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The 2022 Galaxy Community Conference (GCC2022) brings together hundreds of researchers, trainers, tool developers, software engineers, and  computational infrastructure providers, all addressing common challenges in data intensive science using the Galaxy data integration and analysis platform.

  • July 17-23, 2022
  • University of Minnesota, Twin Cities
  • Minneapolis, Minnesota, United States

This annual gathering of the Galaxy community includes training, talks, posters, demos, Birds of a Feather meetups, and many other opportunities for collaboration and networking. GCC2022 will be an in-person meeting with limited support for remote attendees. There is no better event than GCC2022 to share your work and learn form others working in data-intensive science.

Click HERE to Register!

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Friday, July 8
 

12:00am CDT

GCC2022 Training Day
This one day free and virtual training event will be held Friday, July 8, a full week before the GCC2022 conference starts.  The intent of this day is to give community members an introduction to the basics of Galaxy, in preparation for the more advanced, and in-person training offered during the GCC2020 meeting, July 16-19.

Watch this space for details.

Friday July 8, 2022 12:00am - 11:59pm CDT
Online
  A. Training
 
Sunday, July 10
 

9:00am CDT

ISMB 2022, including BOSC 2022
GCC is not affiliated with ISMB, but that meeting is always near to our hearts.  This year we are also near to ISMB in time and space.  ISMB 2022, which includes BOSC 2022, is in Madison, Wisconsin, and is right before the GCC2022 meeting starts: ISMB ends Thursday evening in Madison, and GCC starts Saturday morning in Minneapolis. The two cities are a 70 minute plane trip, or a (pretty) 4 hour drive, or a 6 hour bus ride apart. If you are attending either GCC or ISMB/BOSC then we strongly encourage you to attend both, especially if you are coming from a long distance.




Sunday July 10, 2022 9:00am - Thursday July 14, 2022 6:30pm CDT
Madison, Wisconsin Madison, Wisonsin
 
Thursday, July 14
 

6:40pm CDT

Minnesota Twins vs Chicago White Sox
Just got to town a few days early?  Go watch the Minnesota Twins play their AL Central Division rivals the Chicago White Sox at Target Field.

If you are interested in attending a Twins game while you are here, then please join the #Twins channel in conference chat and plan your trip to the ballgame together.

Thursday July 14, 2022 6:40pm - 9:40pm CDT
Downtown Minneapolis

7:07pm CDT

St. Paul Saints vs Toledo Mud Hens
You could go to watch the Minnesota Twins play major league baseball while you are here, or you could instead (or in addition to!) experience the grandeur of minor league baseball.

Local favorites, the St Paul Saints are playing the legendary Toledo Mud Hens tonight at CHS Field in downtown St. Paul. Go! Watch the baseball! Try the food! Try the beer! Be amazed (or appalled) by the promotional stunts that go on between innings. Nothing quite compares to minor league baseball.

Thursday is Saints World night, which means "Piggy Time! Extra-base hit!" We can't make this up.

If you are interested in attending a Saints game while you are here, then please join the #Saints channel in the conference chat and plan your trip to the ballgame together.

Thursday July 14, 2022 7:07pm - 10:00pm CDT
Greater Minneapolis
 
Friday, July 15
 

7:07pm CDT

St. Paul Saints vs Toledo Mud Hens
You could go to watch the Minnesota Twins play major league baseball while you are here, or you could instead (or in addition to!) experience the grandeur of minor league baseball.

Local favorites, the St Paul Saints are playing the legendary Toledo Mud Hens tonight at CHS Field in downtown St. Paul. Go and experience the mystery that is minor league baseball (just like Bull Durham!).

Friday Night Fireworks will follow the game!  

If you are interested in attending a Saints game while you are here, then please join the #Saints channel in the conference chat and plan your trip to the ballgame together.

Friday July 15, 2022 7:07pm - 10:00pm CDT
Greater Minneapolis

7:10pm CDT

Minnesota Twins vs Chicago White Sox
Just arrived from Paris or Melbourne?  Keep yourself awake by watching the Minnesota Twins play their AL Central Division rivals the Chicago White Sox at Target Field.

If you are interested in attending a Twins game while you are here, then please join the #Twins channel in conference chat and plan your trip to the ballgame together. Go with someone who actually understands baseball and learn the appropriate time to scream "He was robbed!" or to observe "Baseball is a game of inches."

Friday July 15, 2022 7:10pm - 10:10pm CDT
Downtown Minneapolis
 
Saturday, July 16
 

7:07pm CDT

St. Paul Saints vs Toledo Mud Hens
Local favorites, the St Paul Saints are playing the legendary Toledo Mud Hens tonight at CHS Field in downtown St. Paul. Go and experience the mystery that is minor league baseball (just like Bull Durham!).

If you are interested in attending a Saints game while you are here, then please join the #Saints channel in the conference chat and plan your trip to the ballgame together.

Saturday night is Marvel's Defenders of the Diamond night.  The Saints promise that "you're gonna be a little Thor tomorrow."

Saturday July 16, 2022 7:07pm - 10:00pm CDT
Greater Minneapolis
 
Sunday, July 17
 

7:59am CDT

Conference Day 1
Welcome to the first day of the 2022 Galaxy Community Conference (GCC2022). This is our first in-person GCC since 2019 and we are super excited to be meeting in person again. The conference desk will open every day at 8am, and conference sessions at 9am.

Welcome back.

Sunday July 17, 2022 7:59am - 6:00pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks

8:00am CDT

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

Sunday July 17, 2022 8:00am - 6:00pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  F. Help

8:59am CDT

Session 1: GCC2022 Opening & Keynote Presentation: Open Health Natural Language Processing (OHNLP) Collaborative - An open science journey towards real-world implementation of clinical NLP
The opening session of GCC2022.  This session will feature our first Keynote Speaker, Honfang Liu, from the Mayo Clinic.


Welcome back, and welcome to Minneapolis.


Keynote presentation title:
Open Health Natural Language Processing (OHNLP) Collaborative - An open science journey towards real-world implementation of clinical NLP

Abstract
The goal of the Open Health Natural Language Processing (OHNLP) Collaborative is to promote past and current open-source clinical NLP development efforts, encourage participation in advancing future efforts, and focus on an ethical artificial intelligence (AI) framework for dissemination and implementation. In this talk, I will briefly discuss clinical NLP in general, overview some of the systems and applications in clinical NLP, discuss past and ongoing achievements in OHNLP, and provide perspectives of the future directions in clinical NLP research and practice.


Hongfang Liu is professor at the Mayo Clinic in Rochester. She has devoted her research career to leveraging data science, AI, and informatics approaches to support clinical and translational science research. This included advances in natural language processing, algorithm development, and processes of their adoption at the point of care. She is a fellow of the American College of Medical Informatics and a leader of the Natural Language Processing Working Group and the American Medical Informatics Association. 

Moderators
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University

Speakers
avatar for Hongfang Liu

Hongfang Liu

Mayo Clinic


Sunday July 17, 2022 8:59am - 10:00am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:00am CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Sunday July 17, 2022 10:00am - 10:20am CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:19am CDT

Session 2: Poster / Demo Session A
There will be poster / demo sessions on all conference days.  These will be held concurrently with the sponsor sessions.  These are an opportunity to discuss research with community members in small groups and one and one.  Don't miss it.


Sunday July 17, 2022 10:19am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

1. Bottom-Up against F/RE: Comparing bottom-up proteomics and a modified Edman degradation methodology for automated, untargeted protein adductomics analysis within the Galaxy platform.
Andrew T. Rajczewski, University of Minnesota
Efstathios Vryonidis, Stockholm University
Lorena Ndreu, Stockholm University
Gunnar Boysen, University of Arkansas for Medical Sciences
Subina Mehta, University of Minnesota
Pratik D. Jagtap, University of Minnesota
Timothy J. Griffin, University of Minnesota
Isabella Karlsson, Stockholm University
Margareta Törnqvist, Stockholm University
Natalia Y. Tretyakova, University of Minnesota


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

10. Galaxy in AnVIL for Education
Natalie Kucher, Department of Biology, Johns Hopkins University
Ava Hoffman, Department of Biostatistics, Johns Hopkins University
Robert Meller, Department of Neurobiology and Pharmacology, Morehouse School of Medicine
Michael Schatz, Department of Biology, Department of Computer Science, Johns Hopkins University

Speakers
avatar for Natalie Kucher

Natalie Kucher

Project Manager, Johns Hopkins University


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

11. Automating Galaxy Tool Benchmarks
Keith Suderman, Johns Hopkins University
Bridget Carr, Johns Hopkins University
Peyuan Xu, Johns Hopkins University
Victor Wen, Johns Hopkins University
Nuwan Goonasekera, University of Melbourne
Michael Schatz, Johns Hopkins University
Enis Afgan, Johns Hopkins University

Speakers

Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

12. From Newcomer to Contributor: a New Developer Experience with Galaxy
Ahmed Awan, Johns Hopkins University
Tyler Collins, Johns Hopkins University
Michelle Savage, Johns Hopkins University

Speakers

Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

13. GA4GH Task Execution Schema Support in Galaxy
Vipul Chhabra
Alex Kanitz, University of Basel
Kyle Ellrott, Oregon Health and Science University

Speakers

Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

14. Galaxy workflows to BioCompute Objects
Charles Hadley King
Christopher A. Armstrong
Jonathon Keeney
Janisha Patel
Stephanie S. Singleton
Stephen D. Shank
Raja Mazumder


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

2. A unified computing environment for genomics data storage, management, and analysis: NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Space (AnVIL)
Stephen L. Mosher, Department of Biology, Johns Hopkins University, Baltimore, MD
Michael C. Schatz, Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD
Anthony Philippakis, Broad Institute of MIT and Harvard, Cambridge, MA.
AnVIL Team,  The full list of contributors is available at: https://anvilproject.org/about/team

Speakers

Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

3. AlphaFold on Galaxy: fast and accurate modelling of protein structures
Cameron Hyde, Queensland Cyber Infrastructure Foundation; University of the Sunshine Coast, Australia
Grace Hall, Melbourne Bioinformatics, University of Melbourne, Australia
Catherine Bromhead, Melbourne Bioinformatics, University of Melbourne, Australia
Simon Gladman, Melbourne Bioinformatics, University of Melbourne, Australia

Speakers

Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

4. An integrated Galaxy-driven workflow for host-microbiota proteomics and targeted assay development to study host-microbe dynamics in clinical cystic fibrosis samples
Monica E. Kruk, University of Minnesota
Subina Mehta, University of Minnesota
Katherine Do, University of Minnesota
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
Reid Wagner, Minnesota Supercomputing Institute, University of Minnesota
Chris Wendt, Minneapolis Veterans Administration Health Care System and University of Minnesota
John B. O’Connor, Ann & Robert H. Lurie Children’s Hospital of Chicago
Theresa Laguna, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine
Pratik D. Jagtap, University of Minnesota
Timothy J. Griffin, University of Minnesota

Speakers
avatar for Timothy J. Griffin

Timothy J. Griffin

Professor, University of Minnesota


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

5. Automated Reference Genome Assembly in Galaxy in Collaboration with the Vertebrate Genome Project
Delphine Lariviere, Dept. of Biochemistry and Molecular Biology, Penn State University
Giulio Formenti, The Rockefeller University
Alex Ostrovsky, Dept. of Biology, Johns Hopkins University
Cristobal Gallardo, Dept. of Computer Science, University of Freiburg
Linelle Abueg, The Rockefeller University
Nadolina Brajuka, The Rockefeller University
Marc Palmada Flores, Institut de Biologia Evolutiva, Pompeu Fabra University
Anton Nekrutenko, Dept. of Biochemistry and Molecular Biology, Penn State University
Bjorn Grüning, Dept. of Computer Science, University of Freiburg
Michael Schatz, Dept. of Biology, Johns Hopkins University

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Penn State University


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

6. CGH and transcryptome analysis reveals genes related to survival in acute lymphoblastic leukemia
Jessica Alejandra Zapata García, Universidad de Guadalajara, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS)
Adriana Aguilar Lemarroy, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS)
Luis Felipe Jave Suárez, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS)


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

7. Creating Galaxy workflows to empower research into Australia's unique fauna
Anna Syme, Melbourne Bioinformatics, University of Melbourne
Simon Gladman, Melbourne Bioinformatics, University of Melbourne
Catherine Bromhead, Melbourne Bioinformatics, University of Melbourne
Ove Johan Ragnar Gustafsson, Australian BioCommons, University of Melbourne
Mike Thang, Queensland Cyber Infrastructure Foundation, University of Queensland
Tom Harrop, Melbourne Bioinformatics, The University of Melbourne
Gareth Price, Queensland Cyber Infrastructure Foundation, University of Queensland

Speakers
avatar for Anna Syme

Anna Syme

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


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

8. Find and share Galaxy workflows with the community using Dockstore.org
Avani Khadilkar, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Elizabeth Sheets, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Richard Hansen, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Gregory Hogue, Adaptive Oncology, Ontario Institute for Cancer Research
Ash O’Farrell, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Nneka Olunwa, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Charles Overbeck, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Chaz Reid, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Walt Shands, UC Santa Cruz Genomics Institute, University of California Santa Cruz
David Steinberg, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Kathy Tran, Adaptive Oncology, Ontario Institute for Cancer Research
Ben Vizzier, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Steve Von Worley, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Denis Yuen, Adaptive Oncology, Ontario Institute for Cancer Research
Brian O’Connor, Sage Bionetworks
Benedict Paten, UC Santa Cruz Genomics Institute, University of California Santa Cruz
Lincoln Stein, Adaptive Oncology, Ontario Institute for Cancer Research

Speakers
AK

Avani Khadilkar

Bioinformatics Analyst, UCSC


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

9. Galaxy Australia: an Evolving Scientific Instrument
Gareth Price, Queensland Cyber Infrastructure Foundation, University of Queensland
Simon Gladman, Melbourne Bioinformatics, University of Melbourne
Nigel Ward, Australian BioCommons, University of Melbourne
Sarah Nisbet, BioPlatforms Australia, University of Melbourne
Rhys Francis, Australian BioCommons, University of Melbourne
Steven Manon, Australian BioCommons, University of Melbourne
Andrew Lonie, Australian BioCommons, University of Melbourne

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 →


Sunday July 17, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:19am CDT

Session 3: Accepted and Invited Talks
More accepted and invited talks.

This session will also be broadcast live to remote participants.



Moderators
avatar for John Davis

John Davis

software engineer, Johns Hopkins University

Sunday July 17, 2022 11:19am - 12:20pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:20am CDT

Galaxy as a (Science) Gateway to the Command Line
Carrie Ganote, Indiana University
Irene Newton, Indiana University

⇒ Abstract

Speakers
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington


Sunday July 17, 2022 11:20am - 11:27am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:27am CDT

Decentralized Remote Data Handling in Galaxy
John Chilton, Galaxy Project
Marius van den Beek, Galaxy Project

⇒ Abstract

Speakers

Sunday July 17, 2022 11:27am - 11:42am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:42am CDT

GA4GH Task Execution Schema Support in Galaxy
Vipul Chhabra
Alex Kanitz, University of Basel
Kyle Ellrott, Oregon Health and Science University

⇒ Abstract

Speakers

Sunday July 17, 2022 11:42am - 11:49am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:49am CDT

Galaxy Storage Dashboard
Galaxy UI/UX working group

David Lopez, University of Freiburg

⇒ Abstract​​​

Speakers
avatar for Dannon Baker

Dannon Baker

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


Sunday July 17, 2022 11:49am - 11:56am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:56am CDT

Galaxy History Scaling and Modernization
Aysam Guerler, Johns Hopkins University
David López, University of Freiburg
Dannon Baker, Johns Hopkins University
Galaxy UI/UX Working Group

⇒ Abstract​​​

Speakers
avatar for Dannon Baker

Dannon Baker

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


Sunday July 17, 2022 11:56am - 12:11pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

12:11pm CDT

Automating Galaxy Tool Benchmarks
Keith Suderman, Johns Hopkins University
Bridget Carr, Johns Hopkins University
Peyuan Xu, Johns Hopkins University
Victor Wen, Johns Hopkins University
Nuwan Goonasekera, University of Melbourne
Michael Schatz, Johns Hopkins University
Enis Afgan, Johns Hopkins University

⇒ Abstract​​​

Speakers

Sunday July 17, 2022 12:11pm - 12:18pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

12:20pm CDT

Lunch
Lunch is your perfect opportunity to catch up with old friends and collaborators, and to meet new ones.  Get out there and meet people.

Sunday July 17, 2022 12:20pm - 1:20pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

1:19pm CDT

Session 4: Training
GCC2022 features a multi-track training session every day of the conference.  These sessions cover a wide range of topics, and build upon the content presented during the pre-conference training day.  Training sessions are 2 1/2 hours long, and instructors are encouraged to have a short break in the middle.

Not interested in anything being offered? Use this time to catch up on your email, or meet with colleagues, or explore the area, or...

Sunday July 17, 2022 1:19pm - 3:50pm CDT
Various Locations
  A. Training

1:20pm CDT

AnVIL
Description to follow

Speakers
avatar for Mike Schatz

Mike Schatz

Johns Hopkins University


Sunday July 17, 2022 1:20pm - 3:50pm CDT
Discovery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Architecture
Description to follow

Speakers

Sunday July 17, 2022 1:20pm - 3:50pm CDT
Strategy Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

DRM & Clusters
Description to follow

Speakers
avatar for Nate Coraor

Nate Coraor

System Administrator, Galaxy Project, Penn State University


Sunday July 17, 2022 1:20pm - 3:50pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Into to Galaxy & Genomics
Description to follow


Sunday July 17, 2022 1:20pm - 3:50pm CDT
Logic Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Pandemic Research via Proteomics
The Galaxy for proteomics (Galaxy-P) team will conduct a hands-on workshop on the use of MS-based informatics tools to investigate publicly available COVID-19 proteomics data. The attendees will be trained in running well-validated tools and workflows available for proteomic data analysis within Galaxy.

The workshop module will include hands-on experience in using the published workflows that mainly focus on the identification of expressed SARS-CoV-2 proteins/peptides, human host proteins, and potentially co-infecting microbial components from publicly available proteomics data. Tools for visualizing the spectra of the expressed peptides and annotating the peptides and interpreting results will also be discussed.

Attendees will be required to bring their laptop computers so that they can access public Galaxy resources for the training.

Speakers
avatar for Timothy J. Griffin

Timothy J. Griffin

Professor, University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
Metaproteomics . DIA . Proteogenomics
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota


Sunday July 17, 2022 1:20pm - 3:50pm CDT
Gallery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

3:50pm CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Sunday July 17, 2022 3:50pm - 4:10pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:09pm CDT

Session 5: Accepted and Invited Talks
Accepted and invited talks.  The final presentation session of the day.

This session will also be broadcast live to remote participants.



Sunday July 17, 2022 4:09pm - 4:50pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:10pm CDT

Sponsor Talk : Google Cloud
Sunday July 17, 2022 4:10pm - 4:25pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:25pm CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Sunday July 17, 2022 4:25pm - 4:30pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:30pm CDT

Continuous Testing Of Containerized Galaxy Tools
Alexandru Mahmoud, Harvard Medical School
Alex Ostrovsky, Johns Hopkins University
Enis Afgan, Johns Hopkins University

⇒ Abstract

Speakers
avatar for Alex Ostrovsky

Alex Ostrovsky

Johns Hopkins University


Sunday July 17, 2022 4:30pm - 4:37pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:37pm CDT

The Observable Galaxy - a New Notebook Integration with Application to Regulatory Grade Database Construction
Stephen D. Shank
Alex Ostrovsky
Charles Hadley King
Sergei L. Kosakovsky Pond

⇒ Abstract​​​

Speakers

Sunday July 17, 2022 4:37pm - 4:52pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:52pm CDT

Let the Analysis be GiN: Galaxy in Notebooks
Jayadev Joshi, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
Daniel Blankenberg, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.


⇒ Abstract​​​

Speakers

Sunday July 17, 2022 4:52pm - 4:59pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:59pm CDT

Galaxy ProTo 2.0 Redux: Dynamic Tool Prototyping Using Interactive Tools
Sveinung Gundersen
Morten Johansen

⇒ Abstract

Speakers
SG

Sveinung Gundersen

University of Oslo


Sunday July 17, 2022 4:59pm - 5:06pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

5:14pm CDT

Session 6: 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.

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

BoFs this session:

Propose a BoF now.

Sunday July 17, 2022 5:14pm - 6:30pm CDT
Various Locations
  E. BoFs, BoFs

5:15pm CDT

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. Following the BoF of last year, let's meet to see what are the plans and how things are moving.

This BoF will be held jointly in person, and online.

Speakers
avatar for Nate Coraor

Nate Coraor

System Administrator, Galaxy Project, Penn State University
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 →


Sunday July 17, 2022 5:15pm - 6:30pm CDT
Strategy Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs

5:15pm CDT

BOF: microGalaxy
Many efforts on microbial analysis are done in Galaxy. To avoid redundancy and coordinate our efforts, we started microGalaxy, a community focusing on microbial analysis with Galaxy. Whether you are analysing microbiome samples or bacterial isolates, long reads or short, shotgun or 16S, genomics transcriptomics or proteomics, this is the place to be!

We organized quarterly community meeting. What a best occasion than GCC and a BoF for our next meeting? Anyone interested is welcome to join.

This BoF will be held online.  However, if you are participating and you are at GCC, then you are encouraged to gather with your fellow local participants in the assigned room.

Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg


Sunday July 17, 2022 5:15pm - 6:30pm CDT
Gallery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs
 
Monday, July 18
 

7:59am CDT

Conference Day 2
Welcome to the second day of the 2022 Galaxy Community Conference (GCC2022).

Monday July 18, 2022 7:59am - 6:00pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks

8:00am CDT

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

Monday July 18, 2022 8:00am - 6:00pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  F. Help

8:59am CDT

Session 7: Accepted and Invited Talks
This session will feature invited and accepted talks.

This session will also be broadcast live to remote participants.

Moderators
Monday July 18, 2022 8:59am - 10:00am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:00am CDT

Automated Reference Genome Assembly in Galaxy in Collaboration with the Vertebrate Genome Project
Delphine Lariviere, Dept. of Biochemistry and Molecular Biology, Penn State University, College Park, PA, USA
Giulio Formenti, The Rockefeller University, 1230 York Avenue New York, NY 10065, USA
Alex Ostrovsky, Dept. of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
Cristobal Gallardo, Dept. of Computer Science, University of Freiburg, Freiburg, Germany
Linelle Abueg, The Rockefeller University, 1230 York Avenue New York, NY 10065, USA
Nadolina Brajuka, The Rockefeller University, 1230 York Avenue New York, NY 10065, USA
Marc Palmada Flores, Institut de Biologia Evolutiva, Pompeu Fabra University, Barcelona, 08003, Spain
Anton Nekrutenko, Dept. of Biochemistry and Molecular Biology, Penn State University, College Park, PA, USA
Bjorn Grüning, Dept. of Computer Science, University of Freiburg, Freiburg, Germany
Michael Schatz Dept. of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA

⇒ Abstract​​​



Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Penn State University


Monday July 18, 2022 9:00am - 9:15am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:15am CDT

An Integrated Galaxy-Driven Workflow for Host-Microbiota Proteomics and Targeted Assay Development to Study Host-Microbe Dynamics in Clinical Cystic Fibrosis Samples
Monica E. Kruk, University of Minnesota
Subina Mehta, University of Minnesota
Katherine Do, University of Minnesota
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
Reid Wagner, Minnesota Supercomputing Institute, University of Minnesota
Chris Wendt, Minneapolis Veterans Administration Health Care System and University of Minnesota
John B. O’Connor, Ann & Robert H. Lurie Children’s Hospital of Chicago
Theresa Laguna, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine
Pratik D. Jagtap, University of Minnesota
Timothy J. Griffin, University of Minnesota

⇒ Abstract​​​

Speakers
avatar for Timothy J. Griffin

Timothy J. Griffin

Professor, University of Minnesota


Monday July 18, 2022 9:15am - 9:22am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:22am CDT

Advances in Machine Learning for Galaxy
Jeremy Goecks, Oregon Health & Science University
Björn Grüning, University of Freiburg

⇒ Abstract​​​

Speakers
avatar for Jeremy Goecks

Jeremy Goecks

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


Monday July 18, 2022 9:22am - 9:37am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:37am CDT

"Bottom-up Against F/Re”: Comparing Bottom-up Proteomics and a Modified Edman Degradation Methodology for Automated, Untargeted Protein Adductomics Analysis Within the Galaxy Platform
Andrew T. Rajczewski, University of Minnesota
Efstathios Vryonidis, Stockholm University
Lorena Ndreu, Stockholm University
Gunnar Boysen, University of Arkansas for Medical Sciences
Subina Mehta, University of Minnesota
Pratik D. Jagtap, University of Minnesota
Timothy J. Griffin, University of Minnesota
Isabella Karlsson, Stockholm University
Margareta Törnqvist, Stockholm University
Natalia Y. Tretyakova, University of Minnesota
⇒ Abstract​​​



Monday July 18, 2022 9:37am - 9:44am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:44am CDT

Omicron, Delta Waves and Beyond: Galaxy-Generated Variant-Specific Peptide Panels for Diagnosis, Characterization and Surveillance of Emerging Sars-Cov-2 Variants
Subina Mehta- University of Minnesota
Valdemir M. Carvalho - Fluery Group, Brazil
Andrew T. Rajczewski - University of Minnesota
Björn Grüning- University of Freiburg, Freiburg
James E. Johnson- University of Minnesota
Reid Wagner- University of Minnesota
Olivier Pible -DMT, Université Paris Saclay, Bagnols-sur-Cèze, France
Jean Armengaud- DMT, Université Paris Saclay, Bagnols-sur-Cèze, France
Timothy J. Griffin- University of Minnesota
Pratik D. Jagtap - University of Minnesota

⇒ Abstract​​​

Speakers
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota


Monday July 18, 2022 9:44am - 9:59am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:00am CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Monday July 18, 2022 10:00am - 10:20am CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:19am CDT

Session 8: Poster / Demo Session B
There will be poster / demo sessions on all conference days.  These will be held concurrently with the sponsor sessions.  These are an opportunity to discuss research with community members in small groups and one and one.  Don't miss it.


Monday July 18, 2022 10:19am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

15. Galaxy Media Site - a full featured landing site for Galaxy Australia
Cameron Hyde, Queensland Cyber Infrastructure Foundation, University of the Sunshine Coast
Madeline Bassetti, Queensland Cyber Infrastructure Foundation

Speakers

Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

16. Galaxy Pipeline for Quantitative Analysis of Enriched Phosphopeptides
Arthur Eschenlauer, University of Minnesota
Zoi Sychev, University of Minnesota
James Johnson, University of Minnesota
Justin Drake, University of Minnesota

Speakers
avatar for Arthur Eschenlauer

Arthur Eschenlauer

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


Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

17. Let the analysis be GiN: Galaxy in Notebooks
Jayadev Joshi, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic
Daniel Blankenberg, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic

Speakers

Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

18. Microbial strain characterization and subtyping of metagenome-assembled genomes with Sequence Bloom Trees in Galaxy
Fabio Cumbo, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic,
Daniel Blankenberg, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic

Speakers
avatar for Fabio Cumbo

Fabio Cumbo

Postdoctoral Researcher, Cleveland Clinic
Metagenomics, microbiome


Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

19. Molecular Dynamics Simulations of Viral Helicases in Galaxy
Bryan Raubenolt, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic
Daniel Blankenberg, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic

Speakers

Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

20. Multi-Species Bulk RNA sequencing on explanted hiPSC-derived engineered myocardium tissue
Kiera D. Dwyer, Brown University School of Engineering
Rajeev J. Kant, Brown University School of Engineering
Kareen L.K. Coulombe, Brown University School of Engineering

Speakers

Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

21. Secure deployment and hosting of Galaxy workflow using container orchestration tools and infrastructure as Code
Soyean Kim, Simon Fraser University, CINECA, PHA4GE, Statistical Society of Canada, UN task team for Big Data (Global Platform)

Speakers
avatar for Soyean Kim

Soyean Kim

Head of Product, Centre for Infectious Disease Genomics and One Health (CIDGOH)
Soyean Kim is currently the product lead at the Centre for Infectious Disease Genomics and One Health (CIDGOH) and a researcher at Simon Fraser University supporting CIDGOH’s partnership and projects, and being responsible for product development and product strategy. She has over... Read More →


Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

22. Targeting Viral Helicases Through Atomistic Molecular Dynamics Simulations in Galaxy
Bryan Raubenolt, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic
Daniel Blankenberg, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic

Speakers

Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

23. A Global Hub: A home on the web for every Galaxy community
Nick Stoler, Penn State University
Dannon Baker, Johns Hopkins University
Beatriz Serrano-Solano, University of Freiburg
Björn Grüning, University of Freiburg

Speakers

Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

24. RASCL: Rapid Assessment of selection in clades through molecular sequence analysis
Alexander G Lucaci, Institute for Genomics and Evolutionary Medicine, Temple University
Jordan D Zehr, Institute for Genomics and Evolutionary Medicine, Temple University
Stephen D Shank, Institute for Genomics and Evolutionary Medicine, Temple University
Dave Bouvier, Department of Biochemistry and Molecular Biology, The Pennsylvania State University
Alexander Ostrovsky, Department of Biology, Johns Hopkins University
Han Mei, Department of Biochemistry and Molecular Biology, The Pennsylvania State University
Anton Nekrutenko, Department of Biochemistry and Molecular Biology, The Pennsylvania State University
Darren P Martin, Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town
Sergei L Kosakovsky Pond, Institute for Genomics and Evolutionary Medicine, Temple University



Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

25. NCBI Datasets, a new resource for accessing NCBI genome data in Galaxy
Nuala O'Leary, NCBI
Eric Cox, NCBI
Brad Holmes, NCBI
Mirian Tsuchiya, NCBI
Peter Meric, NCBI
Greg Schuler, NCBI
Robert Falk, NCBI
William Anderson, NCBI
Xuan Zhang, NCBI
Vichet Hem, NCBI
Jonathan Cothran, NCBI
Valerie Schneider, NCBI

Speakers
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.


Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

26. RNA Deconvolution with MuSiC
Mehmet Tekman, University of Freiburg
Wendi Bacon, Open University

Speakers
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, University of Freiburg
Single-Cell, Developing Wrappers with Emacs


Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

27. Galaxy ProTo 2.0 Redux: Dynamic tool prototyping using Interactive Tools
Sveinung Gundersen
Morten Johansen

Speakers
SG

Sveinung Gundersen

University of Oslo


Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

40. Introducing the Galaxy Mentor Network
Assunta DeSanto, PSU
Beatriz Serrano-Solano, University of Freiburg
Berenice Batut, University of Freiburg

Speakers
avatar for Assunta DeSanto

Assunta DeSanto

Computational Scientist 3, Penn State University
I'm fairly new to Galaxy and the world of Bioinformatics. Teach me something new!Additionally, I'm a mom, lifelong learner, both a cat and dog person, who loves to read and be outside. Let's chat about common interests :)


Monday July 18, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:19am CDT

Session 9: Accepted and Invited Talks
More accepted and invited talks.

This session will also be broadcast live to remote participants.



Moderators
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington

Monday July 18, 2022 11:19am - 12:20pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:20am CDT

Secure Deployment and Hosting of Galaxy Workflow Using Container Orchestration Tools and Infrastructure as Code
Soyean Kim, Simon Fraser University, CINECA, PHA4GE, Statistical Society of Canada, UN task team for Big Data (Global Platform)

⇒ Abstract​​​

Speakers
avatar for Soyean Kim

Soyean Kim

Head of Product, Centre for Infectious Disease Genomics and One Health (CIDGOH)
Soyean Kim is currently the product lead at the Centre for Infectious Disease Genomics and One Health (CIDGOH) and a researcher at Simon Fraser University supporting CIDGOH’s partnership and projects, and being responsible for product development and product strategy. She has over... Read More →


Monday July 18, 2022 11:20am - 11:27am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:27am CDT

Scaling Galaxy on the Cloud - Data-Local Cancer Analytics on AWS
Allison Creason, Oregon Health and Science University
Jeremy Goecks, Oregon Health and Science University
Qiang Gu, Oregon Health and Science University
Luke Sargent, Oregon Health and Science University
Cameron Watson, Oregon Health and Science University

⇒ Abstract​​​

Speakers
avatar for Luke Sargent

Luke Sargent

Oregon Health and Science University (OHSU)


Monday July 18, 2022 11:27am - 11:42am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:42am CDT

Open Bio Reference Data Catalog for Galaxy and Bioconductor
Enis Afgan, Johns Hopkins University
Alexandru Mahmoud, Harvard Medical School
Nuwan Goonasekera, University of Melbourne
Erin Chu, Amazon Web Services

⇒ Abstract​​​

Speakers
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University



Monday July 18, 2022 11:42am - 11:49am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:49am CDT

Gravity: Painless Process Management for Galaxy Servers
Nate Coraor, Penn State University
Marius van den Beek, Penn State University

⇒ Abstract​​​

Speakers
avatar for Nate Coraor

Nate Coraor

System Administrator, Galaxy Project, Penn State University


Monday July 18, 2022 11:49am - 11:56am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:56am CDT

Metascheduling Galaxy Jobs with Total Perspective Vortex
Nuwan Goonasekera, Melbourne Bioinformatics, University of Melbourne
Catherine Bromhead, Melbourne Bioinformatics, University of Melbourne
Enis Afgan, Johns Hopkins University
Simon Gladman, Melbourne Bioinformatics, University of Melbourne

⇒ Abstract​​​


Monday July 18, 2022 11:56am - 12:11pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

12:11pm CDT

FragPipe in Galaxy: Wrapper Implementation for a Complete Proteomics Tool Suite
Reid Wagner, University of Minnesota
James Johnson, University of Minnesota
Fengchao Yu, University of Michigan
Subina Mehta, University of Minnesota
Pratik Jagtap, University of Minnesota
Alexey I. Nesvizhskii, University of Michigan
Timothy J. Griffin, University of Minnesota

⇒ Abstract​​​

Speakers

Monday July 18, 2022 12:11pm - 12:18pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

12:20pm CDT

Lunch
Lunch is your perfect opportunity to catch up with old friends and collaborators, and to meet new ones.  Get out there and meet people.

Monday July 18, 2022 12:20pm - 1:20pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

1:19pm CDT

Session10: Training
GCC2022 features a multi-track training session every day of the conference.  These sessions cover a wide range of topics, and build upon the content presented during the pre-conference training day.  Training sessions are 2 1/2 hours long, and instructors are encouraged to have a short break in the middle.

Not interested in anything being offered? Use this time to catch up on your email, or meet with colleagues, or explore the area, or...

Monday July 18, 2022 1:19pm - 3:50pm CDT
Various Locations
  A. Training

1:20pm CDT

Assembly
Description to follow

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Penn State University


Monday July 18, 2022 1:20pm - 3:50pm CDT
Logic Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Conda, containers
Description to follow

Speakers
avatar for Bjorn Gruning

Bjorn Gruning

University of Freiburg


Monday July 18, 2022 1:20pm - 3:50pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Contributing to GTN
Description to follow

Speakers

Monday July 18, 2022 1:20pm - 3:50pm CDT
Discovery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Introduction to Metaproteomics
The Galaxy for proteomics (Galaxy-P) team will conduct a hands-on workshop on the use of MS-based informatics tools for metaproteomics research. 

Metaproteomics is the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time. It has the potential to unravel the mechanistic details of microbial interactions with the host / environment by analyzing the functional dynamics of the microbiome. In this metaproteomics tutorial we will identify expressed proteins from a complex bacterial community sample. For this MS/MS data will be matched to peptide sequences provided through a FASTA file.

Attendees will be required to bring their laptop computers so that they can access public Galaxy resources for the training.

Speakers
avatar for Timothy J. Griffin

Timothy J. Griffin

Professor, University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
Metaproteomics . DIA . Proteogenomics
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota


Monday July 18, 2022 1:20pm - 3:50pm CDT
Gallery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Writing tests
Description to follow

Speakers
avatar for John Davis

John Davis

software engineer, Johns Hopkins University


Monday July 18, 2022 1:20pm - 3:50pm CDT
Strategy Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

3:50pm CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Monday July 18, 2022 3:50pm - 4:10pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:09pm CDT

Session 11: Accepted and Invited Talks
Accepted and invited talks.  The final presentation session of the day.

This session will also be broadcast live to remote participants.



Moderators
avatar for Timothy J. Griffin

Timothy J. Griffin

Professor, University of Minnesota

Monday July 18, 2022 4:09pm - 4:50pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:10pm CDT

Sponsor Talk : Amazon
Monday July 18, 2022 4:10pm - 4:35pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:35pm CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Monday July 18, 2022 4:35pm - 4:45pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:45pm CDT

Community Update from PIs
Speakers
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 Mike Schatz

Mike Schatz

Johns Hopkins University


Monday July 18, 2022 4:45pm - 5:30pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

5:29pm CDT

Session 12: 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.

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

BoFs this session:

Propose a BoF now.

Monday July 18, 2022 5:29pm - 6:30pm CDT
Various Locations
  E. BoFs, BoFs

5:30pm CDT

BOF: BYO Board Game 🀄️ 🎲 ♠️
Bring your favorite board game/card game along and get in small groups to play it!

Speakers
avatar for Assunta DeSanto

Assunta DeSanto

Computational Scientist 3, Penn State University
I'm fairly new to Galaxy and the world of Bioinformatics. Teach me something new!Additionally, I'm a mom, lifelong learner, both a cat and dog person, who loves to read and be outside. Let's chat about common interests :)


Monday July 18, 2022 5:30pm - 6:30pm CDT
Strategy Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs

5:30pm CDT

BOF: Sequencing and Genomics of the Future
Earlier this year, the Telomere-to-Telomere (T2T) project yielded the first complete assembly of a human genome. Decades in the making, this puts human genomics on a new trajectory for basic, applied, and medical research. In this BoF, we’ll start off with a brief overview of the T2T project and then suggest some ideas for potential future developments. But most importantly, bring your own ideas because most of the BoF will be devoted to collaborative idea generation and imagining what can be.

Speakers
avatar for Mike Schatz

Mike Schatz

Johns Hopkins University


Monday July 18, 2022 5:30pm - 6:30pm CDT
Gallery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs

5:30pm CDT

BOF: Supporting remote workflows on distributed resources
At Oak Ridge National Laboratory, we are exploring using Galaxy for data analysis of neutron scattering experiments. Our workflows are likely to encompass multiple distributed resources within a single workflow execution. Galaxy provides some capabilities for this, but the accompanying data management and security options that this entails are limited.

We would like to engage with the Galaxy community to discuss and plan for how to enhance Galaxy (and Pulsar) to better support a broader range of workflow environments.


Speakers
SY

Sergey Yakubov

Senior Software Engineer, Oak Ridge National Laboratory


Monday July 18, 2022 5:30pm - 6:30pm CDT
Logic Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs
 
Tuesday, July 19
 

7:59am CDT

Conference Day 3
Welcome to the Third day of the 2022 Galaxy Community Conference (GCC2022).

Tuesday July 19, 2022 7:59am - 6:00pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks

8:00am CDT

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

Tuesday July 19, 2022 8:00am - 6:00pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  F. Help

8:59am CDT

Session 13: Accepted and Invited Talks
This session will feature invited and accepted talks.

This session will also be broadcast live to remote participants.

Tuesday July 19, 2022 8:59am - 10:00am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:00am CDT

From Newcomer to Contributor: a New Developer Experience with Galaxy
Ahmed Awan, Johns Hopkins University
Tyler Collins, Johns Hopkins University
Michelle Savage, Johns Hopkins University


⇒ Abstract

Speakers

Tuesday July 19, 2022 9:00am - 9:07am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:07am CDT

Galaxy Australia: an Evolving Scientific Instrument
Gareth Price, Queensland Cyber Infrastructure Foundation, University of Queensland
Simon Gladman, Melbourne Bioinformatics, University of Melbourne
Nigel Ward, Australian BioCommons, University of Melbourne
Sarah Nisbet, BioPlatforms Australia, University of Melbourne
Rhys Francis, Australian BioCommons, University of Melbourne
Steven Manon, Australian BioCommons, University of Melbourne
Andrew Lonie, Australian BioCommons, University of Melbourne

⇒ Abstract​​​

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 →


Tuesday July 19, 2022 9:07am - 9:22am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:22am CDT

Using Galaxy as a Teaching Platform for the YES for CURE Data Science Track
Alexandru Mahmoud, Channing Division of Network Medicine, Harvard Medical School
Vincent Carey, Channing Division of Network Medicine, Harvard Medical School

⇒ Abstract​​​


Tuesday July 19, 2022 9:22am - 9:29am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:29am CDT

Galaxy in AnVIL for Education
Natalie Kucher, Department of Biology, Johns Hopkins University
Ava Hoffman, Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health
Robert Meller, Department of Neurobiology and Pharmacology, Morehouse School of Medicine
Michael Schatz, Department of Biology, Department of Computer Science, Johns Hopkins University

⇒ Abstract​​​

Speakers
avatar for Natalie Kucher

Natalie Kucher

Project Manager, Johns Hopkins University


Tuesday July 19, 2022 9:29am - 9:36am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:36am CDT

To Seek Out New Talent and New Perspectives: Promoting Functional Analysis of Microbiome Through Online Educational Resources via the Galaxy Platform
Berenice Batut, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg (Germany); Anshu Bhardwaj, CSIR-Institute of Microbial Technology, Chandigarh, Haryana (India); David Clements, Anaconda, Inc., Eugene, Oregon (United States); Bjoern Gruening, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg (Germany); Saskia Hiltemann, Clinical Bioinformatics, Department of Pathology, Erasmus Medical Center, Rotterdam (The Netherlands); James Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota (USA); Manoj Kumar, CSIR-Institute of Microbial Technology, Chandigarh, Haryana (India); Subina Mehta, Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (USA); Helena Rasche, Erasmus Medical Center; Avans Hogeschool, Rotterdam (The Netherlands); Timothy J. Griffin, Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (USA) and Pratik D. Jagtap, Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota (USA)

⇒ Abstract​​​

Speakers
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
Metaproteomics . DIA . Proteogenomics


Tuesday July 19, 2022 9:36am - 9:51am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:51am CDT

Galaxy-E: Ecology Oriented Galaxy Initiative, a 2022 Update!
Coline Royaux, Julien Sananikone, Simon Bénateau, Benjamin Yguel, Olivier Norvez, Romain Lorrillière, Elie Arnaud, Yves Bas, Jean-baptiste Mihoub, Dominique Pelletier, Yvan Le Bras


⇒ Abstract

Speakers

Tuesday July 19, 2022 9:51am - 9:58am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:00am CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Tuesday July 19, 2022 10:00am - 10:20am CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:19am CDT

Session 14: Poster / Demo Session C
There will be poster / demo sessions on all conference days.  These will be held concurrently with the sponsor sessions.  These are an opportunity to discuss research with community members in small groups and one and one.  Don't miss it.


Tuesday July 19, 2022 10:19am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

11. Automating Galaxy Tool Benchmarks
Keith Suderman, Johns Hopkins University
Bridget Carr, Johns Hopkins University
Peyuan Xu, Johns Hopkins University
Victor Wen, Johns Hopkins University
Nuwan Goonasekera, University of Melbourne
Michael Schatz, Johns Hopkins University
Enis Afgan, Johns Hopkins University

Speakers

Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

12. From Newcomer to Contributor: a New Developer Experience with Galaxy
Ahmed Awan, Johns Hopkins University
Tyler Collins, Johns Hopkins University
Michelle Savage, Johns Hopkins University

Speakers

Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

13. GA4GH Task Execution Schema Support in Galaxy
Vipul Chhabra
Alex Kanitz, University of Basel
Kyle Ellrott, Oregon Health and Science University

Speakers

Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

14. Galaxy workflows to BioCompute Objects
Charles Hadley King
Christopher A. Armstrong
Jonathon Keeney
Janisha Patel
Stephanie S. Singleton
Stephen D. Shank
Raja Mazumder


Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

28. Bioconductor Interactive Tools in Galaxy
Alexandru Mahmoud, Channing Division of Network Medicine, Harvard Medical School
Vincent Carey, Channing Division of Network Medicine, Harvard Medical School


Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

29. FragPipe in Galaxy: Wrapper Implementation for a Complete Proteomics Tool Suite
Reid Wagner, University of Minnesota
James Johnson, University of Minnesota
Fengchao Yu, University of Michigan
Subina Mehta, University of Minnesota
Pratik Jagtap, University of Minnesota
Alexey I. Nesvizhskii, University of Michigan
Timothy J. Griffin, University of Minnesota

Speakers

Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

30. What's new in Galaxy's API
Marius van den Beek, PSU
David López, University of Freiburg


Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

31. Galaxy as a (science) gateway to the command line
Carrie Ganote, Indiana University
Irene Newton, Indiana University

Speakers
avatar for Carrie Ganote

Carrie Ganote

Indiana University Bloomington


Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

32. Galaxy History Scaling and Modernization
Aysam Guerler, Johns Hopkins University
David López, University of Freiburg
Dannon Baker, Johns Hopkins University
Galaxy UI/UX Working Group

Speakers
avatar for Dannon Baker

Dannon Baker

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


Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

33. Gravity: Painless Process Management for Galaxy Servers
Nate Coraor, Penn State University
Marius van den Beek, Penn State University

Speakers
avatar for Nate Coraor

Nate Coraor

System Administrator, Galaxy Project, Penn State University


Tuesday July 19, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:19am CDT

Session 15: Accepted and Invited Talks
More accepted and invited talks.

This session will also be broadcast live to remote participants.



Tuesday July 19, 2022 11:19am - 12:20pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:20am CDT

What's New in the API
Marius van den Beek, PSU
David López, University of Freiburg


⇒ Abstract​​​


Tuesday July 19, 2022 11:20am - 11:27am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:27am CDT

Support for the Common Workflow Language in Galaxy: History, Progress and Remaining Challenges
Nicola Soranzo, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
Marius van den Beek, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA
Michael R. Crusoe, VU Amsterdam and ELIXIR-NL
John Chilton, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA

⇒ Abstract​​​

Speakers
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute


Tuesday July 19, 2022 11:27am - 11:42am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:42am CDT

Accelerating Galaxy with Task Queues
Marius van den Beek, PSU
John Chilton, PSU

⇒ Abstract​​​

Speakers

Tuesday July 19, 2022 11:42am - 11:49am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:49am CDT

Securely Storing Sensitive User Preferences in Galaxy
Nuwan Goonasekera, University of Melbourne
Isuru Ranawaka, Indiana University
Enis Afgan, Johns Hopkins University

⇒ Abstract​​​


Tuesday July 19, 2022 11:49am - 11:56am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

11:56am CDT

Galaxy’s New Database Migration System and Data Model Testing Infrastructure
John Davis, Johns Hopkins University

⇒ Abstract

Speakers
avatar for John Davis

John Davis

software engineer, Johns Hopkins University


Tuesday July 19, 2022 11:56am - 12:11pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

12:11pm CDT

Robust, Performant and Resumable Uploads Using tus.io
Marius van den Beek, Penn State University

⇒ Abstract​​​


Tuesday July 19, 2022 12:11pm - 12:18pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks, Dev

12:20pm CDT

Lunch
Lunch is your perfect opportunity to catch up with old friends and collaborators, and to meet new ones.  Get out there and meet people.

Tuesday July 19, 2022 12:20pm - 1:20pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

1:19pm CDT

Session 16: Training
GCC2022 features a multi-track training session every day of the conference.  These sessions cover a wide range of topics, and build upon the content presented during the pre-conference training day.  Training sessions are 2 1/2 hours long, and instructors are encouraged to have a short break in the middle.

Not interested in anything being offered? Use this time to catch up on your email, or meet with colleagues, or explore the area, or...

Tuesday July 19, 2022 1:19pm - 3:50pm CDT
Various Locations
  A. Training

1:20pm CDT

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

Prerequisites
  • Basic understanding of Galaxy from a developer point of view.
  • Python programming.
  • A laptop with a modern web browser (Google Chrome, Firefox and Safari will work best).


Speakers
avatar for Dannon Baker

Dannon Baker

Galaxy Project, Johns Hopkins University
Talk to me about Galaxy Development, especially the UI!
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute


Tuesday July 19, 2022 1:20pm - 3:50pm CDT
Discovery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Debugging Galaxy
We'll cover how to find and fix common types of bugs you may encounter as a contributor to Galaxy.  We'll step through several types of issues and show you how to reproduce them locally, devlop a solution, and commit your edits.  

You'll need a laptop with Mac OS or Linux that can run Galaxy, as well as your favorite IDE or edtor.
Some basic familiarity with Git, as well as Python and JavaScript will be necessary, as well.

Speakers
avatar for John Davis

John Davis

software engineer, Johns Hopkins University
avatar for Assunta DeSanto

Assunta DeSanto

Computational Scientist 3, Penn State University
I'm fairly new to Galaxy and the world of Bioinformatics. Teach me something new!Additionally, I'm a mom, lifelong learner, both a cat and dog person, who loves to read and be outside. Let's chat about common interests :)


Tuesday July 19, 2022 1:20pm - 3:50pm CDT
Strategy Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Genome Annotation
Description to follow

Speakers
avatar for Delphine Lariviere

Delphine Lariviere

Penn State University


Tuesday July 19, 2022 1:20pm - 3:50pm CDT
Logic Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Machine Learning
In this workshop, we provide an overview of the major Deep Learning (DL) architectures, namely feedforward neural networks (FNN), recurrent neural networks (RNN), and convolutional neural networks (CNN). We then do a guided demo of using Galaxy's DL tools to solve an imgae classification problem using CNN.

Speakers
KK

Kaivan Kamali

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


Tuesday July 19, 2022 1:20pm - 3:50pm CDT
Gallery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Pulsar & CVMFS
Description to follow

Speakers

Tuesday July 19, 2022 1:20pm - 3:50pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

3:50pm CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Tuesday July 19, 2022 3:50pm - 4:10pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:09pm CDT

Session 17: Accepted and Invited Talks
Accepted and invited talks.  The final presentation session of the day.

This session will also be broadcast live to remote participants.



Tuesday July 19, 2022 4:09pm - 4:24pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:10pm CDT

Sponsor Talk : PeerJ
Tuesday July 19, 2022 4:10pm - 4:25pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:25pm CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Tuesday July 19, 2022 4:25pm - 4:30pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:30pm CDT

Automatic Updates of Intergalactic Workflow Commission (IWC) Workflows
Simon Bray, Marius van den Beek, John Chilton, Björn Grüning

⇒ Abstract​​​


Tuesday July 19, 2022 4:30pm - 4:37pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:37pm CDT

FragPipe in Headless Mode Enables Seamlessly Analyzing LC-Ms Data in Galaxy Platform
Fengchao Yu, University of Michigan
Guo Ci Teo, University of Michigan
Dmitry Avtonomov, University of Michigan
Sarah Haynes, University of Michigan
Felipe da Veiga Leprevost, University of Michigan
Daniel Geiszler, University of Michigan
Daniel Polasky, University of Michigan
Kevin Yang, University of Michigan
Alexey Nesvizhskii, University of Michigan

⇒ Abstract​​​

Speakers
avatar for Fengchao Yu

Fengchao Yu

Research Investigator, University of Michigan


Tuesday July 19, 2022 4:37pm - 4:52pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:52pm CDT

MSMetaEnhancer: A Galaxy Tool for Mass Spectra Metadata Annotation
Matej Troják, RECETOX, Masaryk University
Helge Hecht, RECETOX, Masaryk University
Martin Čech, RECETOX, Masaryk University
Elliott James Price, RECETOX, Masaryk University


⇒ Abstract

Speakers
avatar for Matej Trojak

Matej Trojak

RECETOX


Tuesday July 19, 2022 4:52pm - 4:59pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:59pm CDT

NCBI Datasets, a New Resource for Accessing NCBI Genome Data in Galaxy
Nuala O'Leary, NCBI;
Eric Cox, NCBI;
Brad Holmes, NCBI;
Mirian Tsuchiya, NCBI;
Peter Meric, NCBI;
Greg Schuler, NCBI;
Robert Falk, NCBI;
William Anderson, NCBI;
Xuan Zhang, NCBI;
Vichet Hem, NCBI;
Jonathan Cothran, NCBI;
Valerie Schneider, NCBI

⇒ Abstract​​​

Speakers
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 19, 2022 4:59pm - 5:06pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

5:06pm CDT

RNA Deconvolution with MuSiC
Mehmet Tekman, University of Freiburg
Wendi Bacon, Open University

⇒ Abstract​​​

Speakers
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, University of Freiburg
Single-Cell, Developing Wrappers with Emacs


Tuesday July 19, 2022 5:06pm - 5:13pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

5:19pm CDT

Session 18: 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.

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

BoFs this session:
Propose a BoF now.

Tuesday July 19, 2022 5:19pm - 6:30pm CDT
Various Locations
  E. BoFs, BoFs

5:20pm CDT

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

This BoF will be held jointly in person (see info below) and online (Zoom).

Speakers
avatar for Hans-Rudolf Hotz

Hans-Rudolf Hotz

Friedrich Miescher Institute for Biomedical Research, Basel
avatar for Nicola Soranzo

Nicola Soranzo

Earlham Institute
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 19, 2022 5:20pm - 6:30pm CDT
Gallery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs

5:20pm CDT

BOF: Building a global database of tool resource requirements
Efficiently executing bioinformatics tools requires careful specification of resource requirements for each job. This specification depends on the job inputs and available resources. Currently, deciding these values is a task mostly left up to the system administrator for each Galaxy instance, which leads to a a lot of repeated effort globally. During this BoF, let's discuss options for building a global database of sensible resource requirement defaults that can be readily reused or customized by anyone.

Speakers
avatar for Enis Afgan

Enis Afgan

Research scientist, Johns Hopkins University


Tuesday July 19, 2022 5:20pm - 6:30pm CDT
Discovery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs

5:20pm CDT

BOF: Yoga 🧘
Let's meet up and get in some downward dog. We'll run through a simple yoga session with an aim to make it accessible for all experience levels. If you have a yoga mat, please bring it with you. If you are unable to, please let me know so I can bring some extras.

Wear comfortable clothing!

This BoF is tentatively scheduled for the Logic Room, but if the weather is nice then we will meet outside.  Watch this space.

Speakers
avatar for Assunta DeSanto

Assunta DeSanto

Computational Scientist 3, Penn State University
I'm fairly new to Galaxy and the world of Bioinformatics. Teach me something new!Additionally, I'm a mom, lifelong learner, both a cat and dog person, who loves to read and be outside. Let's chat about common interests :)


Tuesday July 19, 2022 5:20pm - 6:30pm CDT
Logic Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs

6:30pm CDT

Conference Dinner!
The official conference dinner is Tuesday evening, starting at 6:30pm. A separate registration ticket is required to attend.  Dinner will be in the Courtyard of the hotel.

Tuesday July 19, 2022 6:30pm - 9:30pm CDT
TBA
 
Wednesday, July 20
 

TBA

Aquatennial Starts
Aquatennial, the biggest celebration in Minneapolis's summer, is held July 20-23, nicely overlapping with the last half of GCC2022.  Aquatennial includes parades, concerts, water ski shows (!), Major League Baseball (go Twins), Carifest, and fireworks (to mark the end of GCC!).



Wednesday July 20, 2022 TBA
Greater Minneapolis

7:59am CDT

Conference Day 4
Welcome to the fourth and final day of the 2022 Galaxy Community Conference (GCC2022).

Wednesday July 20, 2022 7:59am - 6:00pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  B. Talks

8:00am CDT

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

Wednesday July 20, 2022 8:00am - 6:00pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  F. Help

8:59am CDT

Session 19: Accepted and Invited Talks
This session will feature invited and accepted talks.

This session will also be broadcast live to remote participants.

Moderators
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
Metaproteomics . DIA . Proteogenomics

Wednesday July 20, 2022 8:59am - 10:00am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:00am CDT

Visualization of Phylogenomic Data in Galaxy with CloudForest
Reid Wagner, Minnesota Supercomputing Institute, University of Minnesota
Benjamin S. Toups, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University
Zhifeng Deng, Dept. of Mathematics, Florida State University
Thomas McGowan, Minnesota Supercomputing Institute, University of Minnesota
Kyle A. Gallivan, Dept. of Mathematics, Florida State University
Jeremy M. Brown, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University
James C. Wilgenbusch, Minnesota Supercomputing Institute, University of Minnesota

⇒ Abstract​​​

Speakers

Wednesday July 20, 2022 9:00am - 9:07am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:07am CDT

A Galaxy Platform for Multiplex Tissue Imaging Analysis in Cancer Research and Translation
Allison Creason, Oregon Health and Science University
Cameron Watson, Oregon Health and Science University
Qiang Gu, Oregon Health and Science University
Daniel Persson, Oregon Health and Science University
Luke Sargent, Oregon Health and Science University
Jeremy Goecks, Oregon Health and Science University

⇒ Abstract​​​

Speakers

Wednesday July 20, 2022 9:07am - 9:22am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:22am CDT

Processing of Small Molecule Gas Chromatography-Mass Spectrometry Data in Galaxy
Helge Hecht, RECETOX, Masaryk University
Martin Čech, RECETOX, Masaryk University
Matej Troják, RECETOX, Masaryk University
Maksym Skoryk, RECETOX, Masaryk University
Jiří Novotný, Institute of Computer Science, Masaryk University
Karolína Trachtová, RECETOX, Masaryk University
Aleš Křenek, Institute of Computer Science, Masaryk University
Elliott James Price, RECETOX, Masaryk University
Jana Klánová, RECETOX, Masaryk University
⇒ Abstract

​​​Various tools for the processing of mass spectrometry (MS) data exist, though few of them have user friendly GUI interfaces, are built with scalability and robustness in mind, or deliver reproducible results. Many of them are also tied to specific frameworks, e.g bioconductor. There is a need for harmonization in data processing for MS based -omics.The Galaxy framework enables user-friendly access to an expandable set of tools and workflows hosted via compute infrastructure, bringing FAIR data principles to -omics data processing. We extended existing Galaxy resources with R and Python packages (i.e apLCMS, xMSannotator, RIAssigner, matchms, WaveICA , MSMetaEnhancer and RAMClustR) and compiled those into comprehensive end-to-end workflows for non-target analysis (NTA). These tools perform several steps (e.g., peak detection & deconvolution, spectral matching & annotation, batch correction & normalization and metadata curation) to enable end-to-end pre-processing of data acquired via gas chromatography (GC) coupled with MS.Through the demo, we will show how to operate various tools in a data processing pipeline to obtain reproducible and shareable results using an example GC-HRMS dataset. We will show how to choose parameters for peak detection & deconvolution specifically for GC-MS in contrast to LC-MS data and how these parameter choices affect the outputs. Subsequently, we will show how to incorporate retention index information from RIAssigner into the annotation using matchms to improve the chemical annotation. Besides the workflow for compound annotation, we also include tools enabling automated curation and expansion of metadata in associated mass spectral libraries.By applying the knowledge gained from the topics covered in this demo, the participants will be able to process their own MS data using Galaxy. All developments covered are open source and hosted on GitHub providing immediate access and creating a platform for scientific collaborations. Access to those resources is provided to the community by hosting a public instance of Galaxy and by uploading tools to the main tool shed.

Speakers
avatar for Helge Hecht

Helge Hecht

Head of Department - Spectrometric Data Processing & Analysis, RECETOX


Wednesday July 20, 2022 9:22am - 9:29am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:29am CDT

Building the Galaxy based X-Ray Imaging of Microstructures Gateway (XIMG) for High Energy X-Ray Diffraction, Imaging, and Microstructure Modeling
Kelly E Nygren, Cornell High Energy Synchrotron Source
Werner Sun, Cornell High Energy Synchrotron Source
Devin Bougie, Cornell High Energy Synchrotron Source
Matt Miller, Cornell High Energy Synchrotron Source
Mehmet Hazar Seren, Cornell High Energy Synchrotron Source
Rolf Verberg, Cornell High Energy Synchrotron Source
Keara Soloway, Cornell High Energy Synchrotron Source
Bob Suter, Carnegie Mellon Department of Physics
Mark Zhuang, Science Gateway Institute. San Diego Supercomputing Center
Mark Miller, Science Gateway Institute. San Diego Supercomputing Center
James Johnson, Minnesota Supercomputing Institute
Jorge Vinals, Minnesota Supercomputing Institute

⇒ Abstract​​​

Speakers

Wednesday July 20, 2022 9:29am - 9:36am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:36am CDT

Targeting Viral Helicases Through Atomistic Molecular Dynamics Simulations in Galaxy
Bryan Raubenolt - Genomic Medicine Institute,
Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
Daniel Blankenberg - Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA

⇒ Abstract​​​

Speakers

Wednesday July 20, 2022 9:36am - 9:51am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

9:51am CDT

Microbial Strain Characterization and Subtyping of Metagenome-Assembled Genomes With Sequence Bloom Trees in Galaxy
Fabio Cumbo, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
Daniel Blankenberg, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA

⇒ Abstract​​​

Speakers
avatar for Fabio Cumbo

Fabio Cumbo

Postdoctoral Researcher, Cleveland Clinic
Metagenomics, microbiome


Wednesday July 20, 2022 9:51am - 9:58am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:00am CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Wednesday July 20, 2022 10:00am - 10:20am CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:19am CDT

Session 20: Poster / Demo Session D
There will be poster / demo sessions on all conference days.  These will be held concurrently with the sponsor sessions.  These are an opportunity to discuss research with community members in small groups and one and one.  Don't miss it.


Wednesday July 20, 2022 10:19am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

25. NCBI Datasets, a new resource for accessing NCBI genome data in Galaxy
Nuala O'Leary, NCBI
Eric Cox, NCBI
Brad Holmes, NCBI
Mirian Tsuchiya, NCBI
Peter Meric, NCBI
Greg Schuler, NCBI
Robert Falk, NCBI
William Anderson, NCBI
Xuan Zhang, NCBI
Vichet Hem, NCBI
Jonathan Cothran, NCBI
Valerie Schneider, NCBI

Speakers
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 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

26. RNA Deconvolution with MuSiC
Mehmet Tekman, University of Freiburg
Wendi Bacon, Open University

Speakers
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, University of Freiburg
Single-Cell, Developing Wrappers with Emacs


Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

27. Galaxy ProTo 2.0 Redux: Dynamic tool prototyping using Interactive Tools
Sveinung Gundersen
Morten Johansen

Speakers
SG

Sveinung Gundersen

University of Oslo


Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

34. MSMetaEnhancer: A Galaxy tool for mass spectra metadata annotation
Matej Troják, RECETOX, Masaryk University
Helge Hecht, RECETOX, Masaryk University
Martin Čech, RECETOX, Masaryk University
Elliott James Price, RECETOX, Masaryk University

Speakers

Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

35. Processing of small molecule gas chromatography-mass spectrometry data in Galaxy
Helge Hecht, RECETOX, Masaryk University
Martin Čech, RECETOX, Masaryk University
Matej Troják, RECETOX, Masaryk University
Maksym Skoryk, RECETOX, Masaryk University
Jiří Novotný, Institute of Computer Science, Masaryk University
Karolína Trachtová, RECETOX, Masaryk University
Aleš Křenek, Institute of Computer Science, Masaryk University
Elliott James Price, RECETOX, Masaryk University
Jana Klánová, RECETOX, Masaryk University

Speakers
avatar for Helge Hecht

Helge Hecht

Head of Department - Spectrometric Data Processing & Analysis, RECETOX


Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

36. Robust, performant and resumable uploads using tus.io
Marius van den Beek, PSU


Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

37. The Observable Galaxy: a new notebook integration with applications to regulatory grade database construction
Stephen D. Shank
Alex Ostrovsky
Charles Hadley King
Sergei L. Kosakovsky Pond

Speakers

Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

38. Visualization of Phylogenomic Data in Galaxy with CloudForest
Reid Wagner, Minnesota Supercomputing Institute, University of Minnesota
Benjamin S. Toups, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University
Zhifeng Deng, Dept. of Mathematics, Florida State University
Thomas McGowan, Minnesota Supercomputing Institute, University of Minnesota
Kyle A. Gallivan, Dept. of Mathematics, Florida State University
Jeremy M. Brown, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University
James C. Wilgenbusch, Minnesota Supercomputing Institute, University of Minnesota

Speakers

Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

39. FragPipe in headless mode enables seamlessly analyzing LC-MS data in Galaxy platform
Fengchao Yu, University of Michigan
Guo Ci Teo, University of Michigan
Dmitry Avtonomov, University of Michigan
Sarah Haynes, University of Michigan
Felipe da Veiga Leprevost, University of Michigan
Daniel Geiszler, University of Michigan
Daniel Polasky, University of Michigan
Kevin Yang, University of Michigan
Alexey Nesvizhskii, University of Michigan

Speakers
avatar for Fengchao Yu

Fengchao Yu

Research Investigator, University of Michigan


Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

10:20am CDT

40. Introducing the Galaxy Mentor Network
Assunta DeSanto, PSU
Beatriz Serrano-Solano, University of Freiburg
Berenice Batut, University of Freiburg

Speakers
avatar for Assunta DeSanto

Assunta DeSanto

Computational Scientist 3, Penn State University
I'm fairly new to Galaxy and the world of Bioinformatics. Teach me something new!Additionally, I'm a mom, lifelong learner, both a cat and dog person, who loves to read and be outside. Let's chat about common interests :)


Wednesday July 20, 2022 10:20am - 11:20am CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

11:19am CDT

Session 21: Keynote Presentation: Comprehensive Rib Fracture Care Map delivered as a Clinical Decision System
This session will feature our second Keynote Speaker, Chris Tignanelli, of UMN.

Keynote presentation title: Comprehensive Rib Fracture Care Map delivered as a Clinical Decision Support System

Abstract
Evidence-based (EB) practices have been shown to improve clinical outcomes, however, EB adherence varies. Clinical decision support systems (CDSS) have been shown to improve EB adherence, reduce health disparities, and improve clinical outcomes. This presentation will discuss the role of clinical informatics to provide cognitive decision support to providers and nurses, show a specific example for how to develop clinical decision support systems, conduct usability testing, implement, and ultimately scale successful CDSS across 10 trauma centers. It will then show how we evaluate such systems using RE-AIM (an implementation science framework). Finally, it will show how we iteratively improve on such systems and develop, validate, and ultimately integrate AI into CDSS to facilitate best practice and optimize patient outcomes.


Christopher Tignanelli is an MD and an associate professor at the medical school at UMN. As an Acute Care Surgeon, he sees patients in trauma, emergency surgery, and critical care. His research focuses on the development and validation of machine learning and AI-enabled decision support systems as well as the implementation, user-centered design, and scaling of interoperable clinical decision support tools. Among other distinctions, in 2021, he was named a “Health Care Hero” by the Minneapolis/St. Paul Business Journal for his innovative use of AI and informatics to improve healthcare for patients with COVID-19.

Moderators
avatar for Subina Mehta

Subina Mehta

Researcher, University of Minnesota

Speakers
avatar for Chris Tignanelli

Chris Tignanelli

Associate Professor of Surgery, UMN


Wednesday July 20, 2022 11:19am - 12:20pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

12:20pm CDT

Lunch
Lunch is your perfect opportunity to catch up with old friends and collaborators, and to meet new ones.  Get out there and meet people.

Wednesday July 20, 2022 12:20pm - 1:20pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

1:19pm CDT

Session 22: Training
GCC2022 features a multi-track training session every day of the conference.  These sessions cover a wide range of topics, and build upon the content presented during the pre-conference training day.  Training sessions are 2 1/2 hours long, and instructors are encouraged to have a short break in the middle.

Not interested in anything being offered? Use this time to catch up on your email, or meet with colleagues, or explore the area, or...

Wednesday July 20, 2022 1:19pm - 3:50pm CDT
Various Locations
  A. Training

1:20pm CDT

Contributing to Galaxy Core
Description to follow

Speakers
avatar for John Davis

John Davis

software engineer, Johns Hopkins University


Wednesday July 20, 2022 1:20pm - 3:50pm CDT
Strategy Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

DBA & Troubleshooting
Description to follow

Speakers
avatar for Nate Coraor

Nate Coraor

System Administrator, Galaxy Project, Penn State University


Wednesday July 20, 2022 1:20pm - 3:50pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Single-cell Transcriptomics
In this session we will be performing the following trainings:
  • An introduction to scRNA-seq data analysis
  This is a presentation that guides the user on the how's and why's of scRNA-seq analysis, and some of the underlying biological and statistic principles needed to understand it.

  • Pre-processing of 10X Single-Cell RNA Datasets
  Here we will generate a tabular count matrix of single cell data from raw FASTQ data, using 10X Genomics sequenced files.

  • Bulk RNA Deconvolution with MuSiC
  This new tutorial will aid users in combining count matrices from bulk RNA and scRNA-seq analyses and performing cell type estimation upon them using the MuSiC suite.

See the transcriptomics training portal for more information

Speakers
avatar for Mehmet Tekman

Mehmet Tekman

Post Doc, University of Freiburg
Single-Cell, Developing Wrappers with Emacs


Wednesday July 20, 2022 1:20pm - 3:50pm CDT
Logic Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Tool Development
Description to follow

Speakers
avatar for Alex Ostrovsky

Alex Ostrovsky

Johns Hopkins University
avatar for Tyler Collins

Tyler Collins

John Hopkins University


Wednesday July 20, 2022 1:20pm - 3:50pm CDT
Discovery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

1:20pm CDT

Visualization Development in Galaxy
Description to follow

Speakers
avatar for Sam Guerler

Sam Guerler

Galaxy Project, Johns Hopkins University
Johns Hopkins University
avatar for Dannon Baker

Dannon Baker

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


Wednesday July 20, 2022 1:20pm - 3:50pm CDT
Gallery Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  A. Training

3:50pm CDT

Break
Stand up! Stretch! Introduce yourself! Talk!

But be sure to be ready for the next session.

Wednesday July 20, 2022 3:50pm - 4:10pm CDT
Lobby Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:09pm CDT

Session 23: GCC2022 Closing
The final session of GCC2022! Accepted and invited talks.  The final presentation session of the day.

This session will also be broadcast live to remote participants.



Speakers
avatar for Timothy J. Griffin

Timothy J. Griffin

Professor, University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
Metaproteomics . DIA . Proteogenomics


Wednesday July 20, 2022 4:09pm - 4:50pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454

4:59pm CDT

Session 24: 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 during this Session:

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

Propose a BoF now.Galaxy Release Process

Wednesday July 20, 2022 4:59pm - 6:30pm CDT
Various Locations
  E. BoFs, BoFs

5:00pm CDT

BOF: Galaxy & Training / teaching
Discussions on using Galaxy for training / teaching and the Galaxy Training Network community:

  • training material and infrastructur (recent and future developments) 
  • using Galaxy for undergraduate instruction
  • training / teaching delivery and events
  • community building (instructors, contributors, users, mentoring)

This BoF will be held jointly in person, and online.



Speakers
avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg


Wednesday July 20, 2022 5:00pm - 6:30pm CDT
Logic Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs

5:00pm CDT

BOF: Galaxy Release Process
Discussion of the Galaxy Release process and any improvements we can make to it.  Topics can include timing, naming, overhauling the release scaffold to integrate the release testing team more formally, and anything else you can think of!.

The location of this BoF has not been set yet.  It will likely be at a nearby public space, like a cafe, restaurant or pub.  Watch this space.

Speakers
avatar for John Davis

John Davis

software engineer, Johns Hopkins University
avatar for Dannon Baker

Dannon Baker

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


Wednesday July 20, 2022 5:00pm - 6:30pm CDT
TBA
  E. BoFs, BoFs

5:00pm CDT

BOF: International Galaxy Proteomics Meeting
The International Galaxy Proteomics Meeting Series (formerly Celestial Masses) is organized by Galaxy communities in the US, Australia, and Europe. Interested researchers meet on a regular basis to discuss Galaxy tools and workflows related to proteomics, metabolomics, and imaging mass spectrometry. We discuss software tools, workflows, new methods, workshops, and topics related to mass spectrometry.

Speakers
avatar for Timothy J. Griffin

Timothy J. Griffin

Professor, University of Minnesota
avatar for Pratik Jagtap

Pratik Jagtap

Research Assistant Professor, University of Minnesota
Metaproteomics . DIA . Proteogenomics


Wednesday July 20, 2022 5:00pm - 6:30pm CDT
Strategy Room Courtyard Minneapolis Downtown, 1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  E. BoFs, BoFs

7:30pm CDT

Aquatennial Torchlight Parade
The first big event of Aquatennial is the Torchlight Parade on Wednesday night in downtown Minneapolis.


Wednesday July 20, 2022 7:30pm - 9:00pm CDT
Downtown Minneapolis

9:30pm CDT

Movies in the Park at The Commons: Black Panther
After the parade, head over to The Commons for Movies in the Park:

Some of the best views of downtown Minneapolis are from The Commons. Enjoy watching Black Panther in this two-block green space. Grab your fellow Galaxians, something to sit on and some food, and head over for a fun evening nestled between the downtown skyline and U.S. Bank Stadium.


Wednesday July 20, 2022 9:30pm - 11:30pm CDT
Downtown Minneapolis
 
Thursday, July 21
 

9:00am CDT

CollaborationFest (CoFest) Day 1
This three day event gathers community members who are interested in contributing to Galaxy's code base, available tool set, documentation, training materials, and anywhere else that expands or improves the Galaxy ecosystem.  You can register for 1, 2 or 3 days of the CoFest.

CoFest participants will coalesce around shared interests and common challenges related to those interests. These clusters form before, at the beginning of, and throughout CollaborationFest and will be fluid and highly interactive with each other.

Goals!

Our goals are to expand the contributor community and the Galaxy Ecosystem.

That's a short sentence, but it is very deliberately worded:

  • Our first goal is to expand the contributor community.  This CoFest is first and foremost about welcoming new contributors and helping you learn the resources and meet the people that will help you contribute. 
  • The second goal is to expand the Galaxy Ecosystem. Not just the code, but the whole ecosystem. That includes training, tools, best practice workflows, documentation, test cases, translations, infrastructure, and yes, even code.
This is a CollaborationFest. Not a hackathon, not a codefest, but a CollaborationFest.

Welcome aboard.

Thursday July 21, 2022 9:00am - 6:00pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  G. CoFest

5:30pm CDT

Music in the Park at The Commons: JoJo Green
After a long day of collaborating, head over to The Commons for Music in the Park:

This week's Music in the Park features JoJo Green:

Strong influences from Motown, Muscle Shoals, and The Summer of Love, JoJo Green gives a nostalgic feeling to a fresh sound, easy on the ears, and exciting to the body. Powerhouse vocals mixed with agile woodwinds, shredding guitars, funky bass, and driving drums.




Thursday July 21, 2022 5:30pm - 6:30pm CDT
Downtown Minneapolis

7:00pm CDT

Twin Cities River Rats Aquatennial Water Ski Show
Join the Twin Cities River Rats for a spectacular show on the Mississippi River! The nationally ranked Twin Cities River Rats Water Ski Show Team puts on an exciting blend of water skiing, acrobatics and high speed thrills!

Right on the banks of the Mississippi River between the Broadway and Plymouth Ave Bridges. Pre-show begins at 6:30pm, main show starts at 7pm.



Thursday July 21, 2022 7:00pm - 8:00pm CDT
Downtown Minneapolis
 
Friday, July 22
 

9:00am CDT

CollaborationFest (CoFest) Day 2
This three day event gathers community members who are interested in contributing to Galaxy's code base, available tool set, documentation, training materials, and anywhere else that expands or improves the Galaxy ecosystem.  You can register for 1, 2 or 3 days of the CoFest.

CoFest participants will coalesce around shared interests and common challenges related to those interests. These clusters form before, at the beginning of, and throughout CollaborationFest and will be fluid and highly interactive with each other.

Goals!

Our goals are to expand the contributor community and the Galaxy Ecosystem.

That's a short sentence, but it is very deliberately worded:

  • Our first goal is to expand the contributor community.  This CoFest is first and foremost about welcoming new contributors and helping you learn the resources and meet the people that will help you contribute. 
  • The second goal is to expand the Galaxy Ecosystem. Not just the code, but the whole ecosystem. That includes training, tools, best practice workflows, documentation, test cases, translations, infrastructure, and yes, even code.
This is a CollaborationFest. Not a hackathon, not a codefest, but a CollaborationFest.

Welcome aboard.

Friday July 22, 2022 9:00am - 6:00pm CDT
Salon ABC Room Courtyard Minneapolis Downtown,1500 Washington Avenue South, Minneapolis, Minnesota, USA, 55454
  G. CoFest

7:00pm CDT

Twin Cities River Rats Aquatennial Water Ski Show
Join the Twin Cities River Rats for a spectacular show on the Mississippi River! The nationally ranked Twin Cities River Rats Water Ski Show Team puts on an exciting blend of water skiing, acrobatics and high speed thrills!

Right on the banks of the Mississippi River between the Broadway and Plymouth Ave Bridges. Pre-show begins at 6:30pm, main show starts at 7pm.



Friday July 22, 2022 7:00pm - 8:00pm CDT
Downtown Minneapolis
 
Saturday, July 23
 

9:00am CDT

CollaborationFest (CoFest) Day 3
This three day event gathers community members who are interested in contributing to Galaxy's code base, available tool set, documentation, training materials, and anywhere else that expands or improves the Galaxy ecosystem.  You can register for 1, 2 or 3 days of the CoFest.

CoFest participants will coalesce around shared interests and common challenges related to those interests. These clusters form before, at the beginning of, and throughout CollaborationFest and will be fluid and highly interactive with each other.

Goals!

Our goals are to expand the contributor community and the Galaxy Ecosystem.

That's a short sentence, but it is very deliberately worded:

  • Our first goal is to expand the contributor community.  This CoFest is first and foremost about welcoming new contributors and helping you learn the resources and meet the people that will help you contribute. 
  • The second goal is to expand the Galaxy Ecosystem. Not just the code, but the whole ecosystem. That includes training, tools, best practice workflows, documentation, test cases, translations, infrastructure, and yes, even code.
This is a CollaborationFest. Not a hackathon, not a codefest, but a CollaborationFest.

Welcome aboard.

Saturday July 23, 2022 9:00am - 6:00pm CDT
University of Minnesota, Twin Cities, East Bank Campus
  G. CoFest

11:00am CDT

Twin Cities Carifest
West River Road between Plymouth Ave. & Broadway Ave.

For more than two decades, Twin Cities Carifest has been the premier Caribbean Festival featuring Caribbean food, music, arts, crafts, and a traditional carnival parade with colorful costumes and dance. Held along the banks of the Mississippi River, you can see the Minneapolis Aquatennial Target Fireworks!
Follow Twin Cities Carifest on Facebook or on Twitter for more information.



Saturday July 23, 2022 11:00am - 10:00pm CDT
Downtown Minneapolis

6:00pm CDT

Aquatennial Fireworks and pre-fireworks festivities
Aquatennial closes with a huge fireworks show and pre-firewoks festivities on the Mississippi River in downtown Minneapolis. If you are still around, then this is a great way to finish your week in Minneapolis.


Saturday July 23, 2022 6:00pm - 10:30pm CDT
Downtown Minneapolis
 
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