotation and analysis of bacterial genomes
Assembly and annotation of bacterial genomes

Prerequisites

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

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

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

Anna Syme

Bioinformatician, Royal Botanic Gardens Melbourne
Plant genomes! 


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

13:20

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
avatar for Simon Gladman

Simon Gladman

Melbourne Bioinformatics, The University of Melbourne
avatar for Nate Coraor

Nate Coraor

Galaxy Project, Penn State University
avatar for Gianmauro Cuccuru

Gianmauro Cuccuru

University of Freiburg
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe


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

13:20

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
avatar for Yvan Le Bras

Yvan Le Bras

Research engineer, French National Museum of Natural History
avatar for Simon Bénateau

Simon Bénateau

Paris, French National Museum of Natural History


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

13:20

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
avatar for Alireza Khanteymoori

Alireza Khanteymoori

Postdoc Researcher, University of Freiburg
avatar for Anup Kumar

Anup Kumar

PhD candidate, University of Freiburg



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

13:20

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
RW

Ralf Weber

University of Birmingham
avatar for Gildas Le Corguillé

Gildas Le Corguillé

CNRS-UPMC - Station Biologique de Roscoff - ABiMS
TN

Thomas N. Lawson

Post doc, University of Birmingham


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

13:20

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
MF

Matthias Fahrner

PhD student, University of Freiburg
MS

Maren Stillger

University of Freiburg
avatar for Melanie Föll

Melanie Föll

PhD student, Institute of Surgical Pathology Freiburg



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

14:50

16: Poster, Demo, and Sponsor Session
Posters and demos will be presented on all three days, concurrently with the sponsor exhibits.

Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 03 C: Galaxy in fields, gardens and greenhouses for better seeds.
→ Abstract, Poster

Michael Faubladier 1, Frederic Sapet 2 and Camille Segard 1

  1. Bioinformatics, Limagrain Vegetables Seeds.Chappes, France
  2. Traits & Technologies, Biostatistics and Bioinformatics Team, Limagrain Field Seeds. Chappes,France

Speakers
avatar for Michael Faubladier

Michael Faubladier

Bioinformatician, Limagrain
avatar for Camille Segard

Camille Segard

Bioinformatician, Limagrain
avatar for Frederic Sapet

Frederic Sapet

Bioinformatics Research Engineer, Limagrain



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

14:50

Poster 09 C: Development and Deployment of a Workflow for the Genomic Analysis of Campylobacter Jejuni
→ Abstract, Poster

José Antonio Barbero Aparicio 1, José Francisco Díez Pastor 1, Beatriz Melero Gil 1, César Ignacio
García Osorio 2

  1. University of Burgos, Spain. Civil Engineering Department. Computer Languages and Systems Area.
  2. University of Burgos, Spain. Department of Biotechnology and Food Science. Food Science Area.



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 12 C: Reproducible and accessible analysis of spatially resolved proteomics and metabolomics data
→ AbstractPoster

Melanie Christine Föll 1,2, Lennart Moritz 1, Thomas Wollmann 3, Maren Nicole Stillger 1,2,4, Niklas Vockert 3, Martin Werner 1,5,6,7, Peter Bronsert 1,5,6,7, Karl Rohr 3, Björn Andreas Grüning 8, Oliver Schilling 1,5,7

  1. Institute of Surgical Pathology, Medical Center –University of Freiburg, Breisacher Straße 115a 79106 Freiburg, Germany
  2. Faculty of Biology, University of Freiburg, Schänzlestraße 1 79104 Freiburg, Germany
  3. Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Im Neuenheimer Feld 267 69120 Heidelberg, Germany
  4. Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Straße 17 79104 Freiburg, Germany
  5. Faculty of Medicine -University of Freiburg, Germany
  6. Tumorbank Comprehensive Cancer Center Freiburg, Medical Center –University of Freiburg, Germany
  7. German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany
  8. Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106 79110 Freiburg, Germany

Speakers
avatar for Melanie Föll

Melanie Föll

PhD student, Institute of Surgical Pathology Freiburg



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 15 C: A new Galaxy Wrapper for MaxQuant
→ Abstract, Poster

Damian Glätzer 1, Melanie Föll 3, Bettina Warscheid 1,2, Oliver Schilling 3, Friedel Drepper1,2

  1. Faculty of Biology; Biochemistry and Functional Proteomics - University of Freiburg
  2. Signaling Research Center CIBSS - University of Freiburg
  3. Institute of Surgical Pathology; University Medical Center; Faculty ofMedicine - University of Freiburg

Speakers


Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 18 C: Applying new model for predicting effects of gene variants in epigenetic regulators within Galaxy environment
Abstract, Poster

Tamara Drljača, Vladimir Perović, Radoslav Davidović, Nevena Veljković and Branislava Gemović

Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade, Serbia

Speakers
TD

Tamara Drljača

Research Trainee, Institute of Nuclear Sciences VINCA
PhD student in Laboratory for Bioinformatics and Computational Chemistry, I mainly focus on genomic data analysis. Recipient of the GCC2019 Fellowship.



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 21 C: Improved Reference Data Management in Galaxy: Towards a Plant Data Analysis Platform
→ AbstractPoster (doi: 10.7490/f1000research.1117086..1)

Ignacio Eguinoa 1,2, Frederik Coppens 1,2

  1. Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
  2. VIB Center for Plant Systems Biology, 9052 Ghent, Belgium

Speakers


Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 24: Galaxy In A Large Scale Production Environment
Sascha Kastens 1, Yadhu Kumar 1, Matthias Neder 1

  1. Eurofins Genomics Europe Sequencing GmbH

Speakers
SK

Sascha Kastens

Bioinformation, Eurofins Genomics Europe Sequencing GmbH



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 27 C: Galaxy on Site: Flexibility without Tears
→ AbstractPoster

Art Eschenlauer 1,2, Mark Esler 2, Tim Griffin 1, Adrian Hegeman 2

  1. Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities.
  2. Department of Horticultural Science, University of Minnesota—Twin Cities

Speakers
avatar for Arthur Eschenlauer

Arthur Eschenlauer

Postdoc, University of Minnesota
Poster Abstract: Untargeted metabolomics contrasts metabolome-scale analyses of samples without first identifying individual metabolites. Workflow4Metabolomics (W4m) provides a suite of Galaxy tools for untargeted metabolomics including univariate and multivariate statistical tools... Read More →



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 30 C: Towards a platform for genomics medicine
→ Abstract, Poster

Wolfgang Maier and Björn Grüning

Speakers
avatar for Wolfgang Maier

Wolfgang Maier

Member of the Galaxy Europe team, University of Freiburg
University of Freiburg



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 33 C: HiCExplorer 3: A toolbox for Hi-C data analysis
→ Abstract, Poster

Joachim Wolff 1,  Leily Rabbani 2,  Gautier Richard 2 , Thomas Manke 2,  Asifa Akhtar 2, Rolf Backofen 1, Fidel Ramirez 3 , BjörnGrüning 1

  1. Bioinformatics Lab, Albert-Ludwigs-Universität Freiburg im Breisgau, Germany
  2. Max-Planck-Institut für Immunbiologie und Epigenetik, Freiburg im Breisgau, Germany
  3. Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß,Germany

Speakers
JW

Joachim Wolff

Albert-Ludwigs-University Freiburg



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 36 C: EDAM: the ontology of bioinformatics operations, types of data, topics, and data formats (2019 update)
Matúš Kalaš, Hervé Ménager, Veit Schwämmle, Jon Ison and Edam Contributors

Speakers
avatar for Matúš Kalaš

Matúš Kalaš

University of Bergen
Open science & society, EDAM ontology, ELIXIR Norway, Bio.Tools, BioXSD|GTrack



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 39 C: Deployment of Genome Databases for Algae Using Galaxy Genome Annotation
→ AbstractPoster

Loraine Brillet-Guéguen 1,2, Delphine Nègre 2, Anthony Bretaudeau 3, Matéo Boudet 4, Helena Rasche 5, Olivier Collin 4, Erwan Corre 2

  1. Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France. Email: loraine.gueguen@sb-roscoff.fr
  2. CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680, Roscoff, France
  3. INRA, UMR IGEPP, BIPAA/GenOuest, Campus Beaulieu, Rennes, France
  4. Plate-forme GenOuest, Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes,France
  5. Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 42 C: Experience of Galaxy training at a biomedical institute
→ AbstractPoster

Maria Doyle 1 and Richard Lupat 2

  1. Research Computing Facility, Peter MacCallum Cancer Centre, Australia
  2. Bioinformatics Core, Peter MacCallum Cancer Centre, Australia

Speakers
MD

Maria Doyle

Application and Training Specialist, Peter MacCallum Cancer Centre



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 45 C: Galaxy-Bricks a Tool for Data Literacy and Scientific Approach Education in the Context of Citizen Science
Simon Bénateau, Sébastien Turpin and Yvan Le Bras

Speakers
avatar for Simon Bénateau

Simon Bénateau

Paris, French National Museum of Natural History



Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 48 C: The ChemicalToolBox - Computational Chemistry in Galaxy
→ Abstract, Poster

Simon Bray and Björn Grüning

Freiburg Galaxy Team, Bioinformatics Group, University of Freibu

Speakers

CTB pdf

Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 51 C: How Usable is Galaxy? A Usability Evaluation of Galaxy
→ AbstractPoster (doi: 10.7490/f1000research.1116995.1)

Daniel Brand 1, Ngoc-Huy Truong 1, Rul von Stülpnagel 1

  1. Center for Cognitive Science, University of Freiburg

Speakers


Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

14:50

Poster 54 C: TrackFind: FAIR Search of Genomic Tracks
→ Abstract, Poster

Dmytro Titov 1, Sveinung Gundersen 1, Radmila Kompova 1, Salvador Capella-Gutierrez 2, Finn
Drabløs 3, José M. Fernández 2 , Kieron Taylor 4, Daniel Zerbino 4, Eivind Hovig 1,5

  1. Center for Bioinformatics, University of Oslo (UiO), Norway
  2. INB Coordination Node / ELIXIR ES, Barcelona Supercomputing Center, Spain
  3. Norwegian University of Science and Technology (NTNU), Norway
  4. European Molecular Biology Laboratory, European Bioinformatics Institute, United Kingdom
  5. Department of Tumor biology, Institute for Cancer Research, Oslo University Hospital (OUH), Norway

Speakers


Thursday July 4, 2019 14:50 - 15:50
Konzerthaus

15:00

Demo 10 C: Interactive Galaxy Visualizations for Multi-omics Research
Ray Sajulga, Praveen Kumar, Caleb Easterly, Subina Mehta, Thomas McGowan, James Johnson, Pratik Jagtap and Timothy J. Griffin

Speakers
avatar for Ray Sajulga

Ray Sajulga

University of Minnesota



Thursday July 4, 2019 15:00 - 15:20
Spain

15:00

Demo 12 C: Visual Refinement of Genome Annotations with Apollo in a Community Environment
Nathan Dunn, Deepak Unni, Colin Diesh, Helena Rasche, Anthony Bretaudeau, Nomi Harris and Ian Holmes

Speakers
avatar for Nathan Dunn

Nathan Dunn

Software Developer, UC Berkeley
I work on the Apollo project, but also have worked on various other projects such as the Monarch Initiative, the (cross-species ontology relations between phenotypes and genomics), the Alliance of Genome resources (major mods curating data), the Gene Ontology, and the Xena Variant... Read More →



Thursday July 4, 2019 15:00 - 15:20
France

15:00

Demo 14 C: Galaxy on Kubernetes
Enis Afgan, Nuwan Goonasekera, Sergey Golitsynskiy and Alexandru Mahmoud

Speakers
avatar for Sergey Golitsynskiy

Sergey Golitsynskiy

software engineer, Johns Hopkins University
avatar for Enis Afgan

Enis Afgan

Galaxy Project, Johns Hopkins University
Everything 'Galaxy on the Cloud' related!
avatar for Alexandru Mahmoud

Alexandru Mahmoud

Galaxy Team, Johns Hopkins University
avatar for Nuwan Goonasekera

Nuwan Goonasekera

Melbourne Bioinformatics / University of Melbourne



Thursday July 4, 2019 15:00 - 15:20
Belgium

15:25

Demo 11 C: NanoGalaxy: A Galaxy toolkit and workflows for long-read sequencing
Willem de Koning, Milad Miladi, Saskia Hiltemann and Bjoern Gruening

Speakers


Thursday July 4, 2019 15:25 - 15:45
Spain

15:25

Demo 13 C: The IRIDA Platform for Microbial Genomics
Aaron Petkau, Thomas Matthews, Franklin Bristow, Josh Adam, Jeff Thiessen, Sukhdeep Sidhu, Peter Kruczkiewicz, Emma Griffiths, Damion Dooley, Dan Fornika, Geoff Winsor, Amogelang Raphenya, Morag Graham, Eduardo Taboada, Andrew McArthur, Robert Beiko, William Hsiao, Fiona Brinkman and Gary Van Domselaar

Speakers
avatar for Aaron Petkau

Aaron Petkau

Bioinformatician, Public Health Agency of Canada



Thursday July 4, 2019 15:25 - 15:45
France

15:50

17: Training Session
Multi-track training, covering full spectrum of bioinformatics tool use, development, and deployment

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

15:50

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
avatar for Kjetil Klepper

Kjetil Klepper

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



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

15:50

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

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

Speakers
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security


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

15:50

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
avatar for Yo Yehudi

Yo Yehudi

Software Developer, InterMine (University of Cambridge)
Integrated genomic data (InterMine)


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

15:50

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
MF

Matthias Fahrner

PhD student, University of Freiburg
MS

Maren Stillger

University of Freiburg
avatar for Melanie Föll

Melanie Föll

PhD student, Institute of Surgical Pathology Freiburg



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

15:50

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
RW

Ralf Weber

University of Birmingham
TN

Thomas N. Lawson

Post doc, University of Birmingham
avatar for Gildas Le Corguillé

Gildas Le Corguillé

CNRS-UPMC - Station Biologique de Roscoff - ABiMS


Thursday July 4, 2019 15:50 - 17:20
France

15:50

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

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

Speakers
avatar for Simon Bénateau

Simon Bénateau

Paris, French National Museum of Natural History
avatar for Yvan Le Bras

Yvan Le Bras

Research engineer, French National Museum of Natural History


Thursday July 4, 2019 15:50 - 17:20
Spain

17:29

Session 18: Closing Plenary
The final session of GCC2019.

Moderators
Thursday July 4, 2019 17:29 - 18:30
Greece

17:30

Invited Talk: UseGalaxy: Elucidating chromatin biology of mouse cardiomyocytes
→ Abstract, Slides

Stephan Nothjunge 1,3
, Björn Grüning 2, Joachim Wolff 2, Theresa Kehl 1, Martin Schwaderer 1 , Lutz Hein 1 , Ralf Gilsbach 1

  1. Institute for Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Germany
  2. Department of Computer Science, University of Freiburg, Germany
  3. present address: Friedrich-Miescher-Institute for Biomedical Research (FMI), Basel, Switzerland

Speakers
avatar for Stephan Nothjunge

Stephan Nothjunge

PostDoc, Friedrich Miescher Institute for Biomedical Research



Thursday July 4, 2019 17:30 - 18:00
Greece

18:00

Galaxy and Training: 2019 updates from the Galaxy Training Network
→ Abstract, Slides

Bérénice Batut 1, Saskia Hiltemann 2, Helena Rasche 1, Subina Mehta 3, Pratik Jagtap 3, Praveen Kumar 3, Timothy Griffin 3, Dave Clements 4, over 100 other GTN contributors 5, Björn Grüning 1

  1. University of Freiburg, Freiburg, Germany
  2. Erasmus Medical Center, The Hague, Netherlands
  3. Galaxy-P Project, University of Minnesota, United States
  4. Galaxy Project, Johns Hopkins University, United States
  5. https://training.galaxyproject.org/training-material/hall-of-fame

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →



Thursday July 4, 2019 18:00 - 18:20
Greece

18:20

Closing
→ Slides



Speakers
avatar for Dave Clements

Dave Clements

Training and Outreach Coordinator, Galaxy Project, Johns Hopkins University
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg
avatar for Anika Erxleben

Anika Erxleben

PostDoc, University of Freiburg



Thursday July 4, 2019 18:20 - 18:30
Greece

19:00

BIKE - Lets Do It! : BoF for Galaxy Bikers (Bicycling).
  1. Meet at the entrance of Konzert Haus at 19:00 on 4th of July.
  2.  Find a bike (example Frelo an App). 
  3. Bike for a little more than an hour. 
  4. Return back to Konzert Haus (or your destination). 
  5. Depending on interest we can all meet for a beer/dinner later in the day.

Interested? Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Melanie Föll

Melanie Föll

PhD student, Institute of Surgical Pathology Freiburg
avatar for Pratik Jagtap

Pratik Jagtap

Research assistant Professor, University of Minnesota
University of Minnesota
avatar for Magnus Palmsblad

Magnus Palmsblad

Associate Professor/Group Leader, Leiden University Medical Center
Analytical chemistry, mass spectrometry, proteomics, metabolomics, text mining, data integration, ontologies

Thursday July 4, 2019 19:00 - 20:30
Offsite

19:00

Galaxy Runners: Thursday Edition
Do you like running? We will take you on a 12km round through Freiburg and along the Dreisam. We will meet at 19:00 in front of the Konzerthaus.
Like to run less? At Tuesday, there will be a 6km round offered.

Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Moderators
avatar for Florian Eggenhofer

Florian Eggenhofer

Postdoc, University of Freiburg (ALU)
University of Freiburg (ALU)
avatar for Anika Erxleben

Anika Erxleben

PostDoc, University of Freiburg

Thursday July 4, 2019 19:00 - 20:30
Offsite

19:00

Birds-of-a-Feather (BoFs), with Your Dinner!
Birds-of-a-feather are informal gatherings or participants with a shared interest. Anyone can organize a BoF session.

BoFs with Your Dinner are held offsite, in a nearby restaurant or other location, that the BoF organizer is responsible for choosing.  There will not be any A/V support during these BoFs.

BoFs offered during this flocking:


Interested?
Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Thursday July 4, 2019 19:00 - 21:00
Offsite

19:00

Intergalactic Utilities Commission (IUC) BoF
The Intergalactic Utilities Commission (IUC) was established in 2012 to enable the pervasive use of the main Galaxy Tool Shed by ensuring the repositories available include contents that are functionally correct and optimized for installation into local Galaxies. When appropriate, the group provides guidance to Galaxy tool developers so that they can improve the quality of their repositories. Maintains a set of high quality Galaxy tools in the GitHub repository. This repo serves as an excellent example and inspiration to all Galaxy tool developers. Cultivates and shares the Galaxy tool development best practices document. Provides support to tool developers on a public Gitter channel.
Preliminary agenda: https://github.com/galaxyproject/tools-iuc/issues/2470

Interested?Sign in / Create an account, and add yourself as a participant.

Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...


We are meeting at the Seapark-Beergarden: https://goo.gl/maps/tjn8M8LaGTEbpZV1A

Speakers
avatar for Björn Grüning

Björn Grüning

University of Freiburg
University of Freiburg
avatar for Marius van den Beek

Marius van den Beek

Institut Curie, Paris
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute
avatar for Saskia Hiltemann

Saskia Hiltemann

Erasmus MC
Metagenomics, Training materials, board games, CTF & security
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →
avatar for Daniel Blankenberg

Daniel Blankenberg

Assistant Professor, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University
avatar for Helena Rasche

Helena Rasche

System Administrator, Galaxy Europe



Thursday July 4, 2019 19:00 - 21:00
Offsite

19:00

The Freiburg City Tour BoF!
Limited Capacity filling up

This BoF will offer a guided Freiburg City tour. It will last for ~1h and 30min and is open for 30 people.  Meet in front of the Konzerthaus.

There is another Freiburg City Tour BoF on Tuesday evening.

Interested?
Sign in / Create an account, and add yourself as a participant. Space is limited.
Please note that adding your name here is considered a firm commitment to attend.


Interested in proposing another idea for a BoF?
Submit your proposal now.  See the list of already scheduled BoFs for inspiration...

Thursday July 4, 2019 19:00 - 21:00
Offsite
 
Friday, July 5
 

08:00

Conference Desk Open
The conference desk will be open all day for CollaborationFest:Core checkin and questions.

Friday July 5, 2019 08:00 - 19:15
Konzerthaus

09:00

CollaborationFest: Core
This two day event will gather community members who are interested in contributing to Galaxy's code base, available tool set, documentation, training materials, and anywhere else that expands the Galaxy ecosystem.

CoFest participants will coalesce around shared interests and address common challenges related to those interests. These clusters form before, at the beginning of, and throughout CollaborationFest. These clusters will be fluid and highly interactive with each other. These groups and clusters will be fluid and highly interactive with each other. There will be a joint gathering of all communities at least once a day.

This event aims to expand the contibutor community as well as the Galaxy ecosystem.

Friday July 5, 2019 09:00 - 19:00
Konzerthaus
 
Saturday, July 6
 

08:00

Conference Desk Open
The conference desk will be open all day for CollaborationFest questions.

Saturday July 6, 2019 08:00 - 19:15
Konzerthaus

09:00

CollaborationFest: Core
This two day event will gather community members who are interested in contributing to Galaxy's code base, available tool set, documentation, training materials, and anywhere else that expands the Galaxy ecosystem.

CoFest participants will coalesce around shared interests and address common challenges related to those interests. These clusters form before, at the beginning of, and throughout CollaborationFest. These clusters will be fluid and highly interactive with each other. These groups and clusters will be fluid and highly interactive with each other. There will be a joint gathering of all communities at least once a day.

This event aims to expand the contibutor community as well as the Galaxy ecosystem.

Saturday July 6, 2019 09:00 - 19:00
Konzerthaus
 
Sunday, July 7
 

08:00

Conference Desk Open
The conference desk will be open all day for CollaborationFest questions.

Sunday July 7, 2019 08:00 - 19:15
University of Freiburg Compute Center

09:00

CollaborationFest: Encore
The first two days, CollaborationFest: Core emphasize collaboration and learning. The next two days, CollaborationFest: Encore lean heavily towards collaboration (although trust us, organizers won't stop you from learning either). We expect CollaborationFest: Encore to be a smaller group of contributors.

It will be at the computing center of the University of Freiburg:

Rechenzentrum der Universität Freiburg
Hermann-Herder-Str.10
79104 Freiburg

Sunday July 7, 2019 09:00 - 19:00
University of Freiburg Compute Center
 
Monday, July 8
 

08:00

Conference Desk Open
The conference desk will be open for CollaborationFest questions.

Monday July 8, 2019 08:00 - Wednesday August 7, 2019 12:00
University of Freiburg Compute Center

09:00

CollaborationFest: Encore
The first two days, CollaborationFest: Core emphasize collaboration and learning. The next two days, CollaborationFest: Encore lean heavily towards collaboration (although, trust us, organizers won't stop you from learning either). We expect CollaborationFest: Encore to be a smaller group of contributors.

Monday July 8, 2019 09:00 - 19:00
University of Freiburg Compute Center