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GCC2021 has ended
GCC2021 is governed by the VIB Conferences Code of Conduct.

The 2021 Galaxy Community Conference (GCC2021) is virtual and global, accessible in any time zone, on every continent, and in every country.  GCC2021 events are held twice, once in the original Ghent time zone (GCC EMEA+APAC), and again 9 hours later (GCC Americas).

 Select your timezone to see events in your local time  

Log in to bookmark your favorites and sync them to your phone or calendar.

Monday, June 28
 

00:00 CEST

GCC2021 Training Week: Galaxy for Administrators Track (Monday-Friday)
Welcome to the second day of GCC2021 Training Week! Today you will learn more about setting up your own server. Help is always available on Slack.

Monday June 28, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Developers Track (Monday-Friday)
GCC2021 training is an online event, spanning all time zones for a week. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers are available 24/7 for online to answer all your questions on Slack (a chat platform).

The Galaxy for Developers Track will teach you how Galaxy works internally (frontend and backend), how to add new features for Galaxy, how to build the best tools and visualisations, how to interact with the Galaxy API using BioBlend, and more!  YOU can choose which of these training modules you want to follow during the week of training.

There are also Scientists and Administrators tracks. The Science and Developer tracks do not have a predetermined path. There are a number of training “modules” covering a variety of topics from which you can build your own training program for the week. All training participants can take any Science and Developer topics you are interested in. (The Administrators track requires a separate registration.)

See the full list of topics in the Galaxy for Developers Track for more information.

Monday June 28, 2021 00:00 - Tuesday June 29, 2021 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Scientists Track (Monday-Friday)
This week of training is an online event, spanning all time zones. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers are available 24/7 for online support and to answer all your questions on Slack (a chat platform).

The Galaxy for Scientists Track covers a wide range of topics including NGS Analysis (DNA & RNA), Proteomics, Microbial Analysis, Machine Learning, using R in Galaxy, Visualisation, Clinical workflows (including COVID-19), Nanopore Analysis, Single-cell RNASeq, Epigenetics, Climate Science, Cheminformatics, Advanced Galaxy features (scaling your analysis) and more! YOU can choose which of these training modules you want to follow during the week of training.

There are also Developers and Administrators tracks. The Science and Developer tracks do not have a predetermined path. There are a number of training “modules” covering a variety of topics from which you can build your own training program for the week. All training participants can take any Science and Developer topics. (The Administrators track requires a separate registration.)

See the full list of topics in the Galaxy for Scientists Track for more information.

Monday June 28, 2021 00:00 - Tuesday June 29, 2021 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack
 
Tuesday, June 29
 

00:00 CEST

GCC2021 Training Week: Galaxy for Administrators Track (Monday-Friday)
GCC2021 training is an online event, spanning all time zones for a week. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers are available 24/7 for online to answer all your questions on Slack (a chat platform).

The Galaxy for Administrators Track eaches you how to be a stellar admin, easily deploying a production-ready Galaxy with Ansible!

There are also tracks for Scientists and Developers. The Science and Developer tracks do not have a predetermined path. There are a number of training “modules” covering a variety of topics from which you can build your own training program for the week. All training participants can take any Science and Developer topics you are interested in. The Administrators track is open to only registered participants

See the full list of topics in the Galaxy for Administrators Track for more information.

Tuesday June 29, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Developers Track (Monday-Friday)
Welcome to the second day of GCC2021 Training Week! Today you can continue with the Developer Track or learn about using Galaxy in the Science Track. Trainers will be on Slack all week to help.

Tuesday June 29, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Scientists Track (Monday-Friday)
Welcome to the second day of GCC2021 Training Week! Explore more topics today. Perhaps advanced use, or mabe new types of analsysis? The Galaxy for Scientists Trackcovers a wide range of topics including NGS Analysis (DNA & RNA), Proteomics, Microbial Analysis, Machine Learning, using R in Galaxy, Visualisation, Clinical workflows (including COVID-19), Nanopore Analysis, Single-cell RNASeq, Epigenetics, Climate Science, Cheminformatics, Advanced Galaxy features (scaling your analysis) and more! YOU can choose which of these training modules you want to follow during the week of training.

There is also Developers if that grabs your interest.

Tuesday June 29, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack
 
Wednesday, June 30
 

00:00 CEST

GCC2021 Training Week: Galaxy for Administrators Track (Monday-Friday)
Third day of GCC2021 Training Week! You are halfway there! Keep at it, and keep asking questions in Slack.

Wednesday June 30, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Developers Track (Monday-Friday)
Third day of GCC2021 Training Week! You are halfway there! Keep at it, and keep asking questions in Slack.

Wednesday June 30, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Scientists Track (Monday-Friday)
Third day of GCC2021 Training Week! You are halfway there! Keep at it, and keep asking questions in Slack.

Wednesday June 30, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack
 
Thursday, July 1
 

00:00 CEST

GCC2021 Training Week: Galaxy for Administrators Track (Monday-Friday)
Day 4 of GCC2021 Training Week! You are halfway there! You are picking up speed!

Thursday July 1, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Developers Track (Monday-Friday)
Day 4 of GCC2021 Training Week! You are halfway there! You are picking up speed!

Thursday July 1, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Scientists Track (Monday-Friday)
Day 4 of GCC2021 Training Week! You are halfway there! You are picking up speed!

Thursday July 1, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

10:00 CEST

Open House
The Meeting and CoFest are happening on the Remo platform. Remo does a good job encouraging interaction, but you will need to learn how to get around. To help with that, we are holding Remo open houses this week, and we encourage you to attend. We will briefly discuss features and then set you loose to meet and talk, wander around, and try things out.

Thursday July 1, 2021 10:00 - 11:00 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

18:00 CEST

Open House
The Meeting and CoFest are happening on the Remo platform. Remo does a good job encouraging interaction, but you will need to learn how to get around. To help with that, we are holding Remo open houses this week, and we encourage you to attend. We will briefly discuss features and then set you loose to meet and talk, wander around, and try things out.

Thursday July 1, 2021 18:00 - 19:00 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.
 
Friday, July 2
 

00:00 CEST

GCC2021 Training Week: Galaxy for Administrators Track (Monday-Friday)
The final day of GCC2021 Training Week! You are going to make it, and you have learrned a lot! And don't forget to do evaluations.

Friday July 2, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Developers Track (Monday-Friday)
The final day of GCC2021 Training Week! You are going to make it, and you have learrned a lot! And don't forget to do evaluations.

Friday July 2, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

00:00 CEST

GCC2021 Training Week: Galaxy for Scientists Track (Monday-Friday)
The final day of GCC2021 Training Week! You are going to make it, and you have learrned a lot! And don't forget to do evaluations.

Friday July 2, 2021 00:00 - 23:59 CEST
Training Slack https://gtnsmrgsbord.slack.com/ Training is asynchronous with videos on YouTube and siupport and chat in this slack

10:00 CEST

Open House
The Meeting and CoFest are happening on the Remo platform. Remo does a good job encouraging interaction, but you will need to learn how to get around. To help with that, we are holding Remo open houses this week, and we encourage you to attend. We will briefly discuss features and then set you loose to meet and talk, wander around, and try things out.

Friday July 2, 2021 10:00 - 11:00 CEST
Social Building

18:00 CEST

Open House
The Meeting and CoFest are happening on the Remo platform. Remo does a good job encouraging interaction, but you will need to learn how to get around. To help with that, we are holding Remo open houses this week, and we encourage you to attend. We will briefly discuss features and then set you loose to meet and talk, wander around, and try things out.

Friday July 2, 2021 18:00 - 19:00 CEST
Social Building
 
Monday, July 5
 

01:00 CEST

Open House!
Open House! Drop by and explore GCC2021 Remo! Explore the different buildings, try out chat, talk, and video, and meet your fellow Galaxy Community Members!

The buildings will reset once every 5 hours or so. When this happens, your Remo tab will become unresponsive. Just wait a minute, and then refresh the tab.


Monday July 5, 2021 01:00 - 21:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.
 
Tuesday, July 6
 

08:59 CEST

EMEA-APAC Conference Day 1
The first day of GCC2021

Tuesday July 6, 2021 08:59 - 17:50 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

09:00 CEST

EMEA-APAC Session 1
The first session of the 2021 Galaxy Community Conference (GCC2021).

Presentations this session:


🙋A presenter or co-author will be available for live Q&A.

Moderators
avatar for Andrew Lonie

Andrew Lonie

Director Australian BioCommons, University of Melbourne

Tuesday July 6, 2021 09:00 - 10:20 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:01 CEST

Welcome
Welcome to the 2021 Galaxy Community Conference (GCC2021)!

We'll introduce the conference, talk about the logistics of this online event, and present last minute news

Speakers
avatar for Frederik Coppens

Frederik Coppens

Project Leader, VIB


Tuesday July 6, 2021 09:01 - 09:20 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:15 CEST

Enabling widespread use of Vertebrate Genome Project assembly pipeline by integration into Galaxy
→ Slides (doi: 10.7490/f1000research.1118636.1)
→ Abstract
→ Video

Delphine Lariviere 2; Alex Ostrovsky 1

  1. Galaxy, Johns Hopkins University, US 
  2. Galaxy, Penn State University, US

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Postdoc, Penn State University


VGP GCC pptx

Tuesday July 6, 2021 09:15 - 09:33 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:33 CEST

Supporting the COVID-19 Data portal: viral data cleaning from human reads and submission to ENA
→ Abstract 
→ Slides (doi: 10.7490/f1000research.1118664.1)
Video

Miguel Roncoroni 1,2; Ignacio Eguinoa 1,2; Bert Droesbeke 1,2; Frederik Coppens 1,2

  1. Department of Plant Biotechnology and Bioinformatics, BE
  2. VIB Center for Plant Systems Biology, BE

Speakers
IE

Ignacio Eguinoa

ELIXIR Belgium - VIB Center for Plant Systems Biology



Tuesday July 6, 2021 09:33 - 09:39 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:39 CEST

Galaxy as a global platform for the analysis of SARS-CoV-2 sequence variants
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118668.1)
→ Video

Wolfgang Maier 1; Anton Nekrutenko 2; Sergei Pond 3, and the covid19.galaxyproject.org, covid19.datamonkey.org and Viral Beacon 4 teams
  1. University  of  Freiburg,  DE
  2. Penn  State University, US
  3. Temple University, US
  4. Centre for Genomic Regulation (CRG), ES

Speakers
avatar for Wolfgang Maier

Wolfgang Maier

University of Freiburg
Interests:- Galaxy tool development- Variant calling tools and pipelines- User trainings


Tuesday July 6, 2021 09:39 - 09:57 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:57 CEST

CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
→ Abstract 
→ Slides (doi: 10.7490/f1000research.1118628.1)
Video

Erika Ferrandi 2; Matteo Chiara 1,2; Federico Zambelli 1,2; Marco Antonio Tangaro 2; Pietro Mandreoli 1,2; David S. Horner 2,3; Graziano Pesole 2,3

  1. Department  of  Biosciences -University  of  Milan,  IT
  2. Institute of Biomembranes, Bioenergetics and Molecular Biotechnology - National  Research  Council,  IT
  3. Department of Biosciences, Biotechnology and Biopharmaceutics - University of Bari "A. Moro", IT

Speakers
EF

Erika Ferrandi

IBIOM - CNR



Tuesday July 6, 2021 09:57 - 10:03 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:03 CEST

Easy access to NCBI data within Galaxy
→ Abstract
→ Slides
Video

Nuala O'Leary 1; Adam Stine 1; Eric Cox 1; Adelaide Rhodes 1

  1. National Center for Biotechnology Information (NCBI), US

Speakers
avatar for Adam Stine

Adam Stine

Curator - Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI)
avatar for Nuala O'Leary

Nuala O'Leary

Product Owner, NCBI
Hi Galaxy Community, I'm Nuala O'Leary and I'm product owner of NCBI Datasets and new resource aimed at making it easier for the biology community to access NCBI sequence data. Please come to our poster, talk and Birds of Feather, bring your questions and suggestions for NCBI.



Tuesday July 6, 2021 10:03 - 10:09 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:09 CEST

Q&A
There will be live question and answer at the end of each session.  Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.


Tuesday July 6, 2021 10:09 - 10:15 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:15 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Tuesday July 6, 2021 10:15 - 10:35 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

10:34 CEST

EMEA-APAC Session 2
Second session of the 2021 Galaxy Community Conference (GCC2021).

Presentations this session:


🙋A presenter or co-author will be available for live Q&A this session.

Speakers
avatar for Lucille Delisle

Lucille Delisle

Post-doc, EPFL SV ISREC UPDUB
Hi,I am a Post-doc in Denis Duboule lab working on gene regulation during development.For the scientific part, I analyzed various NGS methods including Hi-C, ATAC-seq, CUT&RUN. I recently developped a new method for single-cell RNA-seq, named baredSC.For the galaxy part, I develop... Read More →


Tuesday July 6, 2021 10:34 - 11:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:35 CEST

Using Galaxy File Source Plugins to Work with Remote Data including Applications
→ Abstract
→ Slides
→ Video

John  Chilton 1; Luke Sargent 3; David López 4; Alexandru Mahmoud 2; Björn Grüning 4 and the Galaxy Team

  1. Penn  State University, US
  2. Johns Hopkins University, US
  3. Oregon Health & Science University, US
  4. University of Freiburg, DE

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University
avatar for Luke Sargent

Luke Sargent

Average human topics



Tuesday July 6, 2021 10:35 - 12:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:53 CEST

Overhaul and pagination in Data-Libraries
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118606.1)
→ Video

Oleg Zharkov 1; Bjoern Grüning 1

  1. University of Freiburg, DE

Speakers
avatar for Oleg Zharkov

Oleg Zharkov

Albert-Ludwigs-Universität Freiburg



Tuesday July 6, 2021 10:53 - 10:59 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:59 CEST

Recent updates to Nebulizer: a command line utility for Galaxy admins
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118592.1)
→ Video

Peter Briggs 1

  1. University of Manchester, GB

Speakers
avatar for Peter Briggs

Peter Briggs

Computer Officer, Bioinformatics Core Facility, University of Manchester
Software developer supporting a team of informaticians within the Bioinformatics Core Facility (BCF) in the Faculty of Biology Medicine & Health (FBMH) at the University of Manchester. Responsibilities include supporting a number of local Galaxy instances both internally (for local... Read More →



Tuesday July 6, 2021 10:59 - 11:05 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:05 CEST

How UseGalaxy.EU is managed - tips and tricks from inside
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118605.1)
→ Video

Gianmauro Cuccuru 1; Helena Rasche 2

  1. Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106,79110 Freiburg, Germany , DE
  2. Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, NL

Speakers
avatar for Gianmauro Cuccuru

Gianmauro Cuccuru

University of Freiburg



Tuesday July 6, 2021 11:05 - 11:23 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:23 CEST

HPC back-end runner for massive SARS-CoV-2 samples processing
→ Abstract 
→ Slides
→ Video

Hugo Jiménez Hernández 1

  1. Barcelona Supercomputing Center, ES

Speakers
avatar for Hugo Jiménez Hernández

Hugo Jiménez Hernández

Research Engineer, Barcelona Supercomputing Center



Tuesday July 6, 2021 11:23 - 11:29 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:29 CEST

Laniakea - Update 2021
→ Slides (doi: 10.7490/f1000research.1118635.1)
→ Abstract 
→ Video

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

  1. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies - National Research Council, IT
  2. National Institute for Nuclear Physics, Bari Section, IT
  3. Dept. of Biosciences, University of Milan, IT
  4. Dept. of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, IT

Speakers
MA

Marco Antonio Tangaro

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies - National Research Council, Bari, Italy



Tuesday July 6, 2021 11:29 - 11:35 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:35 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Tuesday July 6, 2021 11:35 - 11:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:40 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Tuesday July 6, 2021 11:40 - 12:00 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

11:59 CEST

EMEA-APAC Tuesday Poster / Demo / Sponsor Session
Sponsors and poster / demos are presented in the Poster / Demo / Sponsor Hall in Remo. Sponsors (and the Career Center) are on the first/ground floor. Tuesday's poster / demos are on floors 2 and 3 of that building.


🙋 A presenter will be available during this poster/demo session.

Tuesday July 6, 2021 11:59 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

F1000Research
→ Remo: Poster/Demo/Sponsor Hall, Floor 1
Galaxy Gateway

F1000Research is proud to be a Silver Sponsor for GCC2021! We are an Open Research publishing platform that offers rapid, transparent publication of a range of different article types, including original research articles, to method articles, data notes, and software tool articles. The platform is particularly well suited to publishing software tool articles as the unique versioning system allows small updates at any time, along with proper syntax highlighting and support for LaTeX and markdown submissions.

Our Galaxy Gateway on the platform brings together articles, posters and slides from Galaxy events. The Gateway allows authors to quickly share their work with the community, boosting visibility and giving researchers proper credit for their contribution.

We’re pleased to be running a call for papers for GCC2021 and would like to invite the Galaxy community to submit their articles to the Galaxy Gateway by 20th July 2021. These can be any type of article, such as a new Galaxy workflow or an update to an existing method or software tool. This is a great opportunity to shine a light on your research, improve its impact and be credited with an academic paper for your work. Please submit via the Galaxy gateway.

Please drop by the F100Research table and learn more from Abbie!

Speakers

Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.10: Laniakea@ReCaS: first year of activity of a Laniakea-based Galaxy “on-demand” service
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118652.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


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

  1. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR),Bari, IT
  2. National Institute for Nuclear Physics (INFN), Bari, IT
  3. Department of Biosciences, University of Milan, Milano, IT
  4. Department of Biosc

Speakers
avatar for pietro mandreoli

pietro mandreoli

Dept. of Biosciences, University of Milano



Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.2: Automating Galaxy tool requirement updates with Planemo
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2

Simon Bray 1; Lorraine Coelho 1; Björn Grüning 1

  1. University of Freiburg, DE

Speakers


Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.3: ComPIL 2.0 and MetaNovo Tools for Metaproteomics Searches Within Galaxy: Searching for Needles in a Haystack
→ Abstract
→ 
Poster (doi: 10.7490/f1000research.1118647.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 2

Reid Wagner 1; Peter Thuy-Boun 2; Andrew McArdle 3; Subina Mehta 1; James Johnson 1; Björn Grüning 4; Gianmauro Cuccuru 4; Dennis Wolan 2; Timothy Griffin 1; Pratik Jagtap 1

  1. University of Minnesota, US
  2. Scripps Research, US
  3. Imperial College London, GB
  4. University of Freiburg, DE



Speakers


Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.4: Diversity of pleurocidin-like antimicrobial peptides in a marine bony fish (Sparus aurata) by re-identification in ESTs
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Alberto Serna Duque 1; Alberto Cuesta Peñafiel 1; Maria Angeles Esteban Abad 1

  1. Immunobiology for Aquaculture Group, Department of Cell Biology & Histology, Faculty of Biology, University of Murcia, ES

Speakers
avatar for Jhon Alberto Serna Duque

Jhon Alberto Serna Duque

PhD student, University of Murcia
Study of antimicrobial peptides in marine fish and looking for new biotechnological applications.



Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.5: Galaxy as a global platform for the analysis of SARS-CoV-2 sequence variants
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2

Wolfgang Maier 1; Anton Nekrutenko 2; Sergei Pond 3, and the covid19.galaxyproject.org, covid19.datamonkey.org and Viral Beacon 4 teams

  1. University  of  Freiburg,  DE
  2. Penn  State University, US
  3. Temple University, US
  4. Centre for Genomic Regulation (CRG), ES

Speakers
avatar for Wolfgang Maier

Wolfgang Maier

University of Freiburg
Interests:- Galaxy tool development- Variant calling tools and pipelines- User trainings



Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.6: Easy access to NCBI data within Galaxy
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Nuala O'Leary 1; Adam Stine 1; Eric Cox 1; Adelaide Rhodes 1

  1. National Center for Biotechnology Information (NCBI), US

Speakers
avatar for Adam Stine

Adam Stine

Curator - Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI)
avatar for Nuala O'Leary

Nuala O'Leary

Product Owner, NCBI
Hi Galaxy Community, I'm Nuala O'Leary and I'm product owner of NCBI Datasets and new resource aimed at making it easier for the biology community to access NCBI sequence data. Please come to our poster, talk and Birds of Feather, bring your questions and suggestions for NCBI.



Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.7: Galaxy-E project: 2021 News
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Yvan  Le  Bras 1;  Coline  Royaux 1;  Simon  Bénateau 2

  1. PNDB  research  e-infrastructure,  UMS  PatriNat, Museum National d’Histoire Naturelle (MNHN), Concarneau, France, FR
  2. Centre d’Ecologie et des Sciences de la Conservation, Muséum national d’Histoire naturelle -Sorbonne Université-CNRS, Paris, FR
  3. Existing known colleagues, unknown users and all people interested!, FR

Speakers
avatar for Yvan Le Bras

Yvan Le Bras

Research engineer, French National Museum of Natural History



Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.8: Janis for workflow translation – a potential benefit to the Galaxy ecosystem
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Richard  Lupat 1; Michael Franklin 1,2; Evan Thomas 3; Juny Kesumadewi 1,2; Jiaan Yu 1; Mohammad Bhuyan 3; Tony Papenfuss 1,3; Andrew Lonie 4; Daniel Park 2; Bernard Pope 2; Jason Li 1

  1. Peter MacCallum Cancer Centre, AU
  2. University of Melbourne, AU
  3. Walter and Eliza Hall Institute, AU
  4. Australian BioCommons, AU

Speakers
RL

Richard Lupat

Peter MacCallum Cancer Centre



Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-2.9: Enabling widespread use of Vertebrate Genome Project assembly pipeline by integration into Galaxy
→ Abstract
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Delphine Lariviere 2; Alex Ostrovsky 1

  1. Galaxy, Johns Hopkins University, US 
  2. Galaxy, Penn State University, US

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Postdoc, Penn State University


Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-3.2: Genome-wide predictions and structural modeling of protein-protein interactions using Galaxy
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Aysam Guerler 1, Bjoern Gruening 2, Michael C. Schatz 1 and Anton Nekrutenko 3

  1. Johns Hopkins University, Baltimore, US  
  2. University of Freiburg, DE
  3. Penn State University, State College, US



Speakers
avatar for Aysam Guerler

Aysam Guerler

Galaxy Project, Johns Hopkins University
Johns Hopkins University



Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-3.3: Practical aspects of implementing the IRIDA system as a solution for One Health bioinformatics analyses
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118654.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3

Jeevan Karloss Antony Samy 1,2; Georgios Marselis 1; EveZeyl Fiskebeck 1; Taran Skjerdal 1; Camilla Sekse 1; Karin Lagesen1

  1. Norwegian Veterinary Institute, NO
  2. Norwegian Institute of Public Health, NO

Speakers
avatar for Jeevan Karloss Antony Samy

Jeevan Karloss Antony Samy

Researcher, Norwegian Veterinary Institute
Bioinformatician/frontend developer



Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-3.4: Recent updates to Nebulizer: a command line utility for Galaxy admins
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118593.1)
Remo: Poster/Demo/Sponsor Hall, Floor 3

Peter Briggs 1

  1. University of Manchester, GB

Speakers
avatar for Peter Briggs

Peter Briggs

Computer Officer, Bioinformatics Core Facility, University of Manchester
Software developer supporting a team of informaticians within the Bioinformatics Core Facility (BCF) in the Faculty of Biology Medicine & Health (FBMH) at the University of Manchester. Responsibilities include supporting a number of local Galaxy instances both internally (for local... Read More →


Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-3.5: Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL)
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Stephen Mosher 1; Michael C. Schatz 2,1; Anthony Philippakis 3

  1. Department of Biology, Johns Hopkins University, Baltimore, MD., US
  2. Department of Computer Science, Johns Hopkins University, Baltimore, MD., US
  3. Broad Institute of MIT and Harvard, Cambridge, MA, US

Speakers


Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

Tu-3.6: Use of Galaxy tools for microbiome analysis of breast cancer RNA-seq transcriptomic data
→ Abstract
→ Poster 
(doi: 10.7490/f1000research.1118594.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Dominik Hadzega 1; Katarina Kalavska 2; Marian Karaba 3; Gabriel Minarik 4; Juraj Benca 3,5; Sona Ciernikova 6; Tatiana Sedlackova 4; Daniel Pindak 3; Lubos Klucar 1; Michal Mego 2,7

  1. Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, SK
  2. Translational research unit, Faculty of Medicine, Comenius University and National Cancer Institute, Bratislava, SK
  3. Department of Oncosurgery, National Cancer Institute, Bratislava, SK

Speakers


Tuesday July 6, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

13:20 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Tuesday July 6, 2021 13:20 - 13:40 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

13:25 CEST

Remo Reset
The conference is being run on the Remo.co platform. This has many advantages, and a few disadvantages. One of the disadvantages is that our license allows us to only be up for only 5 hours at a time. This means that every 5 hours, or less, we need to reboot the platform.

When this happens, you will need to log back in to Remo to reconnect. There will be one reset during each conference day, either before or after that day's poster/demo/sponsor session. There will be additional resets in the after hours, before or after BoFs and Socials, as needed.

We apologize for this inconvenience.

Tuesday July 6, 2021 13:25 - 13:25 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

13:39 CEST

EMEA-APAC Session 3
Wrap up the EMEA-APAC region's first day of GCC2021 with a session focused on workflows.

Presentations this session:


🙋A presenter or co-author will be available for live Q&A in this session.

Moderators
Tuesday July 6, 2021 13:39 - 15:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

13:40 CEST

A Galaxy-based multi-omic workflow for discovery and validation of candidate neoantigen peptides for immuno-oncology
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118669.1)
→ Video

Tim Griffin 1; An Duy Dinh Nguyen 1; James Johnson 1; Subina Mehta 1; Andrew Rajczewski 1; Mitchell Hruska 1; Tyler Jubenville 1; Sue Rathe 1; Flavia Popescu 1; Pratik Jagtap 1; David Largaespada 1

  1. University of Minnesota, US

Speakers
avatar for Tim Griffin

Tim Griffin

Professor, University of Minnesota



Tuesday July 6, 2021 13:40 - 13:46 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

13:46 CEST

Enhancing the Whole Workflow Experience from Development through Publication and to Execution
→ Abstract 
→ Slides
Video

John  Chilton 1; Aysam Guerler 2; Marius van den Beek 1

  1. Penn  State  University,  US
  2. Johns Hopkins University, US

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University



Tuesday July 6, 2021 13:46 - 14:04 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:04 CEST

Introducing the Intergalactic Workflow Commission
→ Abstract
→ Slides
→ Video

Marius van den Beek 1; Simon Bray 2; John Chilton 1; Aysam Guerler 3; Ignacio Eguinoa 4; Matthias Bernt 5; Wolfgang Maier 2

  1. Department of Biochemistry and Molecular Biology, Penn State University, University Park PA, US
  2. Bioinformatics Group, Department of Computer Science, Albert Ludwigs University, Freiburg, DE
  3. Department of Biology, Johns Hopkins University, Baltimore MD, US
  4. VIB Center for Plant Systems Biology, BE
  5. Helmholtz Centre for Environmental Research, – UFZ, Leipzig, DE

Speakers
avatar for Marius van den Beek

Marius van den Beek

Penn State University



Tuesday July 6, 2021 14:04 - 14:22 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:22 CEST

Publication of BioCompute Objects (IEEE-2791-2020) created from Galaxy workflow invocations
→ Abstract 
→ Slides (doi: 10.7490/f1000research.1118619.1)
Video

Charles Hadley King 1; Christopher Armstrong 1

  1. George Washington University, US

Speakers
avatar for Charles [Hadley] King

Charles [Hadley] King

Senior Research Associate, George Washington University



Tuesday July 6, 2021 14:22 - 14:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:40 CEST

Developing Pro workflows: lessons learned
→ Abstract 
→ Slides
→ Video

Nathan Roach 1; Randy  Guertin 1; Dannon Baker 1; John Chilton 1; Sam Guerler 1; Stephanie Pond 1; Enis Afgan 1

  1. GalaxyWorks, US

Speakers
avatar for Randy Guertin

Randy Guertin

Computational Biologist, GalaxyWorks



Tuesday July 6, 2021 14:40 - 14:46 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:46 CEST

The WorkflowHub - a registry for workflows
→ Abstract 
→ Slides (doi: 10.7490/f1000research.1118663.1)
→ Video

Ignacio Eguinoa 1,2; WorkflowHub Community 4; Frederik Coppens 1,2; Carole Goble 3

  1. Department of  Plant  Biotechnology  and  Bioinformatics,  Ghent  University,  BE
  2. VIB Center for Plant Systems Biology, BE
  3. Department of Computer Science, The University of Manchester, GB
  4. https://about.workflowhub.eu/acknowledgements/#workflowhub-club, GB

Speakers
IE

Ignacio Eguinoa

ELIXIR Belgium - VIB Center for Plant Systems Biology



Tuesday July 6, 2021 14:46 - 14:52 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:52 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Tuesday July 6, 2021 14:52 - 15:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

15:00 CEST

Break
The first day's formal content is done, but stick around for Birds-of-a-Feather (in 20 minutes) and the Opening Social.

Take a break! Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

See you soon.

Tuesday July 6, 2021 15:00 - 15:20 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

15:19 CEST

Americas Conference Day 1
GCC2021 starts with our first session in the Americas Zone

Tuesday July 6, 2021 15:19 - Wednesday July 7, 2021 02:00 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

15:20 CEST

Birds of a Feather (BOFs)
Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.

BoFs flocking in this session are


Anyone is welcome to propose a BoF! All you need is a title, an organizer, and a brief description.


Tuesday July 6, 2021 15:20 - 16:30 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

15:20 CEST

BoF: Galaxy & Bioinformatics in Africa
While Galaxy has been used by African bioinformaticians for more than 10 years, the African Galaxy user community continues to be scattered. How can we maximise what Galaxy offers for African bioinformatics and what can we do to increase participation of African scientists in the Galaxy community? This BoF will take place either on either Zoom or Google Meet, details will be announced before the time.

Meeting Spaces

Speakers


Tuesday July 6, 2021 15:20 - 16:30 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

15:20 CEST

BoF: Galaxy for Microbiome - Kickoff
Many efforts on microbiome analysis are done in Galaxy but we do not communicate so much together about them. To avoid redundancy and coordinate our efforts, we would like to start a "Galaxy for Microbiome" community.

We started to collect ideas about this community in a shared document. We would like now to properly kickoff this community. What is better to kickoff a community than a BoF at GCC?

Meeting spaces

During BoF

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg


Tuesday July 6, 2021 15:20 - 16:30 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

16:30 CEST

Opening Social
Hey!  Come back!*

GCC2021 is all about community, and while we can't have our usual after hours gatherings, we can still meet new collaborators and spend time with old friends.  This session is an opportunity to do just that. 

We'll start with a few slides (we will highlight our Fellowship recipients) and then do 1-2 short rounds of icebreaker to get the new folks into the groove, and then leave the rest of the session for unstructured socializing.

We really, really hope to see you there (But please bring your own drinks and snacks. Sorry.)

Thanks,
Everyone who is, or ever will be, in the Galaxy Community

* Or, "Hey show up early!"

Tuesday July 6, 2021 16:30 - 17:40 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

17:45 CEST

Remo Reset
The conference is being run on the Remo.co platform. This has many advantages, and a few disadvantages. One of the disadvantages is that our license allows us to only be up for only 5 hours at a time. This means that every 5 hours, or less, we need to reboot the platform.

When this happens, you will need to log back in to Remo to reconnect. There will be one reset during each conference day, either before or after that day's poster/demo/sponsor session. There will be additional resets in the after hours, before or after BoFs and Socials, as needed.

We apologize for this inconvenience.

Tuesday July 6, 2021 17:45 - 17:45 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

18:00 CEST

Americas Session 1
The first session of the 2021 Galaxy Community Conference (GCC2021).

Presentations this session:


🙋 A presenter or co-author will be available for live Q&A in this session.

Moderators
avatar for Frederik Coppens

Frederik Coppens

Project Leader, VIB

Tuesday July 6, 2021 18:00 - 19:15 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:01 CEST

Welcome
Welcome to the 2021 Galaxy Community Conference (GCC2021)!

We'll introduce the conference, talk about the logistics of this online event, and present last minute news

Speakers
avatar for Frederik Coppens

Frederik Coppens

Project Leader, VIB


Tuesday July 6, 2021 18:01 - 18:15 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:15 CEST

Enabling widespread use of Vertebrate Genome Project assembly pipeline by integration into Galaxy
→ Slides (doi: 10.7490/f1000research.1118636.1)
→ 
Abstract
→ Video

Delphine Lariviere 2; Alex Ostrovsky 1

  1. Galaxy, Johns Hopkins University, US 
  2. Galaxy, Penn State University, US

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Postdoc, Penn State University


VGP GCC pptx

Tuesday July 6, 2021 18:15 - 18:33 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:33 CEST

Supporting the COVID-19 Data portal: viral data cleaning from human reads and submission to ENA
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118664.1)
Video

Miguel Roncoroni 1,2; Ignacio Eguinoa 1,2; Bert Droesbeke 1,2; Frederik Coppens 1,2

  1. Department of Plant Biotechnology and Bioinformatics, BE
  2. VIB Center for Plant Systems Biology, BE

Speakers
IE

Ignacio Eguinoa

ELIXIR Belgium - VIB Center for Plant Systems Biology


Tuesday July 6, 2021 18:33 - 18:39 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:39 CEST

Galaxy as a global platform for the analysis of SARS-CoV-2 sequence variants
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118668.1)
Video

Wolfgang Maier 1; Anton Nekrutenko 2; Sergei Pond 3, and the covid19.galaxyproject.org, covid19.datamonkey.org and Viral Beacon 4 teams
  1. University  of  Freiburg,  DE
  2. Penn  State University, US
  3. Temple University, US
  4. Centre for Genomic Regulation (CRG), ES

Speakers
avatar for Wolfgang Maier

Wolfgang Maier

University of Freiburg
Interests:- Galaxy tool development- Variant calling tools and pipelines- User trainings


Tuesday July 6, 2021 18:39 - 18:57 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:57 CEST

CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
→ Abstract 
→ Slides (doi: 10.7490/f1000research.1118628.1)
Video

Erika Ferrandi 2; Matteo Chiara 1,2; Federico Zambelli 1,2; Marco Antonio Tangaro 2; Pietro Mandreoli 1,2; David S. Horner 2,3; Graziano Pesole 2,3

  1. Department  of  Biosciences -University  of  Milan,  IT
  2. Institute of Biomembranes, Bioenergetics and Molecular Biotechnology - National  Research  Council,  IT
  3. Department of Biosciences, Biotechnology and Biopharmaceutics - University of Bari "A. Moro", IT

Speakers
EF

Erika Ferrandi

IBIOM - CNR


Tuesday July 6, 2021 18:57 - 19:03 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:03 CEST

Easy access to NCBI data within Galaxy
→ Abstract
→ Slides
Video

Nuala O'Leary 1; Adam Stine 1; Eric Cox 1; Adelaide Rhodes 1

  1. National Center for Biotechnology Information (NCBI), US

Speakers
avatar for Adam Stine

Adam Stine

Curator - Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI)
avatar for Nuala O'Leary

Nuala O'Leary

Product Owner, NCBI
Hi Galaxy Community, I'm Nuala O'Leary and I'm product owner of NCBI Datasets and new resource aimed at making it easier for the biology community to access NCBI sequence data. Please come to our poster, talk and Birds of Feather, bring your questions and suggestions for NCBI.


Tuesday July 6, 2021 19:03 - 19:09 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:09 CEST

Q&A
There will be live question and answer at the end of each session.  Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.


Tuesday July 6, 2021 19:09 - 19:15 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:15 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Tuesday July 6, 2021 19:15 - 19:35 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

19:34 CEST

Americas Session 2
Second session of the 2021 Galaxy Community Conference (GCC2021).

Presentations this session


🙋 A presenter or co-author will be available for live Q&A this session.

Moderators
avatar for Nate Coraor

Nate Coraor

System Administrator, Galaxy Project, Penn State University

Tuesday July 6, 2021 19:34 - 20:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:35 CEST

Using Galaxy File Source Plugins to Work with Remote Data including Applications
→ Abstract
→ Slides
Video

John  Chilton 1; Luke Sargent 3; David López 4; Alexandru Mahmoud 2; Björn Grüning 4; and the Galaxy Team

  1. Penn  State University, US
  2. Johns Hopkins University, US
  3. Oregon Health & Science University, US
  4. University of Freiburg, DE

Speakers
avatar for Luke Sargent

Luke Sargent

Average human topics
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University


Tuesday July 6, 2021 19:35 - 19:53 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:53 CEST

Overhaul and pagination in Data-Libraries
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118606.1)
Video

Oleg Zharkov 1; Bjoern Grüning 1

  1. University of Freiburg, DE

Speakers
avatar for Oleg Zharkov

Oleg Zharkov

Albert-Ludwigs-Universität Freiburg


Tuesday July 6, 2021 19:53 - 19:59 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:59 CEST

Recent updates to Nebulizer: a command line utility for Galaxy admins
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118592.1)
→ Video

Peter Briggs 1

  1. University of Manchester, GB

Speakers
avatar for Peter Briggs

Peter Briggs

Computer Officer, Bioinformatics Core Facility, University of Manchester
Software developer supporting a team of informaticians within the Bioinformatics Core Facility (BCF) in the Faculty of Biology Medicine & Health (FBMH) at the University of Manchester. Responsibilities include supporting a number of local Galaxy instances both internally (for local... Read More →


Tuesday July 6, 2021 19:59 - 20:05 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:05 CEST

How UseGalaxy.EU is managed - tips and tricks from inside
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118605.1)

Gianmauro Cuccuru 1; Helena Rasche 2

  1. Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106,79110 Freiburg, Germany , DE
  2. Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, NL

Speakers
avatar for Gianmauro Cuccuru

Gianmauro Cuccuru

University of Freiburg


Tuesday July 6, 2021 20:05 - 20:23 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:23 CEST

HPC back-end runner for massive SARS-CoV-2 samples processing
→ Abstract
→ Slides
Video

Hugo Jiménez Hernández 1

  1. Barcelona Supercomputing Center, ES

Speakers
avatar for Hugo Jiménez Hernández

Hugo Jiménez Hernández

Research Engineer, Barcelona Supercomputing Center


Tuesday July 6, 2021 20:23 - 20:29 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:29 CEST

Laniakea - Update 2021
→ Slides (doi: 10.7490/f1000research.1118635.1)
→ Abstract
→ Video

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

  1. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies - National Research Council, IT
  2. National Institute for Nuclear Physics, Bari Section, IT
  3. Dept. of Biosciences, University of Milan, IT
  4. Dept. of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, IT

Speakers
MA

Marco Antonio Tangaro

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies - National Research Council, Bari, Italy


Tuesday July 6, 2021 20:29 - 20:35 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:35 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Tuesday July 6, 2021 20:35 - 20:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:40 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Tuesday July 6, 2021 20:40 - 21:00 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

20:59 CEST

Americas Tuesday Poster / Demo / Sponsor Session
Sponsors and poster / demos are presented in the Poster / Demo / Sponsor Hall in Remo. Sponsors (and the Career Center) are on the first/ground floor.. Tuesday's poster / demos are on floors 2 and 3 of that building.



Tuesday July 6, 2021 20:59 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

F1000Research
→ Remo: Poster/Demo/Sponsor Hall, Floor 1
Galaxy Gateway

F1000Research is proud to be a Silver Sponsor for GCC2021! We are an Open Research publishing platform that offers rapid, transparent publication of a range of different article types, including original research articles, to method articles, data notes, and software tool articles. The platform is particularly well suited to publishing software tool articles as the unique versioning system allows small updates at any time, along with proper syntax highlighting and support for LaTeX and markdown submissions.

Our Galaxy Gateway on the platform brings together articles, posters and slides from Galaxy events. The Gateway allows authors to quickly share their work with the community, boosting visibility and giving researchers proper credit for their contribution.

We’re pleased to be running a call for papers for GCC2021 and would like to invite the Galaxy community to submit their articles to the Galaxy Gateway by 20th July 2021. These can be any type of article, such as a new Galaxy workflow or an update to an existing method or software tool. This is a great opportunity to shine a light on your research, improve its impact and be credited with an academic paper for your work. Please submit via the Galaxy gateway.

Please drop by the F100Research table and learn more from Abbie!

Speakers

Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.10: Laniakea@ReCaS: first year of activity of a Laniakea-based Galaxy “on-demand” service
→ Abstract
→ Poster 
(doi: 10.7490/f1000research.1118652.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 2

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

  1. Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR),Bari, IT
  2. National Institute for Nuclear Physics (INFN), Bari, IT
  3. Department of Biosciences, University of Milan, Milano, IT
  4. Department of Biosc

Speakers
avatar for pietro mandreoli

pietro mandreoli

Dept. of Biosciences, University of Milano


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.2: Automating Galaxy tool requirement updates with Planemo
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Simon Bray 1; Lorraine Coelho 1; Björn Grüning 1

  1. University of Freiburg, DE

Speakers

Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.3: ComPIL 2.0 and MetaNovo Tools for Metaproteomics Searches Within Galaxy: Searching for Needles in a Haystack
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118647.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Reid Wagner 1; Peter Thuy-Boun 2; Andrew McArdle 3; Subina Mehta 1; James Johnson 1; Björn Grüning 4; Gianmauro Cuccuru 4; Dennis Wolan 2; Timothy Griffin 1; Pratik Jagtap 1

  1. University of Minnesota, US
  2. Scripps Research, US
  3. Imperial College London, GB
  4. University of Freiburg, DE



Speakers

Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.4: Diversity of pleurocidin-like antimicrobial peptides in a marine bony fish (Sparus aurata) by re-identification in ESTs
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Alberto Serna Duque 1; Alberto Cuesta Peñafiel 1; Maria Angeles Esteban Abad 1

  1. Immunobiology for Aquaculture Group, Department of Cell Biology & Histology, Faculty of Biology, University of Murcia, ES

Speakers
avatar for Jhon Alberto Serna Duque

Jhon Alberto Serna Duque

PhD student, University of Murcia
Study of antimicrobial peptides in marine fish and looking for new biotechnological applications.


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.5: Galaxy as a global platform for the analysis of SARS-CoV-2 sequence variants
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Wolfgang Maier 1; Anton Nekrutenko 2; Sergei Pond 3, and the covid19.galaxyproject.org, covid19.datamonkey.org and Viral Beacon 4 teams

  1. University  of  Freiburg,  DE
  2. Penn  State University, US
  3. Temple University, US
  4. Centre for Genomic Regulation (CRG), ES

Speakers
avatar for Wolfgang Maier

Wolfgang Maier

University of Freiburg
Interests:- Galaxy tool development- Variant calling tools and pipelines- User trainings


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.6: Easy access to NCBI data within Galaxy
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Nuala O'Leary 1; Adam Stine 1; Eric Cox 1; Adelaide Rhodes 1

  1. National Center for Biotechnology Information (NCBI), US

Speakers
avatar for Adam Stine

Adam Stine

Curator - Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI)
avatar for Nuala O'Leary

Nuala O'Leary

Product Owner, NCBI
Hi Galaxy Community, I'm Nuala O'Leary and I'm product owner of NCBI Datasets and new resource aimed at making it easier for the biology community to access NCBI sequence data. Please come to our poster, talk and Birds of Feather, bring your questions and suggestions for NCBI.


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.7: Galaxy-E project: 2021 News
→ Abstract
→ Poster

→ Remo: Poster/Demo/Sponsor Hall, Floor 2

Yvan  Le  Bras 1;  Coline  Royaux 1;  Simon  Bénateau 2

  1. PNDB  research  e-infrastructure,  UMS  PatriNat, Museum National d’Histoire Naturelle (MNHN), Concarneau, France, FR
  2. Centre d’Ecologie et des Sciences de la Conservation, Muséum national d’Histoire naturelle -Sorbonne Université-CNRS, Paris, FR
  3. Existing known colleagues, unknown users and all people interested!, FR

Speakers
avatar for Yvan Le Bras

Yvan Le Bras

Research engineer, French National Museum of Natural History


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.8: Janis for workflow translation – a potential benefit to the Galaxy ecosystem
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Richard  Lupat 1; Michael Franklin 1,2; Evan Thomas 3; Juny Kesumadewi 1,2; Jiaan Yu 1; Mohammad Bhuyan 3; Tony Papenfuss 1,3; Andrew Lonie 4; Daniel Park 2; Bernard Pope 2; Jason Li 1

  1. Peter MacCallum Cancer Centre, AU
  2. University of Melbourne, AU
  3. Walter and Eliza Hall Institute, AU
  4. Australian BioCommons, AU

Speakers
RL

Richard Lupat

Peter MacCallum Cancer Centre


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-2.9: Enabling widespread use of Vertebrate Genome Project assembly pipeline by integration into Galaxy
→ Abstract
→ Remo: Poster/Demo/Sponsor Hall, Floor 2


Delphine Lariviere 2; Alex Ostrovsky 1

  1. Galaxy, Johns Hopkins University, US 
  2. Galaxy, Penn State University, US

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Postdoc, Penn State University


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-3.2: Genome-wide predictions and structural modeling of protein-protein interactions using Galaxy
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Aysam Guerler 1, Bjoern Gruening 2, Michael C. Schatz 1 and Anton Nekrutenko 3

  1. Johns Hopkins University, Baltimore, US  
  2. University of Freiburg, DE
  3. Penn State University, State College, US



Speakers
avatar for Aysam Guerler

Aysam Guerler

Galaxy Project, Johns Hopkins University
Johns Hopkins University


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-3.3: Practical aspects of implementing the IRIDA system as a solution for One Health bioinformatics analyses
→ Abstract
→ Poster 
(doi: 10.7490/f1000research.1118654.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3

Jeevan Karloss Antony Samy 1,2; Georgios Marselis 1; EveZeyl Fiskebeck 1; Taran Skjerdal 1; Camilla Sekse 1; Karin Lagesen1

  1. Norwegian Veterinary Institute, NO
  2. Norwegian Institute of Public Health, NO

Speakers
avatar for Jeevan Karloss Antony Samy

Jeevan Karloss Antony Samy

Researcher, Norwegian Veterinary Institute
Bioinformatician/frontend developer


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-3.4: Recent updates to Nebulizer: a command line utility for Galaxy admins
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118593.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3

Peter Briggs 1

  1. University of Manchester, GB

Speakers
avatar for Peter Briggs

Peter Briggs

Computer Officer, Bioinformatics Core Facility, University of Manchester
Software developer supporting a team of informaticians within the Bioinformatics Core Facility (BCF) in the Faculty of Biology Medicine & Health (FBMH) at the University of Manchester. Responsibilities include supporting a number of local Galaxy instances both internally (for local... Read More →


Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-3.5: Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL)
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Stephen Mosher 1; Michael C. Schatz 2,1; Anthony Philippakis 3

  1. Department of Biology, Johns Hopkins University, Baltimore, MD., US
  2. Department of Computer Science, Johns Hopkins University, Baltimore, MD., US
  3. Broad Institute of MIT and Harvard, Cambridge, MA, US

Speakers

Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

Tu-3.6: Use of Galaxy tools for microbiome analysis of breast cancer RNA-seq transcriptomic data
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118594.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3

Dominik Hadzega 1; Katarina Kalavska 2; Marian Karaba 3; Gabriel Minarik 4; Juraj Benca 3,5; Sona Ciernikova 6; Tatiana Sedlackova 4; Daniel Pindak 3; Lubos Klucar 1; Michal Mego 2,7

  1. Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, SK
  2. Translational research unit, Faculty of Medicine, Comenius University and National Cancer Institute, Bratislava, SK
  3. Department of Oncosurgery, National Cancer Institute, Bratislava, SK

Speakers

Tuesday July 6, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

22:20 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Tuesday July 6, 2021 22:20 - 22:40 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

22:25 CEST

Remo Reset
The conference is being run on the Remo.co platform. This has many advantages, and a few disadvantages. One of the disadvantages is that our license allows us to only be up for only 5 hours at a time. This means that every 5 hours, or less, we need to reboot the platform.

When this happens, you will need to log back in to Remo to reconnect. There will be one reset during each conference day, either before or after that day's poster/demo/sponsor session. There will be additional resets in the after hours, before or after BoFs and Socials, as needed.

We apologize for this inconvenience.

Tuesday July 6, 2021 22:25 - 22:25 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

22:39 CEST

Americas Session 3
Final session of the first day of the 2021 Galaxy Community Conference (GCC2021).

Presentations in this session focus on workflows.


🙋 A presenter or co-author will be available for live Q&A this session.

Moderators
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota

Tuesday July 6, 2021 22:39 - Wednesday July 7, 2021 00:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

22:40 CEST

A Galaxy-based multi-omic workflow for discovery and validation of candidate neoantigen peptides for immuno-oncology
→ Abstract 
→ Slides (doi: 10.7490/f1000research.1118669.1)
Video

Tim Griffin 1; An Duy Dinh Nguyen 1; James Johnson 1; Subina Mehta 1; Andrew Rajczewski 1; Mitchell Hruska 1; Tyler Jubenville 1; Sue Rathe 1; Flavia Popescu 1; Pratik Jagtap 1; David Largaespada 1

  1. University of Minnesota, US

Speakers
avatar for Tim Griffin

Tim Griffin

Professor, University of Minnesota


Tuesday July 6, 2021 22:40 - 22:46 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

22:46 CEST

Enhancing the Whole Workflow Experience from Development through Publication and to Execution
→ Abstract
→ Slides
Video

John  Chilton 1; Aysam Guerler 2; Marius van den Beek 1

  1. Penn  State  University,  US
  2. Johns Hopkins University, US

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University


Tuesday July 6, 2021 22:46 - 23:04 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:04 CEST

Introducing the Intergalactic Workflow Commission
→ Abstract
→ Slides
→ Video

Marius van den Beek 1; Simon Bray 2; John Chilton 1; Aysam Guerler 3; Ignacio Eguinoa 4; Matthias Bernt 5; Wolfgang Maier 2

  1. Department of Biochemistry and Molecular Biology, Penn State University, University Park PA, US
  2. Bioinformatics Group, Department of Computer Science, Albert Ludwigs University, Freiburg, DE
  3. Department of Biology, Johns Hopkins University, Baltimore MD, US
  4. VIB Center for Plant Systems Biology, BE
  5. Helmholtz Centre for Environmental Research, – UFZ, Leipzig, DE

Speakers
avatar for Marius van den Beek

Marius van den Beek

Penn State University


Tuesday July 6, 2021 23:04 - 23:22 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:22 CEST

Publication of BioCompute Objects (IEEE-2791-2020) created from Galaxy workflow invocations
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118619.1)
Video

Charles Hadley King 1; Christopher Armstrong 1

  1. George Washington University, US

Speakers
avatar for Charles [Hadley] King

Charles [Hadley] King

Senior Research Associate, George Washington University


Tuesday July 6, 2021 23:22 - 23:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:40 CEST

Developing Pro workflows: lessons learned
→ Abstract
→ Slides
Video

Nathan Roach 1; Randy  Guertin 1; Dannon Baker 1; John Chilton 1; Sam Guerler 1; Stephanie Pond 1; Enis Afgan 1

  1. GalaxyWorks, US

Speakers
avatar for Randy Guertin

Randy Guertin

Computational Biologist, GalaxyWorks


Tuesday July 6, 2021 23:40 - 23:46 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:46 CEST

The WorkflowHub - a registry for workflows
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118663.1)
→ Video

Ignacio Eguinoa 1,2; WorkflowHub Community 4; Frederik Coppens 1,2; Carole Goble 3

  1. Department of  Plant  Biotechnology  and  Bioinformatics,  Ghent  University,  BE
  2. VIB Center for Plant Systems Biology, BE
  3. Department of Computer Science, The University of Manchester, GB
  4. https://about.workflowhub.eu/acknowledgements/#workflowhub-club, GB

Speakers
IE

Ignacio Eguinoa

ELIXIR Belgium - VIB Center for Plant Systems Biology


Tuesday July 6, 2021 23:46 - 23:52 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:52 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Tuesday July 6, 2021 23:52 - Wednesday July 7, 2021 00:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.
 
Wednesday, July 7
 

00:00 CEST

Break
The first day's formal content is done, but stick around for Birds-of-a-Feather (in 20 minutes).

Take a break! Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

See you soon.

Wednesday July 7, 2021 00:00 - 00:20 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

00:20 CEST

Birds of a Feather (BOFs)
Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.

Anyone is welcome to propose a BoF! All you need is a title, an organizer, and a brief description. At GCC2020, BoFs will be scheduled before and after the official conference day.

The call for BOFs will go out in June.

Wednesday July 7, 2021 00:20 - 02:00 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

07:59 CEST

EMEA-APAC Conference Day 2
The 2nd day of GCC2021

Wednesday July 7, 2021 07:59 - 17:50 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

08:00 CEST

Birds of a Feather (BOFs)
Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.

BoFs scheduled in this flocking:


Any meeting participant is welcome to propose a BoF! All you need is a title, an organizer, and a brief description.

Wednesday July 7, 2021 08:00 - 08:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

08:00 CEST

BoF: Addressing common misconceptions about Galaxy
Since the beginning of the project, Galaxy has had to fight off all kinds of misconceptions - ranging from "Galaxy is only for Biologists" to "Galaxy does not work". The Global Galaxy Steering Committee has set up a group working on ideas to address those myths.

In this BoF, I would like to invite the wider Galaxy community to help us with this work.

Meeting places
Materials: slides text-doc

Speakers
avatar for Hans-Rudolf Hotz

Hans-Rudolf Hotz

Friedrich Miescher Institute for Biomedical Research, Basel


Wednesday July 7, 2021 08:00 - 08:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

08:00 CEST

BoF: Namaste, Galaxy India!
Please join us for the (soft) launch of the Galaxy India Community.  This community is about enabling data intensive research and instruction in India using the Galaxy platform. As a group, we are/will sponsor

  • Training and workshops, both standalone and at larger meetings
  • Webinars and community calls
  • In person gatherings, once these become prudent
  • Communications channels, including chat and a mailing list
  • An India-focused server hosted by the European Galaxy Team
  • And, later this year, an India-based UseGalaxy server

This BoF will cover community resources, and discuss where the group is planning to go, and where we should be planning to go.

Galaxy India intends to have a full launch, later this year as part of Inbix 2021. Please help us get started.

BoF Places


Jitsi details if you are unable to join through your browser:


Speakers
avatar for Anshu Bhardwaj

Anshu Bhardwaj

Long term Fellow, Senior Scientist, Interdisciplinary Research Center (CRI) and CSIR-Institute of Microbial Technology
avatar for Kiran K Telukunta

Kiran K Telukunta

TMS Foundation
Done PhD from University of Freiburg in Pharmaceutical Bioinformatics. As part of TMS Foundation and Bioclues promoting Galaxy Opensource frame work in India. Working as Cloud Architect. For a detail profile please visit my linkedin page. Following reasons should encourage you to... Read More →
avatar for Prashanth Suravajhala

Prashanth Suravajhala

Senior Scientist and Founder, Bioclues.org, Birla Institute of Scientific Research; Bioclues
Prashanth N Suravajhala is a senior scientist at Birla Institute of Scientific Research, Jaipur. A PhD in Systems Biology, he went on to gain more than 7 years of postdoctoral experience across four different laboratories. He has interests exploring the known unknown regions in the human genome, primarily... Read More →
avatar for Harpreet Singh

Harpreet Singh

Assistant Professor, Hans Raj Mahila Maha Vidyalaya (HMV), Jalandhar
I am the Head, Department of Bioinformatics at one of the best women colleges in India. My research interest include Structural Bioinformatics, Machine Learning and Genomics. I am also the Finance Secretary of one of the biggest Bioinformatics community in India i.e. Bioclues.org... Read More →
avatar for Kirtan Dave

Kirtan Dave

Assistant Professor, GSFC University


Wednesday July 7, 2021 08:00 - 08:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

08:00 CEST

BoF: Rainbow Galaxy People (LGBTQIA)
Members of the LGBTQIA community.

Flocking places


Speakers
avatar for Michael Crusoe

Michael Crusoe

Workflows!Standards!ELIXIR!



Wednesday July 7, 2021 08:00 - 08:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

09:00 CEST

09:01 CEST

Welcome
Welcome to the second day of the 2021 Galaxy Community Conference (GCC2021)!

We'll introduce the day, and present any last minute news


Wednesday July 7, 2021 09:01 - 09:10 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:10 CEST

Detection and functional annotation of lncRNA
→ Abstract 
→ Slides
Video

Bianca Pasat 1,2; Elena Gkotsi 1,2,3; Xara Mastrokalou 1,2; Theodoros Koutsandreas 1,2; Eleutherios Pilalis 1,2; Aristotelis Chatziioannou 1,2

  1. e-NIOS Applications Private Company, GR
  2. Systems Biology, Biomedical Research Foundation of the Academ, GR
  3. Department of Biochemistry and Biotechnology, University of Thessaly, GR

Speakers
avatar for Bianca Pasat

Bianca Pasat

Bioinformatician, eNIOS
I studied Biology and Bioinformatics in Athens.Right now I am a member of Aristotelis Chatziioannou's group at IIBEAA and I work at eNIOS.PhD candidate at NUIG



Wednesday July 7, 2021 09:10 - 09:16 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:16 CEST

Automated Deployment of Genome Databases for Marine Brown Algae Using Galaxy Genome Annotation (GGA)
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118614.1)
Video

Loraine Brillet-Guéguen 1,2; Arthur Le Bars 2; Anthony Bretaudeau 3; J. Mark Cock1; Susana M. Coelho1; Erwan Corre 2

  1. Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, FR
  2. CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680, Roscoff, FR
  3. INRA, UMR IGEPP, BIPAA/GenOuest, Campus, Rennes, FR

Speakers
LG

Loraine Guéguen

Station Biologique de Roscoff



Wednesday July 7, 2021 09:16 - 09:22 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:22 CEST

Galaxy-ML: An Accessible, Reproducible, and Scalable Machine Learning Toolkit for Biomedicine
→ Abstract
→ Slides (doi.: 10.7490/f1000research.1118621.1)
Video

Qiang Gu 1; Anup Kumar 2; Simon Bray 2; Allison Creason 1; Alireza Khanteymoori 2; Vahid Jalili 1; Björn Grüning 2; Jeremy Goecks 1; Kaivan Kamali 3

  1. Oregon  Health  and  Science  University  (OHSU),  US
  2. University of Freiburg, DE
  3. Penn State University, US

Speakers
KK

Kaivan Kamali

Computational Scientist, Penn State University
Computer scientist specializing in AI/ML. Interested in applying AI/ML to bioinformatics problems.



Wednesday July 7, 2021 09:22 - 09:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:40 CEST

The immuneML Portal: a public Galaxy server for machine learning analysis of adaptive immune receptor repertoires
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118651.1)
→ Video

Milena Pavlovic 1; Lonneke Scheffer 1; Victor Greiff 1; Geir Kjetil Sandve 1

  1. University of Oslo, NO

Speakers
avatar for Lonneke Scheffer

Lonneke Scheffer

PhD Candidate, University of Oslo
PhD student | computational immunology | University of Oslo



Wednesday July 7, 2021 09:40 - 09:46 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:46 CEST

The Galaxy Public Health Community
→ Abstract 
Video

Peter van Heusden 5; Abdul Karim Sesay 1; Andrew Page 2; Christophe Antoniewski 3; Stefano Morabito 4

  1. MRC The Gambia, GM
  2. Quadrum Institute, GB
  3. ARTbio Bioinformatics Analysis Facility, Sorbonne Université, FR
  4. EURL for E. coli including VTEC, Istituto Superiore di Sanità, IT
  5. MRC Bioinformatics Unit, SANBI, University of the Western Cape, ZA



Wednesday July 7, 2021 09:46 - 09:52 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:52 CEST

A flexible Galaxy-based platform for the analysis of microbial WGS data in public health
→ AbstractRelated Poster 
→ Slides (doi: 10.7490/f1000research.1118649.1)
→ Video

Bert Bogaerts 1,2; Raf Winand 1; Julien Van Braekel 1; Nancy H. C. Roosens 1; Sigrid C. J. De Keersmaecker 1; Kevin Vanneste 1

  1. Transversal activities in Applied Genomics, Sciensano, BE
  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, BE

Speakers
BB

Bert Bogaerts

UGhent – Department of information Technology, IDLab, imec



Wednesday July 7, 2021 09:52 - 09:58 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:58 CEST

The “ARIES Genomics” Italian public health surveillance system
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118632.1)
 Video

Arnold Knijn 1; Valeria Michelacci 1; Stefano Morabito 1

  1. Istituto Superiore di Sanità, IT

Speakers
avatar for Arnold Knijn

Arnold Knijn

Istituto Superiore di Sanità



Wednesday July 7, 2021 09:58 - 10:04 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:04 CEST

Fostering Public Health Bioinformatics and Collaboration with GalaxyTrakr
→ Abstract
→ Video

Justin Payne 1; Jayanthi Gangiredla 1; Hugh Rand 1; Daniel Benisatto 8; Charles Strittmatter 1; Jimmy Sanders 2; William J. Wolfgang 3; Kevin Libuit 4; James B. Herrick 5; Melanie Prarat 9; Magaly Toro 6; Thomas Farrell 1; Errol Strain 7

  1. US Food and Drug Administration, Center for Food Safety and Applied Nutrition, US
  2. SDS Solutions, Inc., US
  3. Wadsworth Center, US
  4. Libuit Scientific, LLC, US
  5. Center for Genome and Metagenome Studies, James Madison University, US
  6. Laboratorio de Micr

Speakers
avatar for Justin Payne

Justin Payne

Computer Scientist, US Food and Drug Administration
I'm a Python and Java developer, one of the primary developers of the FDA's GenomeTrakr whole-genome pathogen biosurveillance network, an application scientist and admin on GalaxyTrakr, and the primary author of tools such as Bootsie and PoreRefiner. Recently rated "alright" by one... Read More →



Wednesday July 7, 2021 10:04 - 10:10 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:10 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Wednesday July 7, 2021 10:10 - 10:20 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:20 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Wednesday July 7, 2021 10:20 - 10:40 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

10:39 CEST

EMEA-APAC Session 5
Second session of the second day of the 2021 Galaxy Community Conference (GCC2021).  

Presentations this session:


🙋 A presenter or co-author will be available for live Q&A in this session.

Moderators
MD

Maria Doyle

Application and Training Specialist, Peter MacCallum Cancer Centre

Wednesday July 7, 2021 10:39 - 11:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:40 CEST

Analysis of Microscopy Data in Galaxy
→ Abstract
→ Slides 
→ Video

Beatriz Serrano-Solano 1; Yi Sun 2; Jeremy Goecks 3; Jean-Karim Hériché 2

  1. University of Freburg, DE
  2. European Molecular Biology Laboratory, DE
  3. Oregon Health and Science University , US

Speakers
avatar for Beatriz Serrano-Solano

Beatriz Serrano-Solano

Community Coordinator for the European Galaxy Community, University of Freiburg



Wednesday July 7, 2021 10:40 - 10:46 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:46 CEST

Bridging Natural Language Processing and Biomedical Data Analysis
→ Abstract
→ Slides
→ Video

Daniel Blankenberg 1; Nancy Ide 2

  1. Cleveland  Clinic  Genetic  Medical  Institute,  US
  2. Vassar  College, US

Speakers


Wednesday July 7, 2021 10:46 - 11:04 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:04 CEST

French EBV operationalization pilot, where Galaxy can help Biodiversity
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118612.1)
→ Video

Coline Royaux 1; Dominique Pelletier 2; Sandrine Pavoine 3; Jean-Baptiste Mihoub 3; Yvan Le Bras 1

  1. PNDB research e-infrastructure, UMS PatriNat, Museum National d’Histoire Naturelle (MNHN), Concarneau, FR
  2. Institut français de recherche pour l'exploitation de la mer (Ifremer), Nantes, FR
  3. Centre d’Ecologie et des Sciences de la Conse

Speakers
CR

Coline Royaux

French national museum of natural history (MNHN)



Wednesday July 7, 2021 11:04 - 11:10 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:10 CEST

Updates from the Single-Cell Community
→ Slides (doi: 10.7490/f1000research.1118634.1)
→ Abstract 
→ Video

Mehmet Tekman 1; Wendi Bacon 2

  1. Freiburg Galaxy Team, Backofen Group, University Freiburg, DE
  2. The Open University, Milton Keynes MK7 6AA, GB

Speakers
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, University of Freiburg
Single-Cell, Developing Wrappers with Emacs
avatar for Wendi Bacon

Wendi Bacon

Lecturer, Open University



Wednesday July 7, 2021 11:10 - 11:16 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:16 CEST

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118604.1)
→ Video

Willem de Koning 1,2; Milad Miladi 3; Saskia D. Hiltemann 1; Astrid P. Heikema 4; John P. Hays 4; Stephan Flemming 3; Marius van den Beek 5; Dana A. Mustafa 2; Rolf Backofen 3; Björn Grüning 3; Andrew P. Stubbs 1

  1. Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Centre, NL
  2. Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus University Medical Centre, NL
  3. Department of Computer Science, Bioinformatics Group, Univesity of Freiburg, DE
  4. Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, NL
  5. Department of Stem Cells and Tissue Homeostasis, Institut Curie, PSL Research University, FR

Speakers


Wednesday July 7, 2021 11:16 - 11:22 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:22 CEST

Using custom Galaxy workflows to reproducibly search for bacteriophage spanin proteins reveals distinct population distributions
→ Abstract
→ Slides (doi: /10.7490/f1000research.1118590.1)
→ Video

Jason Snowden 1; Curtis Ross 1; Jolene Ramsey 1; Ry Young 1

  1. Center for Phage Technology, Department of Biochemistry & Biophysics, Texas A&M University, US

Speakers
avatar for Jolene Ramsey

Jolene Ramsey

Postdoc, Texas A&M University
I love to study the viruses of bacteria, called bacteriophages, or phages. Ask me about viruses, or my favorite podcast, This Week in Virology.



Wednesday July 7, 2021 11:22 - 11:28 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:28 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Wednesday July 7, 2021 11:28 - 11:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:40 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Wednesday July 7, 2021 11:40 - 12:00 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

11:45 CEST

Remo Reset
The conference is being run on the Remo.co platform. This has many advantages, and a few disadvantages. One of the disadvantages is that our license allows us to only be up for only 5 hours at a time. This means that every 5 hours, or less, we need to reboot the platform.

When this happens, you will need to log back in to Remo to reconnect. There will be one reset during each conference day, either before or after that day's poster/demo/sponsor session. There will be additional resets in the after hours, before or after BoFs and Socials, as needed.

We apologize for this inconvenience.

Wednesday July 7, 2021 11:45 - 11:45 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

11:59 CEST

EMEA-APAC Wednesday Poster / Demo / Sponsor Session
Sponsors and poster / demos are presented in the Poster / Demo / Sponsor Hall in Remo. Sponsors (and the Career Center) are on the first/ground floor.. Wednesday's poster / demos are on floors 3 and 4 of that building.




Wednesday July 7, 2021 11:59 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.3: Galaxy and Research Lifecycle Management technologies for Earth Science Communities and Copernicus users in EOSC
→ Abstract
→ 
Poster (doi: 10.7490/f1000research.1118598.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4

Anne Fouilloux 1; Jean Iaquinta 1

  1. University of Oslo, Department of Geosciences, NO

Speakers
avatar for Anne Fouilloux

Anne Fouilloux

I am a Research Software Engineer working for the Nordic e-Infrastructure Collaboration (NeIC) and working on Galaxy climate (https://climate.usegalaxy.eu/) e.g. providing Galaxy tools for exploiting climate data, models to facilitate climate impact studies and climate modelling... Read More →



Wednesday July 7, 2021 12:00 - 12:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

F1000Research
→ Remo: Poster/Demo/Sponsor Hall, Floor 1
Galaxy Gateway

F1000Research is proud to be a Silver Sponsor for GCC2021! We are an Open Research publishing platform that offers rapid, transparent publication of a range of different article types, including original research articles, to method articles, data notes, and software tool articles. The platform is particularly well suited to publishing software tool articles as the unique versioning system allows small updates at any time, along with proper syntax highlighting and support for LaTeX and markdown submissions.

Our Galaxy Gateway on the platform brings together articles, posters and slides from Galaxy events. The Gateway allows authors to quickly share their work with the community, boosting visibility and giving researchers proper credit for their contribution.

We’re pleased to be running a call for papers for GCC2021 and would like to invite the Galaxy community to submit their articles to the Galaxy Gateway by 20th July 2021. These can be any type of article, such as a new Galaxy workflow or an update to an existing method or software tool. This is a great opportunity to shine a light on your research, improve its impact and be credited with an academic paper for your work. Please submit via the Galaxy gateway.

Please drop by the F100Research table and learn more from Abbie!

Speakers

Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-3.10: Detection and functional annotation of lncRNA
→ Abstract
→ Poster
Demo
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Bianca Pasat 1,2; Elena Gkotsi 1,2,3; Xara Mastrokalou 1,2; Theodoros Koutsandreas 1,2; Eleutherios Pilalis 1,2; Aristotelis Chatziioannou 1,2

  1. e-NIOS Applications Private Company, GR
  2. Systems Biology, Biomedical Research Foundation of the Academ, GR
  3. Department of Biochemistry and Biotechnology, University of Thessaly, GR

Speakers
avatar for Bianca Pasat

Bianca Pasat

Bioinformatician, eNIOS
I studied Biology and Bioinformatics in Athens.Right now I am a member of Aristotelis Chatziioannou's group at IIBEAA and I work at eNIOS.PhD candidate at NUIG



Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-3.11: GalaxyLab: A JupyterLab extension for interactive graphical and programmatic access to Galaxy
→ Abstract
→ 
Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 3

Jayadev Joshi 1; Daniel Blankenberg 1

  1. Cleveland Clinic Foundation, US

Speakers
avatar for jayadev joshi

jayadev joshi

Postdoctoral fellow, Cleveland clinic foundation



Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-3.7: A flexible Galaxy-based platform for the analysis of microbial WGS data in public health
→ AbstractPoster
→ Poster (doi: 10.7490/f1000research.1118648.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Bert Bogaerts 1,2; Raf Winand 1; Julien Van Braekel 1; Nancy H. C. Roosens 1; Sigrid C. J. De Keersmaecker 1; Kevin Vanneste 1

  1. Transversal activities in Applied Genomics, Sciensano, BE
  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, BE

Speakers
BB

Bert Bogaerts

UGhent – Department of information Technology, IDLab, imec



Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-3.8: EDAM ontology, tools, and community
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


EDAM is an ontology of data analysis and data management in life sciences. The structure of EDAM is relatively simple, divided into 4 main sub-ontologies:

  • Topic
  • Operation
  • Data (incl. Identifier)
  • Format

EDAM is used in numerous resources including Galaxy, bio.tools, Debian, WorkflowHub, the ELIXIR Europe training portal TeSS, or BIII (the BioImage Informatics Index). Thanks to the annotations with EDAM, computational tools, workflows, data, and educational materials are easier to find, compare, choose, and integrate.

In Galaxy, EDAM is used for annotation of tools, and of types of data/data formats. There is a new option for administrators of a Galaxy server, to visualise the tools panel by EDAM concepts (galaxyproject/galaxy#10592). 🌌

EDAM contributes to open science also by serving as an ontology for provenance metadata, making the data more understandable, findable, and comparable. EDAM and its applications lower the barrier and effort for scientists and citizens alike, towards doing scientific research in a more open, reliable, and inclusive way.

The EDAM community brings together software engineers and science experts (academic, industrial, citizen), professionals & volunteers. Along with the ontology, this community has developed a number of tools that enhance user experience with EDAM:

  • 🌲 EDAM Browser is a lightweight & fast web-based ontology browser that provides a number of user-oriented features such as aggregated search across various EDAM-annotated resources (e.g. bio.tools, TeSS, …).
  • 🧾 EDAMmap is a tool for text mining EDAM concepts from articles.
  • 🍪 EDAM Popovers is a Firefox add-on for showing details of EDAM concepts found in a website. Great for Galaxy code on GitHub. 🙌


Authors
Melissa Black - Outreachy intern (EDAM), São Paulo, BR; moving to Los Angeles, U.S.
Hager Eldakroury - Ain Shams University, Outreachy intern (EDAM), Cairo, EG
Sakshi Dhamija - ABV - Indian Institute of Information Technology and Management, Gwalior, IN
Rashika Rathi - Indian Institute of Technology, Mandi, IN
Ankita Priya - Birla Institute of Technology, Mesra, IN
Anne Machinda - independent contributor, Bamenda, CM
Uttam Singh Khanduja - Medicaps University, Indore, IN
Gloria Umutesi - independent contributor, Kigali, RW
Anita Op - independent contributor, NG
Precious Chieke - independent contributor, NG
Steve Laurie - Centre Nacional d'Anàlisi Genòmica, Barcelona, ES
Mads Kierkegaard - University of Southern Denmark, Ødense, DK
Veit Schwämmle - University of Southern Denmark, Ødense, DK
Chris Hunter - GigaScience GigaDB, Hong Kong, CN
Jonathan Karr - Icahn School of Medicine at Mount Sinai, New York City, US
Drashti Patoliya - independent contributor, Surat, IN
Sunday Cletus Nkwuda - freelancer, volunteer contributor, Outreachy intern (Debian), Kaduna, NG
Guneet Singh - independent contributor, BV
Pooja Yadav - independent contributor, Outreachy intern (LLVM), Goa, IN
Kelly D'oleo - independent contributor, New York City, US
Marlene Cherop - independent contributor, KE
Tawah Peggy Che Nico - University of Buea, CM
Tosin Bakare - independent contributor, Lagos, NG
Chiamaka Uzuegbu - independent contributor, NG
ellschi - independent contributor, DE
ZM202 - independent contributor, US
Babsbarokah - independent contributor, Lagos, NG
Jon Ison - Institut Français de Bioinformatique (at the time of contribution), FR
Alban Gaignard - University of Nantes, FR
Erik Jaaniso - University of Tartu, EE
Ivan Kuzmin - University of Tartu, EE
Helena Rasche - Erasmus Medical Center, Rotterdam and Avans University of Applied Sciences, NL
Bryan Brancotte - Institut Pasteur, Paris, FR
Matúš Kalaš - University of Bergen, NO
Hervé Ménager - Institut Pasteur, Paris, FR

Speakers
HE

Hager Eldakroury

Outreachy Intern, EDAM
MB

Melissa Black

Outreachy Intern, EDAM
I'm an open science enthusiast with a background in Geography.



Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-3.9: Automated Deployment of Genome Databases for Marine Brown Algae Using Galaxy Genome Annotation (GGA)
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118615.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3

Loraine Brillet-Guéguen 1,2; Arthur Le  Bars 2; Anthony Bretaudeau 3; J. Mark Cock1; Susana M. Coelho1; Erwan Corre 2

  1. Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, FR
  2. CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680, Roscoff, FR
  3. INRA, UMR IGEPP, BIPAA/GenOuest, Campus, Rennes, FR

Speakers
LG

Loraine Guéguen

Station Biologique de Roscoff


Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.10: Using custom Galaxy workflows to reproducibly search for bacteriophage spanin proteins reveals distinct population distributions
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Jason Snowden 1; Curtis Ross 1; Jolene Ramsey 1; Ry Young 1

  1. Center for Phage Technology, Department of Biochemistry & Biophysics, Texas A&M University, US

Speakers
avatar for Jolene Ramsey

Jolene Ramsey

Postdoc, Texas A&M University
I love to study the viruses of bacteria, called bacteriophages, or phages. Ask me about viruses, or my favorite podcast, This Week in Virology.



Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.11: The “ARIES Genomics” Italian public health surveillance system
→ Abstract 
→ Poster (doi:10.7490/f1000research.1118583.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Arnold Knijn 1; Valeria Michelacci 1; Stefano Morabito 1

  1. Istituto Superiore di Sanità, IT

Speakers
avatar for Arnold Knijn

Arnold Knijn

Istituto Superiore di Sanità


Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.2: Driving workforce transition in Australian life science research
→ Abstract
→ 
Poster (doi:10.7490/f1000research.1118591.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4

Anna Syme 1,2; Jeff Christiansen 1; Nigel Ward 1; Simon Gladman 2; Catherine Bromhead 2; Igor Makunin 3; Mike Thang 3; Gareth Price 3; Andrew Lonie 1,2

  1. Australian BioCommons, Faculty of Medicine Dentistry and Health Sciences and School of Computing and Information Systems, University of Melbourne, AU
  2. Melbourne Bioinformatics, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Australia, AU
  3. QCIF Facility for Advanced Bioinformatics, Institute of Molecular Biology, University of Queensland, Australia, AU

Speakers
avatar for Anna Syme

Anna Syme

Bioinformatician, The University of Melbourne
Bioinformatics, Galaxy Training and the GTN, Genome Assembly, Evolution



Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.4: Publication of BioCompute Objects (IEEE-2791-2020) created from Galaxy workflow invocations
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118620.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4

Charles Hadley King 1; Christopher Armstrong 1

  1. George Washington University, US

Speakers
avatar for Charles [Hadley] King

Charles [Hadley] King

Senior Research Associate, George Washington University


Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.5: Gallantries: Scalable, Modular Bioinformatics Curricula
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Helena Rasche 1; Saskia Hiltemann 1; Bérénice Batut 2; Fotis Psomopoulos 3; Anthony Bretaudeau 4;
Yvan Le Bras 5

  1. Erasmus Medical Center, NL
  2. Albert-Ludwigs-Universität Freiburg, DE
  3. INAB|CERTH, GR
  4. Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, FR
  5. Muséum national d’histoire naturelle, FR

Speakers


Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.7: The next-generation Galaxy community site
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Nick Stoler¹; Dannon Baker²

  1. Penn State University, US
  2. Johns Hopkins University, US

Speakers


Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.8: GPU enabled Jupyterlab notebook for deep learning using Tensorflow in Galaxy
Abstract
→ Remo: Poster/Demo/Sponsor Hall, Floor 4
Presentation
→ Video presentation

Anup Kumar 1

  1. Bioinformatics Group Department of Computer Science Albert-Ludwigs-University Freiburg Georges-Köhler-Allee 106 79110 Freiburg, DE

Speakers
avatar for Anup Kumar

Anup Kumar

PhD candidate, University of Freiburg



Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:00 CEST

W-4.9: Taxonomic Classification Analysis of Human Gut Microbiota Using Kraken 2
→ Abstract
→ 
Poster (doi: 10.7490/f1000research.1118672.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4

Nihan Sultan Milat 1; Ab. Matteen Rafiqi 1; Muhammet Çelik 1

  1. Bezmialem Vakıf Üniversitesi, TR



Wednesday July 7, 2021 12:00 - 13:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

13:20 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Wednesday July 7, 2021 13:20 - 13:40 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

13:39 CEST

EMEA-APAC Session 6
Final session of the second day of the 2021 Galaxy Community Conference (GCC2021).

Presentations this session:


A presenter or co-author will be available for live Q&A in this session.

Moderators
avatar for Martin Cech

Martin Cech

ELIXIR CZ

Wednesday July 7, 2021 13:39 - 15:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

13:40 CEST

Galaxy Community Update
Video
→ Slides

Find out what has happened, and what is coming, in the Galaxy.

Speakers
avatar for Andrew Lonie

Andrew Lonie

Director Australian BioCommons, University of Melbourne
avatar for Björn Grüning

Björn Grüning

University of Freiburg
avatar for Anton Nekrutenko

Anton Nekrutenko

Penn State University
Penn State University
avatar for Jeremy Goecks

Jeremy Goecks

Associate Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University
avatar for Dan Blankenberg

Dan Blankenberg

Assistant Professor, Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute
avatar for Mike Schatz

Mike Schatz

Johns Hopkins University



Wednesday July 7, 2021 13:40 - 14:05 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:05 CEST

Modernizing the Galaxy Backend - Data Model
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118653.1)
→ Video

Sergey Golitsynskiy 1

  1. Johns Hopkins University, US

Speakers
avatar for Sergey Golitsynskiy

Sergey Golitsynskiy

software engineer, Johns Hopkins University



Wednesday July 7, 2021 14:05 - 14:11 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:11 CEST

Modernizing the Galaxy Backend - Typing and the API
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118607.1)
→ Video

David López 1; Galaxy Backend Working Group 2

  1. University of Freiburg, DE 
  2. Galaxy Project, Global

Speakers
avatar for David López

David López

Software Developer, University of Freiburg



Wednesday July 7, 2021 14:11 - 14:17 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:17 CEST

Modernizing the Galaxy Backend - Typing and Dependency Injection
→ Abstract
→ Video

John Chilton 1

  1. Penn State Unversity, US
  2. Galaxy Project, Global

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University



Wednesday July 7, 2021 14:17 - 14:23 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:23 CEST

Modernizing the Galaxy Backend - A Task Framework
→ Abstract
→ Slides (https://doi.org/10.7490/f1000research.1118702.1)
Video

Dannon Baker 1; Marius van den Beek 2

  1. Johns Hopkins University, US
  2. Pennsylvania State University, US

Speakers
avatar for Dannon Baker

Dannon Baker

Galaxy Project, Johns Hopkins University
Talk to me about Galaxy Development, especially the UI!



Wednesday July 7, 2021 14:23 - 14:29 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:29 CEST

Galaxy for Protected Datasets
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118665.1)
→ Video

Alexandru Mahmoud 1; Luke Sargent 2; John Chilton 4; Rob Title 5; Dannon Baker 1; Charles Overbeck 6; Nuwan Goonasekera 3; Stephen Mosher 1; Michael Schatz 1; Enis Afgan 1

  1. Johns Hopkins University, US
  2. Oregon Health and Sciences University, US
  3. University of Melbourne, AU
  4. Penn State University, US
  5. Broad Institute, US
  6. USCS, US

Speakers
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University



Wednesday July 7, 2021 14:29 - 14:35 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:35 CEST

Galaxy Language Server - Develop high-quality Galaxy tool wrappers at intergalactic speed
→ Abstract
→ Slides
→ Video

David López 1

  1. University of Freiburg, DE
                                       


Speakers
avatar for David López

David López

Software Developer, University of Freiburg



Wednesday July 7, 2021 14:35 - 14:41 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:41 CEST

Galaxy CloudStor Integration - linking national resources for secure data transfer between services
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118764.1)
→ Video

Nuwan Goonasekera 1; Michael D’Silva 3; Frankie Stevens 3; Gareth Price 2

  1. Melbourne Bioinformatics, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Australia, AU
  2. QCIF Facility for Advanced Bioinformatics, Institute of Molecular Biology, University of Queensland, AU
  3. AARNet, AU

Speakers
avatar for Gareth Price

Gareth Price

Head of Computational Biology, QCIF Facility for Advanced Bioinformatics
Gareth Price has been a Genomics Scientist for over 15 years now. He has involved in experimental design, assay performance, data QC, data analysis and data interpretation from early printed microarrays, to cartridge based GeneChips through to multiple Next Gen platforms. These works... Read More →



Wednesday July 7, 2021 14:41 - 14:47 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:47 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Wednesday July 7, 2021 14:47 - 15:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

15:00 CEST

Break
The first day's formal content is done, but stick around for Birds-of-a-Feather (in 20 minutes) and the Opening Social.

Take a break! Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

See you soon.

Wednesday July 7, 2021 15:00 - 15:20 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

15:19 CEST

Americas Conference Day 2
Second day of GCC2021 in the Americas Zone

Wednesday July 7, 2021 15:19 - Thursday July 8, 2021 02:00 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

15:20 CEST

Birds of a Feather (BOFs)
Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.

BoFs scheduled in this flocking:


Any meeting participant is welcome to propose a BoF! All you need is a title, an organizer, and a brief description.

Wednesday July 7, 2021 15:20 - 16:40 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

15:20 CEST

BoF: Celestial Masses: Galaxy Platform for Mass Spectrometry Research
In this Birds of Feather for Galaxy for Mass Spectrometry interested researchers will meet to discuss Galaxy tools and workflows related to proteomics, metabolomics and imaging mass spectrometry. The group will discuss software tools, workflows, new methods, workshops and topics related to mass spectrometry. See z.umn.edu/celestialmasses for details.

Flocking Spaces:


Speakers
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
avatar for Melanie Föll

Melanie Föll

Institute for Surgical Pathology Freiburg


Wednesday July 7, 2021 15:20 - 16:40 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

15:20 CEST

BoF: Galaxy Public Health Community
Public Health Genomics involves the use of genomic information to benefit public health. The Galaxy Public Health Community invites participation towards building and sharing resources that enhance Galaxy’s utility for those working in public health, including researchers, clinicians, epidemiologists and more. This BoF will be an opportunity for Galaxy Public Health community members to meet, network and plan.

Flocking Places:

Speakers
KL

Karin Lagesen

Norwegian Veterinary Institute
avatar for Arnold Knijn

Arnold Knijn

Istituto Superiore di Sanità


Wednesday July 7, 2021 15:20 - 16:40 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

16:45 CEST

Remo Reset
The conference is being run on the Remo.co platform. This has many advantages, and a few disadvantages. One of the disadvantages is that our license allows us to only be up for only 5 hours at a time. This means that every 5 hours, or less, we need to reboot the platform.

When this happens, you will need to log back in to Remo to reconnect. There will be one reset during each conference day, either before or after that day's poster/demo/sponsor session. There will be additional resets in the after hours, before or after BoFs and Socials, as needed.

We apologize for this inconvenience.

Wednesday July 7, 2021 16:45 - 16:45 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

17:00 CEST

Birds of a Feather (BOFs)
Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.

BoFs flocking in this session are:


Any meeting participant is welcome to propose a BoF! All you need is a title, an organizer, and a brief description.


Wednesday July 7, 2021 17:00 - 17:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

17:00 CEST

BoF: Accessing NCBI Data in Galaxy
National Center for Biotechnology Information (NCBI) at the US National Institutes of Health (NIH) has significantly improved access to sequence and metadata by reimagining our programmatic and web interfaces, data formats for SRA and Genbank and cloud-based tools (e.g. ElasticBLAST). NCBI wants to update users on two new initiatives:

  1. moving the complete Sequence Read Archive (>14 PB ) to AWS ODP and 
  2. improving web, command-line and API access to GenBank data through NCBI Datasets

We welcome you to a discussion of any and all use cases for working with the new data access options!

Flocking places

Speakers
EC

Eric Cox

NIH/NLM/NCBI
avatar for Nuala O'Leary

Nuala O'Leary

Product Owner, NCBI
Hi Galaxy Community, I'm Nuala O'Leary and I'm product owner of NCBI Datasets and new resource aimed at making it easier for the biology community to access NCBI sequence data. Please come to our poster, talk and Birds of Feather, bring your questions and suggestions for NCBI.



Wednesday July 7, 2021 17:00 - 17:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

17:00 CEST

BoF: At the edge of the Galaxy, the lonely life of a (small scale) local Galaxy server admin
Running a local Galaxy server within your institute or offering Galaxy just for your lab is different from managing a big public server (like usegalaxy.*). Very often, you do this as a side-job or even in your free time and you encounter site-specific issues, like disagreements with your IT department or challenges making local data available in your Galaxy server.

In this BoF, I would like to collect such issues and, more importantly, bring Galaxy admins together who might be able to help each other.

Meeting spaces:
Materials: slides text-doc

Speakers
avatar for Hans-Rudolf Hotz

Hans-Rudolf Hotz

Friedrich Miescher Institute for Biomedical Research, Basel
avatar for Lucille Delisle

Lucille Delisle

Post-doc, EPFL SV ISREC UPDUB
Hi,I am a Post-doc in Denis Duboule lab working on gene regulation during development.For the scientific part, I analyzed various NGS methods including Hi-C, ATAC-seq, CUT&RUN. I recently developped a new method for single-cell RNA-seq, named baredSC.For the galaxy part, I develop... Read More →


Wednesday July 7, 2021 17:00 - 17:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

17:00 CEST

BoF: Boost the diversity in your community: Outreachy and other internship-mentorship initiatives
Systemic bias and discrimination in STEM are a persisting threat to productive, diverse communities and a thriving society 👥✨. Outreachy’s mission is to provide anyone who faces underrepresentation an opportunity to make their first contributions to open source. These may involve coding 👾, but non-programming work is very welcome as well, such as design, documentation, content writing, user experience, marketing, or organizing events 🌈.

However, this BoF isn't only about Outreachy, but about any internship and mentorship! 😊

    🧲 Are you interested in bringing new talents to your community or just curious how it works?

    🔮 Or are you an intern or internship applicant wanting to contribute to open source and open science, and to meet others?

    📖 Or do you perhaps want to discuss how to be a mentor, with other fresh mentors-in-progress?

Then come have a friendly chat with past and current interns, internship applicants, and mentors! 🐙

Flocking Spaces:
  • During BoF: Zoom (link removed)
  • Shared notes: HackMD (link to anonymised version will be added in a bit)
  • There is also a dedicated sofa table in the Galactic Cafe, Floor 2 (Outreachy table), to hang around before and after the BoF.
  • Slack: #bof-interns


Speakers
avatar for Matúš Kalaš

Matúš Kalaš

Senior researcher, University of Bergen
Open science|source|society|education, EDAM ontology, ELIXIR Norway, bio.tools, GTrack
HE

Hager Eldakroury

Outreachy Intern, EDAM
MB

Melissa Black

Outreachy Intern, EDAM
I'm an open science enthusiast with a background in Geography.



Wednesday July 7, 2021 17:00 - 17:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

18:00 CEST

Americas Session 4

Moderators
avatar for Jeremy Goecks

Jeremy Goecks

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

Wednesday July 7, 2021 18:00 - 19:20 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:01 CEST

Welcome
Welcome back!

We'll introduce the day, and present last minute news

Speakers
avatar for Jeremy Goecks

Jeremy Goecks

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


Wednesday July 7, 2021 18:01 - 18:10 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:10 CEST

Detection and functional annotation of lncRNA
→ Abstract
→ Slides
Video

Bianca Pasat 1,2; Elena Gkotsi 1,2,3; Xara Mastrokalou 1,2; Theodoros Koutsandreas 1,2; Eleutherios Pilalis 1,2; Aristotelis Chatziioannou 1,2

  1. e-NIOS Applications Private Company, GR
  2. Systems Biology, Biomedical Research Foundation of the Academ, GR
  3. Department of Biochemistry and Biotechnology, University of Thessaly, GR

Speakers
avatar for Bianca Pasat

Bianca Pasat

Bioinformatician, eNIOS
I studied Biology and Bioinformatics in Athens.Right now I am a member of Aristotelis Chatziioannou's group at IIBEAA and I work at eNIOS.PhD candidate at NUIG


Wednesday July 7, 2021 18:10 - 19:20 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:16 CEST

Automated Deployment of Genome Databases for Marine Brown Algae Using Galaxy Genome Annotation (GGA)
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118614.1)
Video

Loraine Brillet-Guéguen 1,2; Arthur Le  Bars 2; Anthony Bretaudeau 3;  J. Mark Cock1; Susana M. Coelho1; Erwan Corre 2

  1. Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, FR
  2. CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680, Roscoff, FR
  3. INRA, UMR IGEPP, BIPAA/GenOuest, Campus, Rennes, FR

Speakers
LG

Loraine Guéguen

Station Biologique de Roscoff


Wednesday July 7, 2021 18:16 - 18:22 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:22 CEST

Galaxy-ML: An Accessible, Reproducible, and Scalable Machine Learning Toolkit for Biomedicine
→ Abstract
→ Slides (doi.: 10.7490/f1000research.1118621.1)
Video

Qiang Gu 1; Anup Kumar 2; Simon Bray 2; Allison Creason 1; Alireza Khanteymoori 2; Vahid Jalili 1; Björn Grüning 2; Jeremy Goecks 1; Kaivan Kamali 3

  1. Oregon  Health  and  Science  University  (OHSU),  US
  2. University of Freiburg, DE
  3. Penn State University, US

Speakers
KK

Kaivan Kamali

Computational Scientist, Penn State University
Computer scientist specializing in AI/ML. Interested in applying AI/ML to bioinformatics problems.


Wednesday July 7, 2021 18:22 - 18:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:40 CEST

The immuneML Portal: a public Galaxy server for machine learning analysis of adaptive immune receptor repertoires
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118651.1)
→ Video

Milena Pavlovic 1; Lonneke Scheffer 1; Victor Greiff 1; Geir Kjetil Sandve 1

  1. University of Oslo, NO

Speakers
avatar for Lonneke Scheffer

Lonneke Scheffer

PhD Candidate, University of Oslo
PhD student | computational immunology | University of Oslo


Wednesday July 7, 2021 18:40 - 18:46 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:46 CEST

The Galaxy Public Health Community
→ Abstract
Video

Peter van Heusden 5; Abdul Karim Sesay 1; Andrew Page 2; Christophe Antoniewski 3; Stefano Morabito 4

  1. MRC The Gambia, GM
  2. Quadrum Institute, GB
  3. ARTbio Bioinformatics Analysis Facility, Sorbonne Université, FR
  4. EURL for E. coli including VTEC, Istituto Superiore di Sanità, IT
  5. MRC Bioinformatics Unit, SANBI, University of the Western Cape, ZA


Wednesday July 7, 2021 18:46 - 18:52 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:52 CEST

A flexible Galaxy-based platform for the analysis of microbial WGS data in public health
→ AbstractRelated Poster
→ Slides (doi: 10.7490/f1000research.1118649.1)
Video


Bert Bogaerts 1,2; Raf Winand 1; Julien Van Braekel 1; Nancy H. C. Roosens 1; Sigrid C. J. De Keersmaecker 1; Kevin Vanneste 1

  1. Transversal activities in Applied Genomics, Sciensano, BE
  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, BE

Speakers
BB

Bert Bogaerts

UGhent – Department of information Technology, IDLab, imec


Wednesday July 7, 2021 18:52 - 18:58 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

18:58 CEST

The “ARIES Genomics” Italian public health surveillance system
→ Abstract 
→ Slides (doi: 10.7490/f1000research.1118632.1)
Video

Arnold Knijn 1; Valeria Michelacci 1; Stefano Morabito 1

  1. Istituto Superiore di Sanità, IT

Speakers
avatar for Arnold Knijn

Arnold Knijn

Istituto Superiore di Sanità


Wednesday July 7, 2021 18:58 - 19:04 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:04 CEST

Fostering Public Health Bioinformatics and Collaboration with GalaxyTrakr
→ Abstract
→ Video

Justin Payne 1; Jayanthi Gangiredla 1; Hugh Rand 1; Daniel Benisatto 8; Charles Strittmatter 1; Jimmy Sanders 2; William J. Wolfgang 3; Kevin Libuit 4; James B. Herrick 5; Melanie Prarat 9; Magaly Toro 6; Thomas Farrell 1; Errol Strain 7

  1. US Food and Drug Administration, Center for Food Safety and Applied Nutrition, US
  2. SDS Solutions, Inc., US
  3. Wadsworth Center, US
  4. Libuit Scientific, LLC, US
  5. Center for Genome and Metagenome Studies, James Madison University, US
  6. Laboratorio de Micr

Speakers
avatar for Justin Payne

Justin Payne

Computer Scientist, US Food and Drug Administration
I'm a Python and Java developer, one of the primary developers of the FDA's GenomeTrakr whole-genome pathogen biosurveillance network, an application scientist and admin on GalaxyTrakr, and the primary author of tools such as Bootsie and PoreRefiner. Recently rated "alright" by one... Read More →


Wednesday July 7, 2021 19:04 - 19:10 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:10 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Wednesday July 7, 2021 19:10 - 19:20 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:20 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Wednesday July 7, 2021 19:20 - 19:40 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

19:39 CEST

Americas Session 5
Session 5 of the 2021 Galaxy Community Conference (GCC2021) focuses on applications of Galaxy.

Presentations this session:


🙋 A presenter or co-author will be available for live Q&A this session,

Speakers
avatar for Anne Fouilloux

Anne Fouilloux

I am a Research Software Engineer working for the Nordic e-Infrastructure Collaboration (NeIC) and working on Galaxy climate (https://climate.usegalaxy.eu/) e.g. providing Galaxy tools for exploiting climate data, models to facilitate climate impact studies and climate modelling... Read More →


Wednesday July 7, 2021 19:39 - 20:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:40 CEST

Analysis of Microscopy Data in Galaxy
→ Abstract
→ Slides
→ Video

Beatriz Serrano-Solano 1; Yi Sun 2; Jeremy Goecks 3; Jean-Karim Hériché 2

  1. University of Freburg, DE
  2. European Molecular Biology Laboratory, DE
  3. Oregon Health and Science University , US

Speakers
avatar for Beatriz Serrano-Solano

Beatriz Serrano-Solano

Community Coordinator for the European Galaxy Community, University of Freiburg


Wednesday July 7, 2021 19:40 - 19:46 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

19:46 CEST

Bridging Natural Language Processing and Biomedical Data Analysis
→ Abstract
→ Slides
Video

Daniel Blankenberg 1; Nancy Ide 2

  1. Cleveland  Clinic  Genetic  Medical  Institute,  US
  2. Vassar  College, US

Speakers

Wednesday July 7, 2021 19:46 - 20:04 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:04 CEST

French EBV operationalization pilot, where Galaxy can help Biodiversity
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118612.1)
→ Video

Coline Royaux 1; Dominique Pelletier 2; Sandrine Pavoine 3; Jean-Baptiste Mihoub 3; Yvan Le Bras 1

  1. PNDB research e-infrastructure, UMS PatriNat, Museum National d’Histoire Naturelle (MNHN), Concarneau, FR
  2. Institut français de recherche pour l'exploitation de la mer (Ifremer), Nantes, FR
  3. Centre d’Ecologie et des Sciences de la Conse

Speakers
CR

Coline Royaux

French national museum of natural history (MNHN)


Wednesday July 7, 2021 20:04 - 20:10 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:10 CEST

Updates from the Single-Cell Community
→ Slides (doi: 10.7490/f1000research.1118634.1)
Abstract
 Video

Mehmet Tekman 1; Wendi Bacon 2

  1. Freiburg Galaxy Team, Backofen Group, University Freiburg, DE
  2. The Open University, Milton Keynes MK7 6AA, GB

Speakers
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, University of Freiburg
Single-Cell, Developing Wrappers with Emacs
avatar for Wendi Bacon

Wendi Bacon

Lecturer, Open University


Wednesday July 7, 2021 20:10 - 20:16 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:16 CEST

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118604.1)
Video

Willem de Koning 1,2; Milad Miladi 3; Saskia D. Hiltemann 1; Astrid P. Heikema 4; John P. Hays 4; Stephan Flemming 3; Marius van den Beek 5; Dana A. Mustafa 2; Rolf Backofen 3; Björn Grüning 3; Andrew P. Stubbs 1

  1. Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Centre, NL
  2. Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus University Medical Centre, NL
  3. Department of Computer Science, Bioinformatics Group, Univesity of Freiburg, DE
  4. Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, NL
  5. Department of Stem Cells and Tissue Homeostasis, Institut Curie, PSL Research University, FR

Speakers

Wednesday July 7, 2021 20:16 - 20:22 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:22 CEST

Using custom Galaxy workflows to reproducibly search for bacteriophage spanin proteins reveals distinct population distributions
→ Abstract
→ Slides (doi: /10.7490/f1000research.1118590.1)
→ Video

Jason Snowden 1; Curtis Ross 1; Jolene Ramsey 1; Ry Young 1

  1. Center for Phage Technology, Department of Biochemistry & Biophysics, Texas A&M University, US

Speakers
avatar for Jolene Ramsey

Jolene Ramsey

Postdoc, Texas A&M University
I love to study the viruses of bacteria, called bacteriophages, or phages. Ask me about viruses, or my favorite podcast, This Week in Virology.


Wednesday July 7, 2021 20:22 - 20:28 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:28 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Wednesday July 7, 2021 20:28 - 20:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

20:40 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Wednesday July 7, 2021 20:40 - 21:00 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

20:45 CEST

Remo Reset
The conference is being run on the Remo.co platform. This has many advantages, and a few disadvantages. One of the disadvantages is that our license allows us to only be up for only 5 hours at a time. This means that every 5 hours, or less, we need to reboot the platform.

When this happens, you will need to log back in to Remo to reconnect. There will be one reset during each conference day, either before or after that day's poster/demo/sponsor session. There will be additional resets in the after hours, before or after BoFs and Socials, as needed.

We apologize for this inconvenience.

Wednesday July 7, 2021 20:45 - 20:45 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

20:59 CEST

Americas Wednesday Poster / Demo / Sponsor Session
Sponsors and poster / demos are presented in the Poster / Demo / Sponsor Hall in Remo. Sponsors (and the Career Center) are on the first/ground floor..  Wednesday's poster / demos are on floors 3 and 4 of that building.




Wednesday July 7, 2021 20:59 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

F1000Research
→ Remo: Poster/Demo/Sponsor Hall, Floor 1
Galaxy Gateway

F1000Research is proud to be a Silver Sponsor for GCC2021! We are an Open Research publishing platform that offers rapid, transparent publication of a range of different article types, including original research articles, to method articles, data notes, and software tool articles. The platform is particularly well suited to publishing software tool articles as the unique versioning system allows small updates at any time, along with proper syntax highlighting and support for LaTeX and markdown submissions.

Our Galaxy Gateway on the platform brings together articles, posters and slides from Galaxy events. The Gateway allows authors to quickly share their work with the community, boosting visibility and giving researchers proper credit for their contribution.

We’re pleased to be running a call for papers for GCC2021 and would like to invite the Galaxy community to submit their articles to the Galaxy Gateway by 20th July 2021. These can be any type of article, such as a new Galaxy workflow or an update to an existing method or software tool. This is a great opportunity to shine a light on your research, improve its impact and be credited with an academic paper for your work. Please submit via the Galaxy gateway.

Please drop by the F100Research table and learn more from Abbie!

Speakers

Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-3.10: Detection and functional annotation of lncRNA
→ Abstract
→ Poster
→ Demo

→ Remo: Poster/Demo/Sponsor Hall, Floor 3

Bianca Pasat 1,2; Elena Gkotsi 1,2,3; Xara Mastrokalou 1,2; Theodoros Koutsandreas 1,2; Eleutherios Pilalis 1,2; Aristotelis Chatziioannou 1,2

  1. e-NIOS Applications Private Company, GR
  2. Systems Biology, Biomedical Research Foundation of the Academ, GR
  3. Department of Biochemistry and Biotechnology, University of Thessaly, GR

Speakers
avatar for Bianca Pasat

Bianca Pasat

Bioinformatician, eNIOS
I studied Biology and Bioinformatics in Athens.Right now I am a member of Aristotelis Chatziioannou's group at IIBEAA and I work at eNIOS.PhD candidate at NUIG


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-3.11: GalaxyLab: A JupyterLab extension for interactive graphical and programmatic access to Galaxy
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Jayadev Joshi 1; Daniel Blankenberg 1

  1. Cleveland Clinic Foundation, US

Speakers
avatar for jayadev joshi

jayadev joshi

Postdoctoral fellow, Cleveland clinic foundation


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-3.7: A flexible Galaxy-based platform for the analysis of microbial WGS data in public health
→ AbstractPoster
→ Poster 
(doi: 10.7490/f1000research.1118648.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Bert Bogaerts 1,2; Raf Winand 1; Julien Van Braekel 1; Nancy H. C. Roosens 1; Sigrid C. J. De Keersmaecker 1; Kevin Vanneste 1

  1. Transversal activities in Applied Genomics, Sciensano, BE
  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, BE

Speakers
BB

Bert Bogaerts

UGhent – Department of information Technology, IDLab, imec


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-3.8: EDAM ontology, tools, and community
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


EDAM is an ontology of data analysis and data management in life sciences. The structure of EDAM is relatively simple, divided into 4 main sub-ontologies:

  • Topic
  • Operation
  • Data (incl. Identifier)
  • Format

EDAM is used in numerous resources including Galaxy, bio.tools, Debian, WorkflowHub, the ELIXIR Europe training portal TeSS, or BIII (the BioImage Informatics Index). Thanks to the annotations with EDAM, computational tools, workflows, data, and educational materials are easier to find, compare, choose, and integrate.

In Galaxy, EDAM is used for annotation of tools, and of types of data/data formats. There is a new option for administrators of a Galaxy server, to visualise the tools panel by EDAM concepts (galaxyproject/galaxy#10592). 🌌

EDAM contributes to open science also by serving as an ontology for provenance metadata, making the data more understandable, findable, and comparable. EDAM and its applications lower the barrier and effort for scientists and citizens alike, towards doing scientific research in a more open, reliable, and inclusive way.

The EDAM community brings together software engineers and science experts (academic, industrial, citizen), professionals & volunteers. Along with the ontology, this community has developed a number of tools that enhance user experience with EDAM:

  • 🌲 EDAM Browser is a lightweight & fast web-based ontology browser that provides a number of user-oriented features such as aggregated search across various EDAM-annotated resources (e.g. bio.tools, TeSS, …).
  • 🧾 EDAMmap is a tool for text mining EDAM concepts from articles.
  • 🍪 EDAM Popovers is a Firefox add-on for showing details of EDAM concepts found in a website. Great for Galaxy code on GitHub. 🙌


Authors
Melissa Black - Outreachy intern (EDAM), São Paulo, BR; moving to Los Angeles, U.S.
Hager Eldakroury - Ain Shams University, Outreachy intern (EDAM), Cairo, EG
Sakshi Dhamija - ABV - Indian Institute of Information Technology and Management, Gwalior, IN
Rashika Rathi - Indian Institute of Technology, Mandi, IN
Ankita Priya - Birla Institute of Technology, Mesra, IN
Anne Machinda - independent contributor, Bamenda, CM
Uttam Singh Khanduja - Medicaps University, Indore, IN
Gloria Umutesi - independent contributor, Kigali, RW
Anita Op - independent contributor, NG
Precious Chieke - independent contributor, NG
Steve Laurie - Centre Nacional d'Anàlisi Genòmica, Barcelona, ES
Mads Kierkegaard - University of Southern Denmark, Ødense, DK
Veit Schwämmle - University of Southern Denmark, Ødense, DK
Chris Hunter - GigaScience GigaDB, Hong Kong, CN
Jonathan Karr - Icahn School of Medicine at Mount Sinai, New York City, US
Drashti Patoliya - independent contributor, Surat, IN
Sunday Cletus Nkwuda - freelancer, volunteer contributor, Outreachy intern (Debian), Kaduna, NG
Guneet Singh - independent contributor, BV
Pooja Yadav - independent contributor, Outreachy intern (LLVM), Goa, IN
Kelly D'oleo - independent contributor, New York City, US
Marlene Cherop - independent contributor, KE
Tawah Peggy Che Nico - University of Buea, CM
Tosin Bakare - independent contributor, Lagos, NG
Chiamaka Uzuegbu - independent contributor, NG
ellschi - independent contributor, DE
ZM202 - independent contributor, US
Babsbarokah - independent contributor, Lagos, NG
Jon Ison - Institut Français de Bioinformatique (at the time of contribution), FR
Alban Gaignard - University of Nantes, FR
Erik Jaaniso - University of Tartu, EE
Ivan Kuzmin - University of Tartu, EE
Helena Rasche - Erasmus Medical Center, Rotterdam and Avans University of Applied Sciences, NL
Bryan Brancotte - Institut Pasteur, Paris, FR
Matúš Kalaš - University of Bergen, NO
Hervé Ménager - Institut Pasteur, Paris, FR

Speakers
HE

Hager Eldakroury

Outreachy Intern, EDAM
MB

Melissa Black

Outreachy Intern, EDAM
I'm an open science enthusiast with a background in Geography.


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-3.9: Automated Deployment of Genome Databases for Marine Brown Algae Using Galaxy Genome Annotation (GGA)
→ Abstract
→ 
Poster (doi: 10.7490/f1000research.1118615.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 3


Loraine Brillet-Guéguen 1,2; Arthur Le  Bars 2; Anthony Bretaudeau 3; J. Mark Cock1; Susana M. Coelho1; Erwan Corre 2

  1. Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, FR
  2. CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680, Roscoff, FR
  3. INRA, UMR IGEPP, BIPAA/GenOuest, Campus, Rennes, FR

Speakers
LG

Loraine Guéguen

Station Biologique de Roscoff


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.10: Using custom Galaxy workflows to reproducibly search for bacteriophage spanin proteins reveals distinct population distributions
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Jason Snowden 1; Curtis Ross 1; Jolene Ramsey 1; Ry Young 1

  1. Center for Phage Technology, Department of Biochemistry & Biophysics, Texas A&M University, US

Speakers
avatar for Jolene Ramsey

Jolene Ramsey

Postdoc, Texas A&M University
I love to study the viruses of bacteria, called bacteriophages, or phages. Ask me about viruses, or my favorite podcast, This Week in Virology.


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.11: The “ARIES Genomics” Italian public health surveillance system
→ Abstract
→ Poster 
(doi:10.7490/f1000research.1118583.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Arnold Knijn 1; Valeria Michelacci 1; Stefano Morabito 1

  1. Istituto Superiore di Sanità, IT

Speakers
avatar for Arnold Knijn

Arnold Knijn

Istituto Superiore di Sanità


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.2: Driving workforce transition in Australian life science research
→ Abstract
→ Poster 
(doi:10.7490/f1000research.1118591.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4

Anna Syme 1,2; Jeff Christiansen 1; Nigel Ward 1; Simon Gladman 2; Catherine Bromhead 2; Igor Makunin 3; Mike Thang 3; Gareth Price 3; Andrew Lonie 1,2

  1. Australian BioCommons, Faculty of Medicine Dentistry and Health Sciences and School of Computing and Information Systems, University of Melbourne, AU
  2. Melbourne Bioinformatics, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Australia, AU
  3. QCIF Facility for Advanced Bioinformatics, Institute of Molecular Biology, University of Queensland, Australia, AU

Speakers
avatar for Anna Syme

Anna Syme

Bioinformatician, The University of Melbourne
Bioinformatics, Galaxy Training and the GTN, Genome Assembly, Evolution


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.3: Galaxy and Research Lifecycle Management technologies for Earth Science Communities and Copernicus users in EOSC
→ Abstract
→ Poster 
(doi: 10.7490/f1000research.1118598.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4

Anne Fouilloux 1; Jean Iaquinta 1

  1. University of Oslo, Department of Geosciences, NO

Speakers
avatar for Anne Fouilloux

Anne Fouilloux

I am a Research Software Engineer working for the Nordic e-Infrastructure Collaboration (NeIC) and working on Galaxy climate (https://climate.usegalaxy.eu/) e.g. providing Galaxy tools for exploiting climate data, models to facilitate climate impact studies and climate modelling... Read More →


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.4: Publication of BioCompute Objects (IEEE-2791-2020) created from Galaxy workflow invocations
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118620.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Charles Hadley King 1; Christopher Armstrong 1

  1. George Washington University, US

Speakers
avatar for Charles [Hadley] King

Charles [Hadley] King

Senior Research Associate, George Washington University


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.5: Gallantries: Scalable, Modular Bioinformatics Curricula
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Helena Rasche 1; Saskia Hiltemann 1; Bérénice Batut 2; Fotis Psomopoulos 3; Anthony Bretaudeau 4;
Yvan Le Bras 5

  1. Erasmus Medical Center, NL
  2. Albert-Ludwigs-Universität Freiburg, DE
  3. INAB|CERTH, GR
  4. Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, FR
  5. Muséum national d’histoire naturelle, FR

Speakers

Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.7: The next-generation Galaxy community site
→ Abstract, Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Nick Stoler¹; Dannon Baker²

  1. Penn State University, US
  2. Johns Hopkins University, US

Speakers


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.8: GPU enabled Jupyterlab notebook for deep learning using Tensorflow in Galaxy
Abstract
→ Remo: Poster/Demo/Sponsor Hall, Floor 4
Presentation
→ Video presentation


Anup Kumar 1

  1. Bioinformatics Group Department of Computer Science Albert-Ludwigs-University Freiburg Georges-Köhler-Allee 106 79110 Freiburg, DE

Speakers
avatar for Anup Kumar

Anup Kumar

PhD candidate, University of Freiburg



Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

21:00 CEST

W-4.9: Taxonomic Classification Analysis of Human Gut Microbiota Using Kraken 2
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118672.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 4


Nihan Sultan Milat 1; Ab. Matteen Rafiqi 1; Muhammet Çelik 1 

  1. Bezmialem Vakıf Üniversitesi, TR


Wednesday July 7, 2021 21:00 - 22:20 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

22:20 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Wednesday July 7, 2021 22:20 - 22:40 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

22:39 CEST

Americas Session 6
Session 6 of the 2021 Galaxy Community Conference (GCC2021).

Presentations this session:


🙋 A presenter or co-author will be available for live Q&A this session.

Moderators
avatar for Brad Langhorst

Brad Langhorst

Developmenet Group Leader, NEB

Wednesday July 7, 2021 22:39 - Thursday July 8, 2021 00:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

22:40 CEST

Galaxy Community Update
Video
→ Slides


Speakers
avatar for Andrew Lonie

Andrew Lonie

Director Australian BioCommons, University of Melbourne
avatar for Björn Grüning

Björn Grüning

University of Freiburg
avatar for Anton Nekrutenko

Anton Nekrutenko

Penn State University
Penn State University
avatar for Jeremy Goecks

Jeremy Goecks

Associate Professor of Biomedical Engineering and Computational Biology, Oregon Health & Science University
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University
avatar for Dan Blankenberg

Dan Blankenberg

Assistant Professor, Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute
avatar for Mike Schatz

Mike Schatz

Johns Hopkins University


Wednesday July 7, 2021 22:40 - 23:05 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:05 CEST

Modernizing the Galaxy Backend - Data Model
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118653.1)
→ Video

Sergey Golitsynskiy 1

  1. Johns Hopkins University, US

Speakers
avatar for Sergey Golitsynskiy

Sergey Golitsynskiy

software engineer, Johns Hopkins University


Wednesday July 7, 2021 23:05 - 23:11 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:11 CEST

Modernizing the Galaxy Backend - Typing and the API
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118607.1)
Video

David López 1; Galaxy Backend Working Group 2

  1. University of Freiburg, DE 
  2. Galaxy Project, Global

Speakers
avatar for David López

David López

Software Developer, University of Freiburg


Wednesday July 7, 2021 23:11 - 23:17 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:17 CEST

Modernizing the Galaxy Backend - Typing and Dependency Injection
→ Abstract
→ Video

John Chilton 1

  1. Penn State Unversity, US
  2. Galaxy Project, Global

Speakers
avatar for John Chilton

John Chilton

Galaxy Project, Penn State University


Wednesday July 7, 2021 23:17 - 23:23 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:23 CEST

Modernizing the Galaxy Backend - A Task Framework
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118702.1)
→ 
Video

Dannon Baker 1; Marius van den Beek 2

  1. Johns Hopkins University, US
  2. Pennsylvania State University, US

Speakers
avatar for Dannon Baker

Dannon Baker

Galaxy Project, Johns Hopkins University
Talk to me about Galaxy Development, especially the UI!


Wednesday July 7, 2021 23:23 - 23:29 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:29 CEST

Galaxy for Protected Datasets
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118665.1)
→ 
Video

Alexandru Mahmoud 1; Luke Sargent 2; John Chilton 4; Rob Title 5; Dannon Baker 1; Charles Overbeck 6; Nuwan Goonasekera 3; Stephen Mosher 1; Michael Schatz 1; Enis Afgan 1

  1. Johns Hopkins University, US
  2. Oregon Health and Sciences University, US
  3. University of Melbourne, AU
  4. Penn State University, US
  5. Broad Institute, US
  6. USCS, US

Speakers
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University


Wednesday July 7, 2021 23:29 - 23:35 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:35 CEST

Galaxy Language Server - Develop high-quality Galaxy tool wrappers at intergalactic speed
→ Abstract
→ Slides
→ Video

David López 

  1. University of Freiburg, DE
                                       


Speakers
avatar for David López

David López

Software Developer, University of Freiburg


Wednesday July 7, 2021 23:35 - 23:41 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:41 CEST

Galaxy CloudStor Integration - linking national resources for secure data transfer between services
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118764.1)
Video

Nuwan Goonasekera 1; Michael D’Silva 3; Frankie Stevens 3; Gareth Price 2

  1. Melbourne Bioinformatics, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Australia, AU
  2. QCIF Facility for Advanced Bioinformatics, Institute of Molecular Biology, University of Queensland, AU
  3. AARNet, AU

Speakers
avatar for Gareth Price

Gareth Price

Head of Computational Biology, QCIF Facility for Advanced Bioinformatics
Gareth Price has been a Genomics Scientist for over 15 years now. He has involved in experimental design, assay performance, data QC, data analysis and data interpretation from early printed microarrays, to cartridge based GeneChips through to multiple Next Gen platforms. These works... Read More →


Wednesday July 7, 2021 23:41 - 23:47 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

23:47 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Wednesday July 7, 2021 23:47 - Thursday July 8, 2021 00:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.
 
Thursday, July 8
 

00:00 CEST

Break
The first day's formal content is done, but stick around for Birds-of-a-Feather (in 20 minutes).

Take a break! Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

See you soon.

Thursday July 8, 2021 00:00 - 00:20 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

00:10 CEST

Remo Reset
The conference is being run on the Remo.co platform. This has many advantages, and a few disadvantages. One of the disadvantages is that our license allows us to only be up for only 5 hours at a time. This means that every 5 hours, or less, we need to reboot the platform.

When this happens, you will need to log back in to Remo to reconnect. There will be one reset during each conference day, either before or after that day's poster/demo/sponsor session. There will be additional resets in the after hours, before or after BoFs and Socials, as needed.

We apologize for this inconvenience.

Thursday July 8, 2021 00:10 - 00:10 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

00:20 CEST

Birds of a Feather (BOFs)
Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.

BoFs flicking this session:


Anyone is welcome to propose a BoF! All you need is a title, an organizer, and a brief description.

Thursday July 8, 2021 00:20 - 02:00 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

00:20 CEST

BoF: Galaxy community roadmap planning
Galaxy is a freely available, global scientific good, sustained by multiple collaborating funded projects and a large and growing community of users and contributors. Planning is coordinated in technical and community streams by means of published roadmaps The new community governance body, the GGSC seeks your input in figuring out it can best understand, nurture, manage and expand the communities engaging with this novel and increasingly important global scientific resource.

This BoF will provide an opportunity for anyone interested and willing to discuss, plan and lead Galaxy community initiatives and contribute to developing a roadmap for future community development activities. Technical roadmap input will be gathered in community consultations managed by the Technical board.

"It takes a village to do a complex scientific analysis"

Meeting spaces:

Speakers


Thursday July 8, 2021 00:20 - 02:00 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

07:59 CEST

EMEA-APAC Conference Day 3
Last day of the meeting part of GCC2021

Thursday July 8, 2021 07:59 - 17:50 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

08:00 CEST

Birds of a Feather (BOFs)
Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.

BoFs flocking in this session:


Anyone is welcome to propose a BoF! All you need is a title, an organizer, and a brief description.

Thursday July 8, 2021 08:00 - 08:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

08:00 CEST

BoF: Galaxy & Training / Teaching
Discussions on using Galaxy for training / teaching and the Galaxy Training Network community:

  • training material (recent and future developments) 
  • using Galaxy for undergraduate instruction
  • training / teaching delivery and events 
  • community building (instructors, contributors, users, mentoring)

Flocking Spaces:



Speakers
avatar for Björn Grüning

Björn Grüning

University of Freiburg
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
avatar for Beatriz Serrano-Solano

Beatriz Serrano-Solano

Community Coordinator for the European Galaxy Community, University of Freiburg



Thursday July 8, 2021 08:00 - 08:50 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.
  E. Social / Networking
  • Zone EMEA-APAC
  • Category BoF
  • about Community, Outreach, Imaging in Galaxy, EOSC, ELIXIR<br><br>

09:00 CEST

EMEA-APAC Session 7
The first session of the last day of the 2021 Galaxy Community Conference (GCC2021).

Presentations in this session center around community and education:


🙋 A presenter or co-author will be available for live Q&A in this session

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg


Thursday July 8, 2021 09:00 - 10:25 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:01 CEST

Welcome
Hey! It's the last day of the GCC2021 Conference.

We'll introduce the day and present last minute news

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg


Thursday July 8, 2021 09:01 - 09:10 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:10 CEST

Galaxy Training Network (GTN) Community Update
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118622.1)
→ Video

Saskia Hiltemann 1; Helena Rasche 1,2; Bérénice Batut 3

  1. Erasmus MC, NL
  2. Avans Hogeschool, NL
  3. Albert Ludwig University of Freiburg, DE



Thursday July 8, 2021 09:10 - 09:28 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:28 CEST

Using the Galaxy (Australia) Database to Aid an Undergraduate Investigation of RNF43 Mutations as Biomarkers for ctDNA Surveillance of Colorectal Cancer
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118611.1)
→ Video

Jordon Lima 1; Parry Guilford 1; Robert Day 1

  1. University of Otago, NZ

Speakers
JL

Jordon Lima

PhD Student, University of Otago



Thursday July 8, 2021 09:28 - 09:34 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:34 CEST

Open Life Science: An Open Research mentoring and training program
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118603.1)
Video

Muhammet Celik 1; Bérénice Batut 2; Malvika Sharan 2; Emmy Tsang 2; Yo Yehudi 2

  1. Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, TR
  2. Open Life Science, GB



Thursday July 8, 2021 09:34 - 09:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:40 CEST

Galaxy Australia - the influx state of a national eResearch service
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118656.1)
→ Video

Simon Gladman 2; Gareth Price 3; Catherine Bromhead 2; Nicholas Rhodes 3; Steven Manos 1; Nigel Ward 1; Andrew Lonie1

  1. Australian BioCommons, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, AU
  2. Melbourne Bioinformatics, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, AU
  3. QCIF Facility for Advanced Bioinformatics, Institute of Molecular Biology, University of Queensland, AU

Speakers
avatar for Gareth Price

Gareth Price

Head of Computational Biology, QCIF Facility for Advanced Bioinformatics
Gareth Price has been a Genomics Scientist for over 15 years now. He has involved in experimental design, assay performance, data QC, data analysis and data interpretation from early printed microarrays, to cartridge based GeneChips through to multiple Next Gen platforms. These works... Read More →



Thursday July 8, 2021 09:40 - 09:58 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

09:58 CEST

Community engagement and how it influences Galaxy Australia Innovation
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118660.1)
→ Video

Johan Gustafsson 1; Gareth Price 2; Andrew Lonie 1

  1. Australian BioCommons, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, AU
  2. QCIF Facility for Advanced Bioinformatics, Institute of Molecular Biology, University of Queensland, AU

Speakers


Thursday July 8, 2021 09:58 - 10:16 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:16 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Thursday July 8, 2021 10:16 - 10:25 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:25 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Thursday July 8, 2021 10:25 - 10:45 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

10:44 CEST

EMEA-APAC Session 8

Moderators
avatar for Anshu Bhardwaj

Anshu Bhardwaj

Long term Fellow, Senior Scientist, Interdisciplinary Research Center (CRI) and CSIR-Institute of Microbial Technology

Thursday July 8, 2021 10:44 - 11:55 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

10:45 CEST

Quantitative Metaproteomics using Galaxy Platform: Measuring Functional Microbiome via Data-Dependent and Data-Independent Acquisition Mass Spec
→ Abstract
→ Slides (doi:10.7490/f1000research.1118609.1)
→ Video

Subina Mehta 1; Miranda Mudge 2; James Johnson 1; Reid Wagner 1; Emma Leith 1; Andrew McCardle 3; Jacqueline Padilla-Gamiño 2; Brian Searle 4; Brook Nunn 2; Timothy Griffin 1; Pratik Jagtap 1

  1. University of Minnesota, US
  2. University of Washington, US
  3. Imperial College London, London, UK
  4. Ohio State University, US

Speakers
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota



Thursday July 8, 2021 10:45 - 11:03 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:03 CEST

A Galaxy-based evaluation of optimal peptide targets for MS-based detection of SARS-CoV-2 in clinical samples
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118682.1)
→ Video

Andrew Rajczewski 1; Subina Mehta 1; Dinh Duy An Nguyen 1; Björn Grüning 3; James Johnson 2; Thomas McGowan 2; Timothy Griffin 1; Pratik Jagtap 1

  1. University of Minnesota, US
  2. Minnesota Supercomputing Institute, US
  3. University of Freiberg, DE

Speakers
AT

Andrew T Rajczewski

University of Minnesota



Thursday July 8, 2021 11:03 - 11:21 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:21 CEST

MaxQuant and MSstats in Galaxy enable reproducible quantitative high-throughput proteomics for everyone
→ Abstract
→ Slides
→ Video

Niko Pinter 1; Damian Glätzer 2; Matthias Fahrner 1; Klemens Fröhlich 1; James Johnson 3; Björn Grüning 4; Bettina Warscheid 2; Oliver Schilling 1; Melanie Föll 1

  1. Institute for Surgical Pathology, Medical Center –University of Freiburg, DE
  2. Faculty of Biology, University of Freiburg, DE
  3. Minnesota Supercomputing Institute, University of Minnesota, US
  4. Department of Computer Science,University of Freiburg, DE

Speakers
avatar for Melanie Föll

Melanie Föll

Institute for Surgical Pathology Freiburg



Thursday July 8, 2021 11:21 - 11:27 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:27 CEST

Peptide mass spectrometry imaging of pancreatic cancers – A data analysis workflow in Galaxy
→ Abstract
→ Video

Maren Stillger 1,2,3; Melanie Foell 1; Martin Dieterle 4; Martin Werner 1,4,5,6; Pia Hoenscheid 7; Peter Bronsert 1,4,5,6; Oliver Schilling 1,4,5,6

  1. Institute of Surgical Pathology, Medical Center – University of Freiburg, Germany
  2. Faculty of Biology, University of Freiburg, Germany
  3. Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Germany
  4. Faculty of Medicine - University of Freiburg, Germany
  5. Tumorbank Comprehensive Cancer Center Freiburg, Medical Center – University of Freiburg, Germany
  6. German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany
  7. Institute Pathology, University Hospital Carl Gustav Carus, Technical University Dresden and National Center for Tumor Diseases Partner Site Dresden, Germany

Speakers
MS

Maren Stillger

University of Freiburg



Thursday July 8, 2021 11:27 - 11:33 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:33 CEST

XIMG-CHESS: a Galaxy based Science Gateway for X-ray Diffraction Imaging and Microstructure Modeling
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118601.1)
→ Video

Kelly Nygren 1; Matthew Miller 1; Robert Suter 4; Mark Zhuang 2; Mark Miller 2; James Johnson 3; Jorge Vinals 3

  1. Cornell High Energy Synchrotron Source/Cornell University, US
  2. San Diego Supercomputing Center/University California San Diego, US
  3. Minnesota Supercomputing Institute/University of Minnesota, US
  4. Carnegie Mellon University, US

Speakers


Thursday July 8, 2021 11:33 - 11:39 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:39 CEST

Muon Galaxy – extending Galaxy for muon science
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118613.1)
Video

Eli Chadwick 1; Leandro Liborio 1; Simone Sturniolo 1; Alejandra Gonzalez Beltran 1

  1. Science and Technology Facilities Council, GB

Speakers
avatar for Eli Chadwick

Eli Chadwick

Scientific Computing Graduate, Science and Technology Facilities Council



Thursday July 8, 2021 11:39 - 11:45 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:45 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Thursday July 8, 2021 11:45 - 11:55 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

11:55 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Thursday July 8, 2021 11:55 - 12:15 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

12:05 CEST

Remo Reset
The conference is being run on the Remo.co platform. This has many advantages, and a few disadvantages. One of the disadvantages is that our license allows us to only be up for only 5 hours at a time. This means that every 5 hours, or less, we need to reboot the platform.

When this happens, you will need to log back in to Remo to reconnect. There will be one reset during each conference day, either before or after that day's poster/demo/sponsor session. There will be additional resets in the after hours, before or after BoFs and Socials, as needed.

We apologize for this inconvenience.

Thursday July 8, 2021 12:05 - 12:05 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

12:14 CEST

EMEA-APAC Thursday Poster / Demo / Sponsor Session
Sponsors and poster / demos are presented in the Poster / Demo / Sponsor Hall in Remo. Sponsors (and the Career Center) are on the first/ground floor.. Thursday's poster / demos are on floors 5 and 6 of that building.


Thursday July 8, 2021 12:14 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

F1000Research
→ Remo: Poster/Demo/Sponsor Hall, Floor 1
Galaxy Gateway

F1000Research is proud to be a Silver Sponsor for GCC2021! We are an Open Research publishing platform that offers rapid, transparent publication of a range of different article types, including original research articles, to method articles, data notes, and software tool articles. The platform is particularly well suited to publishing software tool articles as the unique versioning system allows small updates at any time, along with proper syntax highlighting and support for LaTeX and markdown submissions.

Our Galaxy Gateway on the platform brings together articles, posters and slides from Galaxy events. The Gateway allows authors to quickly share their work with the community, boosting visibility and giving researchers proper credit for their contribution.

We’re pleased to be running a call for papers for GCC2021 and would like to invite the Galaxy community to submit their articles to the Galaxy Gateway by 20th July 2021. These can be any type of article, such as a new Galaxy workflow or an update to an existing method or software tool. This is a great opportunity to shine a light on your research, improve its impact and be credited with an academic paper for your work. Please submit via the Galaxy gateway.

Please drop by the F100Research table and learn more from Abbie!

Speakers

Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-5.2: Addressing the demand for secure and scalable on-demand Galaxy platforms
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118667.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 5

Enis Afgan 1; Dannon Baker 1; Dan Blankenberg 1; John Chilton 1; Nate Coraor 1; Jeremy Goecks 1; Nuwan Goonasekera 1; Sam Guerler 1; Anton Nekrutenko 1; Mike Sauria 1

  1. GalaxyWorks, US

Speakers
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-5.3: An automatic tool installer with integrated testing for a public Galaxy
→ Poster (doi: 10.7490/f1000research.1118633.1)
→ 
Abstract
→ Remo: Poster/Demo/Sponsor Hall, Floor 5

Catherine Bromhead 1; Thom Cuddihy 2; Simon Gladman 1

  1. Melbourne Bioinformatics, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Australia, AU
  2. QCIF Facility for Advanced Bioinformatics, Institute of Molecular Biology, University of Queensland, Australia, AU

Speakers
CB

Catherine Bromhead

University of Melbourne



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-5.4: ARIAWeb: a new web service for automated NMR structure calculation with ARIA
→ Abstract
→ Poster / Demo
→ Remo: Poster/Demo/Sponsor Hall, Floor 5


Fabien Mareuil 1; Fabrice Allain 2; Hervé Ménager 1; Michael Nilges 2; Benjamin Bardiaux 2

  1. Bioinformatics and Biostatistics Hub -Department of Computational Biology -Institut Pasteur, FR
  2. Structural BioinformaticsUnit -Department of Structural Biology and Chemistry -Institut Pasteur, FR

Speakers
FM

Fabien Mareuil

Research Engineer, Institut Pasteur



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-5.5: Augmenting Galaxy with GPU Support for Speeding Up Scientific Applications
→ Abstract
→ Poster
Demo
→ Remo: Poster/Demo/Sponsor Hall, Floor 5


Gulsum Gudukbay 1; Jashwant Raj Gunasekaran 1; Mahmut T. Kandemir 1; Anton Nekrutenko1

  1. Pennsylvania State University, US

See Gudukbay, G., Gunasekaran, J. R., Feng, Y., Kandemir, M. T., Nekrutenko, A., Das, C. R., Medvedev, P., Gruning, B., Coraor, N., Roach, N., & Afgan, E. (2021). GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping. 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 194–203. https://doi.org/10.1109/IPDPSW52791.2021.00037

Speakers
avatar for Gulsum Gudukbay

Gulsum Gudukbay

Ph.D. Student, Pennsylvania State University
I am a Ph.D. student at The Pennsylvania State University in Computer Science and Engineering department. I work in computer architecture, more specifically, adding GPU support to platforms like Galaxy and to applications in different domains.



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-5.6: Building a Disaster Recovery option for Galaxy Australia
→ Abstract
Poster / Demo
→ Remo: Poster/Demo/Sponsor Hall, Floor 5


Nicholas Rhodes 2; Catherine Bromhead 1; Gareth Price 2; Simon Gladman 1

  1. Melbourne Bioinformatics, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, AU
  2. QCIF Facility for Advanced Bioinformatics, AU

Speakers
avatar for Nicholas Rhodes

Nicholas Rhodes

IT Wrangler, Galaxy Australia
Talk to me about your Galaxy implementation!



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-5.7: Comparative genomic analysis of the pink pigmented facultative methylotrophs (PPFMs)
→ Abstract
→ Remo: Poster/Demo/Sponsor Hall, Floor 5


Ola Alessa 1;Yoshitoshi Ogura2; Yoshiko Fujitani1; Hideto Takami3; Tetsuya Hayashi4; Akio Tani1.
  1. Institute  of  plant  research  science  and  resources,  Okayama  University,  JP
  2. School  of  Medicine,  Kurume University, JP
  3. Research Institute, Marine Microbiology, Tokyo University, JP.
  4. Graduate School of Medical Sciences, Kyushu University, JP
  5. Mugla Sitki Kocman University, TR

Speakers
avatar for Ola Alessa

Ola Alessa

PhD, Okayama University
Hello, I am Ola from Syria, currently in Japan doing a PhD. in Plant-Microbe interaction. I have been using galaxy for one year and a half now. I was able to analyze whole genome data with the help of many tutorials available on the galaxy website.  My PhD. as you read the title... Read More →



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-5.8: CloudForest: Dockerized Galaxy as a Platform for an Integrated Phylogenomics Software Workflow
→ Abstract
→ 
Poster (doi: 10.7490/f1000research.1118655.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 5

Reid Wagner 1; Benjamin S. Toups 2; Zhifeng Deng 3; Kyle A. Gallivan 3; Jeremy M. Brown 2; James C. Wilgenbusch 1

  1. Minnesota Supercomputing Institute, University of Minnesota, US
  2. Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University, US
  3. Dept. of Mathematics, Florida State University, US

Speakers


Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-6.2: Efficient Tool Development within Enterprise
→ Abstract
→ Poster/Demo
→ Remo: Poster/Demo/Sponsor Hall, Floor 6


Peter Selten 1; Jan-Christoph Richter 1
  1. KWS SAAT SE & Co. KGaA

Speakers
PS

Peter Selten

Scientist RD-IT, KWS SAAT SE & Co. KGaA



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-6.3: Galaxy Genome Annotation (GGA) environment in the cloud
→ Abstract
→ Poster (doi: 10.7490/f1000research.1118732.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 6


Romain Dallet 1; Gildas Le Corguillé 1; Loraine Brillet-Guéguen 1,2; Erwan Corre 1

  1. Sorbonne Université, CNRS, FR2424, ABiMS, Station Biologique de Roscoff, FR
  2. Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, FR

Speakers
RD

Romain Dallet

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



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-6.4: From the landscape to the plant: Integrating, visualizing and analyzing plant environment, phenotype and genotype using CartograPlant, WildType and Tripal Galaxy
→ Abstract 
→ Poster (doi: 10.7490/f1000research.1118599.1)
→ Remo: Poster/Demo/Sponsor Hall, Floor 6


Irene Cobo-Simon 1; Nic Herndon 2; Margaret Staton 3; Emily Grau 1; Sean Buehler 1; Peter Richter 1; Risharde Ramnath 1; Charles Demurjian 1; Abdullah Almsaeed 3; Stephen Duncanson 1; Barnaly Pande 1; Emily Strickland 1; Jessica Gunoskey 1; Jill Wegrzyn 1

  1. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, US
  2. Department of Computer Science, East Carolina University, NC, US
  3. Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, US

Speakers
IC

Irene Cobo-Simon

Postdoctoral Research Associate, University of Connecticut



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-6.5: Galaxy GFF3 tool suite for manipulation, conversion and deposition of genome data
→ Abstract
→ Poster/Demo
→ Remo: Poster/Demo/Sponsor Hall, Floor 6


Anthony Criscione 1; Curtis Ross 1; Cory Maughmer 1; Jolene Ramsey 1; Mei Liu 1; Jason Gill 1

  1. Center for Phage Technology, Texas A&M University, US

Speakers
AC

Anthony Criscione

Programmer, Center for Phage Technology



Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-6.6: MaxQuant and MSstats in Galaxy enable reproducible quantitative high-throughput proteomics for everyone
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 6


Niko Pinter 1; Damian Glätzer 2; Matthias Fahrner 1; Klemens Fröhlich 1; James Johnson 3; Björn Grüning 4; Bettina Warscheid 2; Oliver Schilling 1; Melanie Föll 1

  1. Institute for Surgical Pathology, Medical Center –University of Freiburg, DE
  2. Faculty of Biology, University of Freiburg, DE
  3. Minnesota Supercomputing Institute, University of Minnesota, US
  4. Department of Computer Science,University of Freiburg, DE

Speakers


Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-6.7: New User Welcome: A customizable, beginner-friendly introduction into Galaxy
→ Abstract
→ Poster
→ Remo: Poster/Demo/Sponsor Hall, Floor 6


Alexander Ostrovsky 1; Dannon Baker 1

  1. Galaxy Project, Johns Hopkins, US

Speakers


Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

12:15 CEST

Th-6.8: Peptide mass spectrometry imaging of pancreatic cancers – A data analysis workflow in Galaxy
Abstract
→ Remo: Poster/Demo/Sponsor Hall, Floor 6


Maren Stillger 1,2,3; Melanie Foell 1; Martin Dieterle 4; Martin Werner 1,4,5,6; Pia Hoenscheid 7; Peter Bronsert 1,4,5,6; Oliver Schilling 1,4,5,6

  1. Institute of Surgical Pathology, Medical Center – University of Freiburg, Germany
  2. Faculty of Biology, University of Freiburg, Germany
  3. Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Germany
  4. Faculty of Medicine - University of Freiburg, Germany
  5. Tumorbank Comprehensive Cancer Center Freiburg, Medical Center – University of Freiburg, Germany
  6. German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany
  7. Institute Pathology, University Hospital Carl Gustav Carus, Technical University Dresden and National Center for Tumor Diseases Partner Site Dresden, Germany

Speakers
MS

Maren Stillger

University of Freiburg


Thursday July 8, 2021 12:15 - 13:35 CEST
Poster / Demo / Sponsor Hall https://live.remo.co/e/galaxy-poster-session This building has sponsors and the Career Center on the first/ground floor, and posters/demos on the 2-6 floors. Take the elevator!

13:35 CEST

Break
Take a break!  Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

Just be sure to be back in 20 minutes.

Thursday July 8, 2021 13:35 - 13:55 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

13:54 CEST

EMEA-APAC Session 9
Final session of the 2021 Galaxy Community Conference (GCC2021).

Presentations in this session:


🙋 A presenter or co-author will be available for live Q&A in this session.

Moderators
Thursday July 8, 2021 13:54 - 15:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

13:55 CEST

A single stack for dev, testing, and production: Galaxy Helm Chart v4
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118608.1)
→ Video

Nuwan Goonasekera 1; Alexandru Mahmoud 2; Luke Sargent 3; Keith Suderman 2; Enis Afgan 2

  1. University of Melbourne, AU
  2. Johns Hopkins University, US
  3. Oregon Health and Sciences University, US



Thursday July 8, 2021 13:55 - 14:13 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:13 CEST

Browser Development Environment for Galaxy Powered by Kubernetes
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118748.1)
→ Video

Alexandru Mahmoud 1; Nuwan Goonasekera 2; John Chilton 3; Enis Afgan 1

  1. Johns Hopkins University, US
  2. Melbourne Bioinformatics, US
  3. Penn State University, US

Speakers
avatar for Alexandru Mahmoud

Alexandru Mahmoud

Galaxy Team, Johns Hopkins University



Thursday July 8, 2021 14:13 - 14:19 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:19 CEST

Interactive Tools in Galaxy on Kubernetes
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118747.1)
Video

Alexandru Mahmoud
1; Nuwan Goonasekera 2; Enis Afgan 1; Luke Sargent 3; John Chilton 1

  1. Johns Hopkins University, US
  2. Melbourne Bioinformatics, AU
  3. Oregon Health and Sciences University, US
  4. Penn State University, US

Speakers
avatar for Alexandru Mahmoud

Alexandru Mahmoud

Galaxy Team, Johns Hopkins University



Thursday July 8, 2021 14:19 - 14:25 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:25 CEST

An automatic tool installer with integrated testing for a public Galaxy
→ Abstract
→ Slides (doi: 10.7490/f1000research.1118641.1)
→ Video

Catherine Bromhead 1; Thom Cuddihy 2; Simon Gladman 1

  1. Melbourne Bioinformatics, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Australia, AU
  2. QCIF Facility for Advanced Bioinformatics, Institute of Molecular Biology, University of Queensland, Australia, AU

Speakers
CB

Catherine Bromhead

University of Melbourne


Thursday July 8, 2021 14:25 - 14:31 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:31 CEST

Q&A
There will be live question and answer at the end of each session. Presenters will be present at their end of their session in at least one hemisphere.  Watch this space.

Thursday July 8, 2021 14:31 - 14:40 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

14:40 CEST

Closing
→ Slides


Thursday July 8, 2021 14:40 - 15:00 CEST
Meeting Hall https://live.remo.co/e/galaxy-main-event GCC2021 Meeting sessions happen in the Galaxy Meeting Hall, on Remo.

15:00 CEST

Break
The first day's formal content is done, but stick around for Birds-of-a-Feather (in 20 minutes) and the Opening Social.

Take a break! Meet your fellow participants, check your email, grab some food, acknowledge your family and pets, ...

See you soon.

Thursday July 8, 2021 15:00 - 15:20 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

15:19 CEST

Americas Conference Day 3
The last day of the meeting portion of GCC2021 in the Americas Zone.

Thursday July 8, 2021 15:19 - 23:59 CEST
Remo+Slack The 3 day GCC2021 meeting is happening in Remo and Slack.

15:20 CEST

Birds of a Feather (BOFs)
Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of interest.

BoFs flocking in this session include


Any meeting participant is welcome to propose a BoF! All you need is a title, an organizer, and a brief description. 
 




Thursday July 8, 2021 15:20 - 16:15 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

15:20 CEST

BoF: Community Hubs: Helping the Hubmakers
The new Galaxy Community Hub (preview.galaxyproject.org) is mainly designed to ease the task of authoring. One key way is through automating the task of crossposting news and events between community sites. This is a space for those interested in standardizing data sharing between sites, or any other way that a Hub platform could make life easier.

Flocking Spaces


Speakers

Thursday July 8, 2021 15:20 - 16:15 CEST
Poster / Demo / Sponsor Building

15:20 CEST

BoF: Galaxy community roadmap planning
Please use the zoom link below to join - the event will be there, not Remo
Galaxy is a freely available, global scientific good, sustained by multiple collaborating funded projects and a large and growing community of users and contributors. Planning is coordinated in technical and community streams by means of published roadmaps The new community governance body, the GGSC seeks your input in figuring out it can best understand, nurture, manage and expand the communities engaging with this novel and increasingly important global scientific resource.
This BoF will provide an opportunity for anyone interested and willing to discuss, plan and lead Galaxy community initiatives and contribute to developing a roadmap for future community development activities. Technical roadmap input will be gathered in community consultations managed by the Technical board.

"It takes a village to do a complex scientific analysis"

Meeting spaces:

Speakers


Thursday July 8, 2021 15:20 - 16:15 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

15:20 CEST

BoF: Galaxy on Kubernetes
Talking about the deployment stack for Kubernetes as well as existing services using it.

This BoF is being held twice, at two different times to be convenient to everyone who is interested.

Meeting Spaces:

Speakers
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University
avatar for Alexandru Mahmoud

Alexandru Mahmoud

Galaxy Team, Johns Hopkins University


Thursday July 8, 2021 15:20 - 16:15 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

15:20 CEST

BoF: GTN-Español - Bioinformatics resources in human-translated Spanish
We're trying to move beyond Google-translate into manually translated tutorials, slide-decks, and videos in Spanish for a workshop. Anyone who speaks Spanish and would be keen to get involved in developing or testing these resources would be very welcome! And double gold star if you know anything about translation or automated translation, as long-term we want to see how we can power this up bigger scale.

Flocking Places:


Speakers
avatar for Beatriz Serrano-Solano

Beatriz Serrano-Solano

Community Coordinator for the European Galaxy Community, University of Freiburg
avatar for Wendi Bacon

Wendi Bacon

Lecturer, Open University


Thursday July 8, 2021 15:20 - 16:15 CEST
Galactic Cafe https://live.remo.co/e/galaxy-social-event Training, BoFs and Social hours will use the Galactic Cafel as a base for conversation. Training groups and BoFs may link out to external spaces like Zoom or Google meet, as needed.

15:20 CEST

BoF: IDC - Intergalactic (reference) Data Commission
IDC is the entry point to contribute to the community-maintained CVMFS data repository. However, it seems that this project has not been updated recently. GCC2021 could be the occasion to discuss what could be updated, who, how?

Flocking Places


Speakers
avatar for Lucille Delisle

Lucille Delisle

Post-doc, EPFL SV ISREC UPDUB
Hi,I am a Post-doc in Denis Duboule lab working on gene regulation during development.For the scientific part, I analyzed various NGS methods including Hi-C, ATAC-seq, CUT&RUN. I recently developped a new method for single-cell RNA-seq, named baredSC.For the galaxy part, I develop... Read More →