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GCC2019
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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!
Schedule
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A. Training
All
Admin / Dev
Diverse Communities
Epigenetics
Introduction / General
Metagenomics / Assembly
Proteomics / Metabolomics
Transciptomics / Genome Variation
B. Talks: Admin / Dev
All
Session 2
Session 7
Session 8
B. Talks: Epigenetics
All
Session 6
B. Talks: General
B. Talks: Outside the Genome & Community
All
Session 13
Session 2
Session 6
B. Talks: Proteomics / Metabolomics
All
Session 13
Session 14
B. Talks: Transcriptomics / Genomics
All
Session 7
Session 8
B. Talks: Variation / Metagenomics / Assembly
All
Session 14
C. Posters / Demos / Sponsors
All
Demos
Posters
Sponsors
D. Break / Social / Networking / Meal
All
BoFs
Break
Demos
Meal
Sponsors
E. Help
F. CollaborationFest: Core
G. CollaborationFest: Encore
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Filter sessions
Monday
, July 1
Germany
10:00 •
Introduction to Using Galaxy (Galaxy 101)
13:00 •
Beyond the Intro: Further Adventures in Using Galaxy
15:30 •
Analyzing Large / Complex Experimental Designs with Galaxy
Greece
10:00 •
Introduction to Galaxy Administration I
13:00 •
Introduction to Galaxy Administration II
15:30 •
Introduction to Galaxy Administration III
Italy
09:00 •
Nanopore Loading Zone!
09:00 •
Beer Decoded, Here and Now!
Konzerthaus
09:00 •
Conference Desk Open
12:00 •
Lunch
15:00 •
Break
Offsite
18:00 •
Birds-of-a-Feather (BoFs), with Your Dinner!
18:00 •
Genome Annotation BoF
18:00 •
BOF: Single Cell
18:00 •
The Computational Chemistry BoF
Tuesday
, July 2
Belgium
13:20 •
16S analysis with mothur
15:50 •
Metatranscriptomics and multi-omics functional microbiome analysis
Czechia
12:15 •
Arts & Crafts
France
12:15 •
BoF: Remote computation with Pulsar
13:20 •
EWAS data analysis for population epigenetics integrated into Galaxy - Epigenetics
15:00 •
Demo 03 A: Analysing and organising large-scale metabolome annotation studies with Django, ISA and Galaxy
15:25 •
Demo 04 A: GalaxyCloudRunner: Streamlined Cloud Bursting for Galaxy
Germany
10:59 •
Session 2: Outside the Genome & Community Track
11:00 •
Galaxy Computational Chemistry
11:20 •
Climate Analysis with Galaxy
11:40 •
Galaxy Image Analysis: Web-based microscopy image analysis and cellular phenotyping
13:20 •
Quality control of HTS data
15:50 •
Machine Learning with Galaxy - Predict age from RNA-seq dataset
17:29 •
Session 6: Outside the Genome & Community Track
17:30 •
Using Galaxy for Creation and Execution of Text Mining Workflows in the OpenMinTeD platform
17:50 •
To Better Benefit from Shared Tasks in Biomedical Text Mining
17:57 •
The LAPPS Grid/Galaxy Platform for Mining Scientific Publications
18:17 •
Infrastructure for Healthier Living: Galaxy at Quadram Institute Bioscience
18:24 •
How Usable is Galaxy? A Usability Evaluation of Galaxy
Greece
08:59 •
Session 1: Opening Plenary
09:00 •
Welcome
09:10 •
Invited Talk: Evolution of X chromosome recognition during Drosophila Dosage Compensation
09:40 •
Galaxy Australia – inside the national vision of a data commons
10:00 •
A Machine Learning Tool Suite for Galaxy
10:20 •
An Update on Galaxy Workflows: More Accessible, Expressive, Robust, and Scalable
10:59 •
Session 2: Administration & Development
11:00 •
GalaxyCloudRunner: Streamlined Cloud Bursting for Galaxy
11:07 •
Laniakea: A Galaxy-on-demand Provider Platform Through Cloud Technologies
11:27 •
Enabling Single Sign-On for Multiple Galaxy Instances
11:34 •
How – And How not – to manage successful local Galaxies deployments
11:54 •
Building a Pulsar Network across Europe
13:20 •
How to create a Galaxy Tool
15:50 •
Scripting Galaxy through BioBlend
17:29 •
Session 6: Epigenetics Track & Late Breaking Lightning Talks
17:30 •
HiCExplorer 3: A toolbox for Hi-C data analysis
17:50 •
Histone Deacetylases 1/2 In Microglia Function During Development And Neurodegeneration
17:57 •
Analysis and visualization of the human cardiac myocyte epigenome using Galaxy
18:17 •
Late Breaking Lightning Talks
18:17 •
Training Infrastructure as a Service
Italy
12:15 •
BoF: Using Galaxy in automated production setups
13:20 •
ChIP-seq data analysis
15:50 •
Hi-C analysis
Konzerthaus
08:00 •
Conference Desk Open
10:30 •
Break / Sponsors
12:00 •
Lunch
12:15 •
Birds-of-a-Feather (BoFs), with Lunch
13:19 •
Session 3: Training
14:50 •
Poster 19 A: EpiGeEC allows fast comparison of user datasets with thousands of public epigenomic datasets through Galaxy
14:50 •
Poster 49 A: Mining hot topics in stem cells by combining text mining and scientometrics
14:50 •
Poster 25 A: Building a Galaxy Trusted Server to Ensure Privacy and Ownership in Genomic Research
14:50 •
Poster 13 A: Evaluation of tools and workflows for database construction for environmental metaproteomics
14:50 •
Poster 31 A: Development and implementation of a Galaxy instance geared towards microbiological applications within an applied public health setting
14:50 •
Poster 16 A: Predicting Gene Expression from Histone Modifications and Chronological Age by RNA-Seq Data using Galaxy Machine Learning Tools
14:50 •
Poster 34 A: A Newly Opened Galaxy Platform at Clermont Auvergne University
14:50 •
Poster 40 A: Aequatus.js: a plugin to visualise gene trees in Galaxy
14:50 •
Poster 10 A: Dima: Data-driven recommendation for a high-performing imputation algorithm
14:50 •
Session 4: Posters, Demos, and Sponsors
14:50 •
Poster 52 A: Poster: Science Data Center BioDATEN in relation to the Galaxy Community
14:50 •
Poster 46 A: Galaxy-E project: 2019 news
14:50 •
Poster 37 A: Galaxy Genome Annotation Project: Easier Genome Annotation Using Galaxy and GMOD Tools
14:50 •
Poster 43 A: Galaxy and Training: 2019 updates from the Galaxy Training Network
14:50 •
Poster 07 A: Knockdown Effects of MAGOHB on Alternative Splicing Via RNA-Seq Analysis
14:50 •
Poster 28 A: InteractoMIX integration in Galaxy
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
14:50 •
Poster 01 A: Alternative Splicing Analysis: The Silencing of the Human Colon Oxidase Complex
14:50 •
Poster 22 A: Laniakea: A Galaxy-on-demand Provider Platform Through Cloud Technologies
15:49 •
Session 5: Training
17:20 •
Group Picture
Offsite
19:00 •
Galaxy Runners: Tuesday Edition
19:00 •
Birds-of-a-Feather (BoFs), with Your Dinner!
19:00 •
The Freiburg City Tour BoF!
FULL
19:00 •
The Galaxy Training Network BoF!
Spain
12:15 •
BOF: Galaxy Workflow Discovery (IWC)
13:20 •
Variant calling I - from sequenced reads to variant lists
15:00 •
Demo 01 A: Galaxy Computational Chemistry
15:25 •
Demo 02 A: Climate Analysis with Galaxy
15:50 •
Variant Calling II - causative variant discovery
Wednesday
, July 3
Belgium
15:00 •
Demo 05 B: Combat-tb Workbench, A Customizable Platform For Variant Discovery And Annotation, Phylogeny Construction And Variant Prioritisation
15:25 •
Demo 06 B: ProteoRE, a Galaxy-based platform for the annotation and the interpretation of proteomics data in biomedical research
Czechia
12:15 •
Arts & Crafts
France
12:15 •
BoF: Multi-omics
13:20 •
The RNA workbench, best practices for RNA and high-throughput sequencing bioinformatics in Galaxy - RNA and transcriptomics
15:50 •
Visualisation development in Galaxy
Germany
08:59 •
Session 7: Transcriptomics & Genomics Track
09:00 •
Invited Talk: Pou5f3, SoxB1 and Nanog control the Zygotic Genome Activation in Zebrafish by Chromatin Remodeling
09:30 •
Single-cell RNA Analysis in Galaxy on 10X Datasets
09:50 •
Biology-driven classification of Single-Cells RNAseq data in Galaxy
10:10 •
Improving Transcriptome Analysis with Molecular Indices and Galaxy
10:17 •
Transposon Insertion Sequencing Analysis in Galaxy
10:59 •
Session 8: Transcriptomics & Genomics Track
11:00 •
Aequatus.js: a plugin to visualise gene trees in Galaxy
11:20 •
Visual Refinement of Genome Annotations with Apollo in a Community Environment
11:27 •
Architectural and Systems Improvements to G-OnRamp, a Collaborative Eukaryotic Genome Annotation Platform
11:34 •
ChiRA: an integrated framework for Chimeric Read Annotation
11:54 •
Training experience on “Data analysis and interpretation for clinical genomics” using Galaxy
13:20 •
Single cell RNA-seq analysis
15:50 •
Single cell RNA-seq analysis II
Greece
08:59 •
Session 7: Administration & Development Track
09:00 •
Containerizing Galaxy server as a Singularity application on HPC clusters for GenAP
09:20 •
Galaxy on Kubernetes: where we are and future challenges
09:40 •
A Minimal Docker Image for Galaxy
09:47 •
CVMFS-CSI for Galaxy: Efficient Access to Read-only Data in Kubernetes
09:54 •
gxadmin: usegalaxy.* administration wisdom
10:14 •
Galaxy container for Hinxton Single Cell Interactive Analysis Portal (HiSciAP)
10:59 •
Session 8: Administration & Development Track
11:00 •
Working Effectively with Remote Data in Galaxy - A Progress Report
11:07 •
Testing and Visualizing the State of Galaxy Tools and Workflows
11:27 •
Setting up a Galaxy Platform in a HPC Infrastructure for Genomics Implementation into Diagnosis Routines for a Health Reference Center
11:34 •
RealTimeTools: Integrating, Customizing, and Accessing UI-based Tools in Galaxy
11:54 •
Creating a Universe of Galaxies: The UseGalaxy.* Project
13:20 •
Galaxy Code Architecture
15:50 •
Running Galaxy on Kubernetes
17:29 •
Session 12: Plenary
17:30 •
Invited Talk: Galaxy Community Update
18:00 •
Tool Prediction in Galaxy Workflows using Deep Learning
18:07 •
Street Science Community: make science tangible & accessible by bringing it to the “street” with open science workshops
Italy
12:15 •
BoF: Galactic Visualisation!
13:20 •
Visualization of HTS Data in Galaxy
15:00 •
Demo 15 B: CWL in Galaxy, 2019-06 snapshot
15:50 •
Beyond the Intro: Further Adventures in Using Galaxy
Konzerthaus
08:00 •
Conference Desk Open
10:30 •
Break / Sponsors
12:00 •
Lunch
12:15 •
Birds-of-a-Feather (BoFs), with Lunch
13:19 •
Session 9: Training
14:50 •
Poster 14 B: Modulation of Nav1.5 mechanosensitivity by β1 and β3 subunits
14:50 •
Poster 20 B: Testing and Visualizing the State of Galaxy Tools and Workflows
14:50 •
Poster 53 B: UseGalaxy.eu: Community, Training, Infrastructure, and Users
14:50 •
Poster 08 B: Transposon Insertion Sequencing Analysis in Galaxy
14:50 •
Poster 50 B: Using Galaxy for Creation and Execution of Text Mining Workflows in the OpenMinTeD platform
14:50 •
Poster 35 B: NanoGalaxy: A Galaxy toolkit and workflows for long-read sequencing
14:50 •
Poster 11 B: LC-MS/MS tool and interactive visualizations integration on Galaxy Workflow4Metabolomics infrastructure
14:50 •
Poster 23 B: Galaxy on Kubernetes: where we are and future challenges
14:50 •
Poster 47 B: Climate Analysis with Galaxy
14:50 •
Poster 26 B: RealTimeTools: Integrating, Customizing, and Accessing UI-based Tools in Galaxy
14:50 •
Session 10: Posters, Demos, and Sponsors
14:50 •
Poster 29 B: ARIAWeb: a new web service for automated NMR structure calculation with ARIA
14:50 •
Poster 02 B: Galaxy container for Hinxton Single Cell Interactive Analysis Portal (HiSciAP)
14:50 •
Poster 38 B: Visual Refinement of Genome Annotations with Apollo in a Community Environment
14:50 •
Poster 44 B: A brief overview on how bilille is using Galaxy for sharing knowledge, computational resources & tools.
14:50 •
Poster 05 B: Improving Transcriptome Analysis with Molecular Indices and Galaxy
14:50 •
Poster 17 B: Analysis and visualization of the human cardiac myocyte epigenome using Galaxy
14:50 •
Poster 41 B: Training experience on “Data analysis and interpretation for clinical genomics” using Galaxy
14:50 •
Poster 32 B: The IRIDA Platform for Microbial Genomics
15:49 •
Session 11: Training
Offsite
19:30 •
Conference Dinner
Spain
12:15 •
EOSC-Life roadmap BOF
13:20 •
Train the Galaxy Trainer
15:00 •
Demo 07 B: Knockdown Effects of MAGOHB on Alternative Splicing Via RNA-Seq Analysis
15:25 •
Demo 08 B: Tool Prediction in Galaxy Workflows using Deep Learning
15:50 •
Making your open source project awesome
Thursday
, July 4
Belgium
12:15 •
BoF: Text Mining / NLP
13:20 •
Proteomic data analysis with Galaxy
15:00 •
Demo 14 C: Galaxy on Kubernetes
15:50 •
MALDI imaging of peptides data analysis
Czechia
12:15 •
Arts & Crafts
France
12:15 •
Galaxy containers BoF
13:20 •
Metabolomics data analysis I
15:00 •
Demo 12 C: Visual Refinement of Genome Annotations with Apollo in a Community Environment
15:25 •
Demo 13 C: The IRIDA Platform for Microbial Genomics
15:50 •
Metabolomics data analysis II
Germany
08:59 •
Session 13:Outside the Genome & Community Track
09:00 •
Invited Talk: Data visualisation by citizen science participants: the case of birds and bats monitoring schemes and Galaxy-E
09:30 •
Galaxy-Bricks a Tool for Data Literacy and Scientific Approach Education in the Context of Citizen Science
09:37 •
CITIZEN SCIENCE PROJECT in ECOLOGY with the GALAXY-E PLATFORM
09:44 •
Galaxy-E project: 2019 news
10:04 •
The ChemicalToolBox - Computational Chemistry in Galaxy
10:11 •
Improved Reference Data Management in Galaxy: Towards a Plant Data Analysis Platform
10:18 •
Use Galaxy, Right Now!
10:25 •
Galaxy Publication Library
10:59 •
Session 14: Variation, Metagenomics & Assembly Track
11:00 •
The IRIDA Platform for Microbial Genomics
11:20 •
Combat-tb Workbench, A Customizable Platform For Variant Discovery And Annotation, Phylogeny Construction And Variant Prioritisation
11:27 •
High throughput HIV next generation sequence analysis in Galaxy
11:47 •
NanoGalaxy: A Galaxy toolkit and workflows for long-read sequencing
11:54 •
MITOLINK: An integrated Web-based Workflow System to Evaluate Genotype-Phenotype Correlations in Human Mitochondrial Diseases
13:20 •
Machine Learning with Galaxy - Predict age from DNA-methylation dataset
15:50 •
Handling integrated biological data using Python, Jupyter, and InterMine
Greece
08:59 •
Session 13: Proteomics & Metabolomics & Late Breaking Track
09:00 •
Metaproteomics Powered By Metatranscriptomics: Towards a Multi-omic Functional Microbiome Analysis Within Galaxy
09:20 •
Interactive Galaxy Visualizations for Multi-omics Research
09:27 •
ProteoRE, a Galaxy-based platform for the annotation and the interpretation of proteomics data in biomedical research
09:47 •
Galaxy Wrapper for MaxQuant
09:54 •
Application of Halogen Bonding in Molecular and Drug Design Facilitated by a Galaxy Webserver
10:14 •
Rootless Galaxy Docker, with Backup, for our Lab Intranet
10:14 •
Late Breaking Lightning Talks
10:21 •
CFSAN GalaxyTrakr
10:59 •
Session 14: Proteomics & Metabolomics
11:00 •
Analysing and organising large-scale metabolome annotation studies with Django, ISA and Galaxy
11:20 •
Reproducible and accessible analysis of spatially resolved proteomics and metabolomics data
11:40 •
Workflow4Metabolomics: an international computing infrastructure for Metabolomics
13:20 •
CVMFS and Pulsar
15:50 •
Genomic assembly and data analysis in Galaxy with Nanopore ONT long read sequencing
17:29 •
Session 18: Closing Plenary
17:30 •
Invited Talk: UseGalaxy: Elucidating chromatin biology of mouse cardiomyocytes
18:00 •
Galaxy and Training: 2019 updates from the Galaxy Training Network
18:20 •
Closing
Italy
12:15 •
BoF: Metabolomics: Tools, Resources, and Needs
13:20 •
Assembly, annotation and analysis of bacterial genomes
15:50 •
ELIXIR Galaxy AAI: Authentication and Authorisation Infrastructure
Konzerthaus
08:00 •
Conference Desk Open
10:30 •
Break / Sponsors
12:00 •
Lunch
12:15 •
Birds-of-a-Feather (BoFs), with Lunch
13:20 •
15: Training Session
14:50 •
Poster 51 C: How Usable is Galaxy? A Usability Evaluation of Galaxy
14:50 •
Poster 21 C: Improved Reference Data Management in Galaxy: Towards a Plant Data Analysis Platform
14:50 •
Poster 03 C: Galaxy in fields, gardens and greenhouses for better seeds.
14:50 •
16: Poster, Demo, and Sponsor Session
14:50 •
Poster 48 C: The ChemicalToolBox - Computational Chemistry in Galaxy
14:50 •
Poster 33 C: HiCExplorer 3: A toolbox for Hi-C data analysis
14:50 •
Poster 36 C: EDAM: the ontology of bioinformatics operations, types of data, topics, and data formats (2019 update)
14:50 •
Poster 54 C: TrackFind: FAIR Search of Genomic Tracks
14:50 •
Poster 09 C: Development and Deployment of a Workflow for the Genomic Analysis of Campylobacter Jejuni
14:50 •
Poster 45 C: Galaxy-Bricks a Tool for Data Literacy and Scientific Approach Education in the Context of Citizen Science
14:50 •
Poster 27 C: Galaxy on Site: Flexibility without Tears
14:50 •
Poster 42 C: Experience of Galaxy training at a biomedical institute
14:50 •
Poster 39 C: Deployment of Genome Databases for Algae Using Galaxy Genome Annotation
14:50 •
Poster 30 C: Towards a platform for genomics medicine
14:50 •
Poster 18 C: Applying new model for predicting effects of gene variants in epigenetic regulators within Galaxy environment
14:50 •
Poster 15 C: A new Galaxy Wrapper for MaxQuant
14:50 •
Poster 12 C: Reproducible and accessible analysis of spatially resolved proteomics and metabolomics data
14:50 •
Poster 06 C: miRGalaxy: Galaxy tool for miRNA Analysis of NGS datasets (sRNA-seq)
14:50 •
Poster 24: Galaxy In A Large Scale Production Environment
15:50 •
17: Training Session
Offsite
19:00 •
BIKE - Lets Do It! : BoF for Galaxy Bikers (Bicycling).
19:00 •
Galaxy Runners: Thursday Edition
19:00 •
Birds-of-a-Feather (BoFs), with Your Dinner!
19:00 •
Intergalactic Utilities Commission (IUC) BoF
19:00 •
The Freiburg City Tour BoF!
FILLING
Spain
13:20 •
Import, handle, visualize and analyze biodiversity data in Galaxy
15:00 •
Demo 10 C: Interactive Galaxy Visualizations for Multi-omics Research
15:25 •
Demo 11 C: NanoGalaxy: A Galaxy toolkit and workflows for long-read sequencing
15:50 •
Population genomics with RADseq
Friday
, July 5
Konzerthaus
08:00 •
Conference Desk Open
09:00 •
CollaborationFest: Core
Saturday
, July 6
Konzerthaus
08:00 •
Conference Desk Open
09:00 •
CollaborationFest: Core
Sunday
, July 7
University of Freiburg Compute Center
08:00 •
Conference Desk Open
09:00 •
CollaborationFest: Encore
Monday
, July 8
University of Freiburg Compute Center
08:00 •
Conference Desk Open
09:00 •
CollaborationFest: Encore
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GCC2019
Europe/Berlin
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Monday
, July 1
Tuesday
, July 2
Wednesday
, July 3
Thursday
, July 4
Friday
, July 5
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, July 6
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, July 7
Types
A. Training
All
Admin / Dev
Diverse Communities
Epigenetics
Introduction / General
Metagenomics / Assembly
Proteomics / Metabolomics
Transciptomics / Genome Variation
B. Talks: Admin / Dev
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Session 7
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Session 14
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University of Freiburg Compute Center
