Daily schedule

The schedule is where you can discover what’s happening when at GCC2024. List of talks as well as list of posters are available lower on the page and you can download the abstract book here.

DayTimeEventRoom(s)
Monday, Jun 248:30 - 8:45Open and welcomeBCD
8:45 - 9:45Keynote by Jana KlánováBCD
9:45 - 10:00Morning breakAtrium
10:00 - 12:00Talks (single track)BCD
12:00 - 13:00LunchRestaurant Lucullus
13:00 - 14:00Trainings IB, C, D, M1, M2
14:00 - 16:00Posters + coffeeA
16:00 - 18:00Trainings IIB, C, D, M1, M2
18:00 - 19:00BoFsB, C, D, M1, M2
19:00 - 21:00GCC2024 Welcome Happy HourSiesta Lobby & Wine Restaurant
Tuesday, Jun 258:45 - 9:00Overview of dinner toursBCD
9:00 - 9:45What's up in the Galaxy: Community update talkBCD
9:45 - 10:10Morning breakAtrium
10:10 - 12:00Talks (2 tracks)BC, D
12:00 - 13:00LunchRestaurant Lucullus
13:00 - 14:00Trainings IB, C, D, M1, M2
14:00 - 16:00Posters + coffeeA
16:00 - 18:00Trainings IIB, C, D, M1, M2
18:00 - 19:00BoFsB, C, D
19:00 - 22:00Conference dinnerMendel's Abbey
Wednesday, Jun 268:30 - 8:45Overview of activities on Wednesday afternoonBCD
8:45 - 9:45Keynote by Ute GunsenheimerBCD
9:45 - 10:10Morning breakAtrium
10:10 - 10:30Gold sponsor talk: JXTX FoundationBCD
10:30 - 12:00Panel discussionBCD
12:00 - 12:10Group photographAtrium
12:10 - 13:00LunchBox lunch
13:00 - ...Tour of Villa Tugendhat. Walking tour of Brno. Fun BoFs.Brno
Thursday, Jun 278:30 - 8:45Feedback sessionBCD
8:45 - 9:45Keynote by Daria OnichtchoukBCD
9:45 - 10:10Morning breakAtrium
10:10 - 12:00Talks (2 tracks)BC, D
12:00 - 13:00LunchRestaurant Lucullus
13:00 - 14:00Trainings IB, C, D, M1, M2
14:00 - 14:30Afternoon breakAtrium
14:30 - 16:30Trainings IIB, C, D, M1, M2
16:30 - 17:30Talks (single track) & conference closingBCD
17:30 - 19:00BoFsB, C, D, M1
Friday, Jun 289:00 - 18:00CoFestOPEN GARDENS
Saturday, Jun 299:00 - 18:00CoFestOPEN GARDENS

Talks

Monday: 10:00 - 12:00

Single track (room BCD)
BioDigs: a GDSCN Project; Tyler Collins, Alex Ostrovsky
Galaxy activities in Czech Republic; Miroslav Ruda, Aleš Křenek
Galaxy-ML2: Simple, Powerful, and Robust Machine Learning Tools for Galaxy; Junhao Qui, et al.
Community Lightning Talks: SPOC, GGA, SSA, Imaging, microGalaxy, & GCB; Wendi Bacon, et al.
Empowering Users to Bring Their Own Storage; John Chilton
Maintaining and improving a large collection of workflows; Marius van den Beek
Driving Decisions with Data: Introducing the Key Usage Indicators (KUI) for Galaxy Project Governance; Enis Afgan, Nuwan Goonasekera
The AquaINFRA platform: A research data infrastructure for marine and inland waters; Markus Konkol, et al.
Developing Interactive Neutron Science Applications using Galaxy; Sergey Yakubov, et al.
ABRomics: a Galaxy-based One Health Antimicrobial Resistance Platform; Pierre Marin, et al.

Tuesday: 10:10 - 12:00

Analysis track (room D)Enablement track: workflows & administration (room BC)
Genomics and transcriptomics of Fusarium musae from human and banana; Luca Degradi, et al.Upgrading User Experience: Introducing the New Galaxy UI; Aysam Guerler, et al.
MAdLand computational resources through Galaxy; Deepti Varshney, et al.Visualizing Workflow Runs in Galaxy: The Graph View for Workflow Invocations; Ahmed Awan
Genomic and evolutionary analysis of the cytochrome P450 gene family in a ground -herb of Amazonian riparian forests with a waterflooding gradient; Drielli Canal, et al.Enhanced Workflow Management in Galaxy; Alireza Heidari, Laila Los, Aysam Guerler
The Galaxy Platform: Applications to Catalysis Workflows; Patrick Austin, et al.A Galaxy Workflow Developer's Companion in your Browser; David López
A Toolset for Building and Simulating Transmembrane Proteins in Galaxy; Bryan Raubenolt, Jayadev Joshi, Daniel BlankenbergGalaxy CoDex for finding tools, workflows, and training; Bérénice Batut
Ab-initio Semi-Empirical Mass Spectra Predictions with Galaxy; Wudmir Rojas, et al.DevOps techniques for developing and integrating tools in Galaxy; Serena Lorenzini, Giuseppe Profiti
Bridging the Gap: A Systematic Workflow to Convert Low-Resolution GC-MS Libraries to High-Resolution in Silico for Enhanced Chemical Profiling; Zargham Ahmad, et al.TES job submission and streamlined data transfers; Aleš Křenek, et al.
Automated Reference Genome Assembly in Galaxy - An Update; Delphine Larivière, et al.Metascheduling with TPV: Weighting jobs on multiple constraints for distributed deployment over local and remote resources; Catherine Bromhead, Justin Lee, Nuwan Goonasekera
Long-read genomes from diverse outbred dogs; Tyler Collins, Alex OstrovskyData access architecture at "Galactic" scale: what's new and what's next; John Davis
Using Galaxy and Integrated Genome Browser to study tardigrade biology; Paige Kulzer, Nowlan Freese, Ann LoraineIntegrating OGC API services into Galaxy; Markus Konkol, Alexander Pilz

Thursday: 10:10 - 12:00

Analysis track (room D)Enablement track: outreach & automation (room BC)
Navigating the variant landscape: integrating MAVE data analysis into Galaxy; Polina PoluninaUpdates from the Global Galaxy Training Network (GTN); Saskia Hiltemann, Helena Rasche, Bérénice Batut
A Galaxy-based immunopeptidogenomic pipeline for neoantigen discovery; Subina Mehta, et al.Automating Social Media Outreach: A GitHub Workflow for Galaxy Community; Arash Kadkhodaei
Clinical metaproteomics workflow to study host-microbiome dynamics; Katherine Do, et al.Addressing user needs in single-cell analysis; internship and obstacles; Morgan Howells, et al.
MitoLink2.0: A generic integrated web-based workflow system to evaluate genotype-phenotype correlations in human mitochondrial diseases; Shweta Pandey, et al.Galaxy as a Gateway to Bioinformatics: an updated scRNA-seq analysis training suite; Julia Jakiela, et al.
Viral pathogen data analysis with Galaxy; Wolfgang Maier, et al.Persist-seq: a set of reproducible single cell RNA-seq analysis pipelines for understanding early persister cells in cancer; Pablo Moreno, et al.
PathoGFAIR: FAIR Workflows for Pathogen Detection & Samples Comparison; Engy Nasr, et al.Image Analysis in Galaxy: Recent Developments and Highlights; Leonid Kostrykin, Karl Rohr
FAIR viral quasispecies reconstruction from short reads - possibilities and limitations; Stephen Shank, et al.Interactivity as a tool power-up – Interactive Client Tools reimplemented in the frontend; Sveinung Gundersen, Morten Johansen
BREW3R - a workflow to get more reads in genes in 3'-end sequencing methods; Lucille Lopez-Delisle, Denis DubouleCommunity-driven standards development for reference genome generation; Tom Brown, et al.
Reconstructing cell type specification trajectories in the last common animal ancestor; Natalia E Padillo-AnthemidesUseGalaxy France: an example of a national UseGalaxy server; Anthony Bretaudeau, et al.
Structural annotation of repeated regions in the Psidium guajava L. genome and development of molecular markers for regulatory regions; Giovanna Pinto Pires, et al."Smarter" job scheduling using user provided infrastructure; Paul De Geest, Frederik Coppens, Sebastian Luna-Valero

Thursday: 16:30 - 17:15

Posters

Monday: 14:00 - 16:00

Poster #Title
1BioDigs: a GDSCN Project; Tyler Collins, Alex Ostrovsky
2Galaxy activities in Czech Republic; Miroslav Ruda, Aleš Křenek
3Galaxy-ML2: Simple, Powerful, and Robust Machine Learning Tools for Galaxy; Junhao Qui, et al.
4Maintaining and improving a large collection of workflows; Marius van den Beek
5Driving Decisions with Data: Introducing the Key Usage Indicators (KUI) for Galaxy Project Governance; Enis Afgan, Nuwan Goonasekera
6The AquaINFRA platform: A research data infrastructure for marine and inland waters; Markus Konkol, et al.
7Developing Interactive Neutron Science Applications using Galaxy; Sergey Yakubov, et al.
8ABRomics: a Galaxy-based One Health Antimicrobial Resistance Platform; Pierre Marin, et al.
9Investigation of Plasmids of Lactoplantibacillus plantarium L3 strain Using Whole Genome Sequencing and Bioinformatics Assay; Vladimir Tolchkov, et al.
10Community-driven standards development for reference genome generation; Tom Brown, et al.
11Pairing Data Analysis Methods with Sequencing Products to Meet Scientist’s Needs. What Do People Want?; Adrian Reich, Ariel Erijman, Bradley Langhorst
12WALL·E – Prevent Abuse of Interactive Research Environments; Mira Kuntz
13Galaxy's Future: Bridging Interoperability and Execution Challenges; Jean Iaquinta, et al.
14Democratizing access to genomics data science education through GDSCN; Shurjo Sen
15In silico analysis of the ribosomal DNA copy number in animal species; Jana Sochorová, Aleš Kovařík
16Exploring the Richness of the French Galaxy Ecosystem; Bérénice Batut, et al.
17microGalaxy SIG: microbial data analysis resources in Galaxy; Paul Zierep, et al.
18Expanding Horizons: Single-Cell Multiomics Analysis Tools in Galaxy; Pavankumar Videm
19MetaSBT in Galaxy: towards a comprehensive investigation and characterization of the microbial dark matter; Fabio Cumbo, Daniel Blankenberg
20Automating Social Media Outreach: A GitHub Workflow for Galaxy Community; Arash Kadkhodaei
21Takeaways from teaching long-read genome assembly using Galaxy; Linelle Abueg, Giulio P. Formenti, Erich D. Jarvis
22Enhancements to UseGalaxy.org Client-Facing Error Reporting for Optimized Functionality and Risk Mitigation; Michelle Savage, et al.
23Bacterial Community Associated with Native Blowflies (Diptera: Calliphoridae) of Pahang National Park, Malaysia: A Metagenomic approach; Ahmad Azani Othman, et al.
24GHGA - Standardizing and harmonizing NGS analysis workflows to create a unified omics data resource for Germany; Florian Heyl, et al.
25Exploring the metatranscriptome of two moss species (terrestrial and aquatic) using Galaxy platform; Vesselin Baev, et al.
26Hosting Galaxy at the Edge: Directly in Your Pocket!; Mehmet Tekman
27Enabling access to scalable bioinformatics with Galaxy in AnVIL; Natalie Kucher, et al.

Tuesday: 14:00 - 16:00

Poster #Title
28TES job submission and streamlined data transfers; Aleš Křenek, et al.
29MAdLand computational resources through Galaxy; Deepti Varshney, et al.
30The Galaxy Platform: Applications to Catalysis Workflows; Patrick Austin, et al.
31Automated Reference Genome Assembly in Galaxy - An Update; Delphine Larivière, et al.
32Long-read genomes from diverse outbred dogs; Tyler Collins, Alex Ostrovsky
33Using Galaxy and Integrated Genome Browser to study tardigrade biology; Paige Kulzer, Nowlan Freese, Ann Loraine
34Visualizing Workflow Runs in Galaxy: The Graph View for Workflow Invocations; Ahmed Awan
35Upgrading User Experience: Introducing the New Galaxy UI; Aysam Guerler, et al.
36Data access architecture at "Galactic" scale: what's new and what's next; John Davis
37DevOps techniques for developing and integrating tools in Galaxy; Serena Lorenzini, Giuseppe Profiti
38Genomics and transcriptomics of Fusarium musae from human and banana; Luca Degradi, et al.
39Infrastructure for Estimating Cloud Computing Costs for Bioinformatics Workloads; Keith Suderman, et al.
40Colabfold: Fast and Accurate Protein Folding in Galaxy; Alex Ostrovsky, et al.
41Expansion and Updates of the Galaxy Mass Spectrometry Imaging Tool Collection: New Statistical Tools and a New Workflow for Region Specific Analysis; Maren Stillger, et al.
42Integration of ANPDB with Usegalaxy: Empowering Drug Discovery; Shreya Agarwal, Fidele Ntie-Kang, Kiran K Telukunta
43Galaxy @Sciensano: Implementation of Galaxy as a bioinformatics tools portal in an applied public health context; Bert Bogaerts, et al.
44Giving the Single Cell Community the Tools It Needs on Galaxy – an ELIXIR Staff Exchange Project; Marisa Loach
45Transcriptome Analysis of Triphyophyllum peltatum, a Liana producing Naphthylisoquinoline Alkaloids using Galaxy Framework; Darshana Joshi, Karin Fester, Kiran K Telukunta
46Portability of a variant analysis workflow to Galaxy: Rabdomyzer case study; Federica Isidori, et al.
47Galaxy workflow for bacterial genomics exploration and chitin utilization enzyme identification: A case study exploring the Streptomyces albogriseolus PMB5 genome; Vesselin Baev, et al.
48Aqua Metagenomic Analyses Using Galaxy Reveals an Admixture of Organisms Associated with Diverse Environments; Srishti Singh, et al.
49Exploring Earth’s Aerobiome through Similarity Search Analysis; Michal Winnicki, et al.
50Implementing a new Galaxy integration to export datasets to COPO; Nicola Soranzo, Felix Shaw
51In Silico Analysis on Antimalarial Properties of Satureja Myrtifolia and Helichrysum Taenari; Swathi Nataraj, Kiran K. Telukunta
52Automating Galaxy: Enhancing Production Pipelines with Galaxy-wf-executor; Anil S Thanki, Pablo Moreno
53EDAM enables findability – from biomolecular sciences to imaging, ecology, and society; Claire Rioualen, et al.
54Toolkit Galaxy MLA computational intelligence toolset for biological sciences that is expandable, reproducible, and easily approachable; Reyed Reyed
55An Update on the FragPipe Galaxy Tool for Proteomics Workflows; Reid Wagner, et al.
56The potential of GlobalFungi and GlobalAMFungi databases for Galaxy; Tomáš Větrovský

BoFs

Monday: 18:00 - 19:00

Title: microGalaxy SIG with BioDIGS and GDSCN (room B)
Description: The microGalaxy Special Interest Group (SIG) is a group of researchers and bioinformaticians who collaborate to develop and optimise scientific analytical for microbial data using the Galaxy platform. This SIG aims to (i) develop, maintain, and sustain microbial data analysis in Galaxy, (ii) establish and implement standardised "best practices", (iii) expand documentation and training resources, (iv) coordinate collaborative efforts to avoid redundancy and prioritise tools, workflows, and training (v) outreach to the microbiology research communities both within and outside the Galaxy. In this BoF, we will talk about the recent efforts of the community (tools, workflows, training, resource catalog, papers) and plan efforts for the next months.
We will also discuss the GDSCN and BioDIGS projects, which are looking to get interested researchers and students involved in soil metagenomics.
Organizers: Alex Ostrovsky, Tyler Collins, Michael Schatz
Title: Efficient Data Management in Galaxy: Accessing and Processing Large Externally Stored Data (room C)
Description: In the era of big data, the ability to manage and process vast, often distributed datasets efficiently is crucial for scientific research and data-driven decision-making. In this Birds of a Feather (BoF) session we want to discuss the challenges and strategies associated with handling large amounts of data stored externally - on tape, an HPC filesystem, experimental facility, cloud platforms, etc., within the Galaxy platform. A crucial aspect of this session will be the collection of requirements and experiences from diverse scientific domains, including photon, neutron, muon science, astronomy, and others. We will also exchange experiences from various institutions, such as Oak Ridge National Laboratory (ORNL) who developed the Rucio object store plugin for data management. By understanding the unique needs and challenges of these fields, we aim to gather valuable insights to discuss with Galaxy developers about what can be done to develop more tailored and effective solutions for data management in Galaxy. We would also like to discuss Galaxy deferred datasets and see to what extent they can help address the issue.
Organizers: Denys Savchenko, Volodymyr Savchenko, Sergey Yakubov
Title: Key Usage Indicators for Galaxy (room D)
Description: The Key Usage Indicators dashboard for Galaxy (available at gxy.io/kui) is new community resource that focuses on exposing usegalaxy service usage data for easy consumption. In this BoF, we will discuss topics such as what data to capture, how to visualize it, how to use it, as well as go over the technical implementation details in search of improvements. Join this BoF if you are interested in using service usage data to craft the future of Galaxy.
Organizer: Enis Afgan
Title: The Art of Phylogeny: Where Science Meets Creativity (room M1)
Description: Join us for an engaging Birds of a Feather (BoF) session where we delve into the fascinating intersection of art and science through the lens of phylogenetic trees. Discussions will cover the artistic softwares and techniques used to enhance their visual appeal, and real-world applications in both research and education. We will explore how these trees, which represent evolutionary relationships, can be both scientifically informative and visually captivating. This session is designed to inspire and attract enthusiasts from diverse fields, sparking conversations on the creative potential of scientific visualization.
Organizer: Drielli Canal
Title: Small scale Galaxy Admins Community of Practice (room M2)
Description: We are a group of admins who maintain a (small) (local) Galaxy server. In this BoF we would like to attract other Galaxy admins to join us. After a general introduction of our community, we would like to discuss (and solve) any current issue we face as a Galaxy admin - in a similar style (though in person) to our on-line meetings which we have every two months.
Organizers: Lucille Delisle, Hans-Rudolf Hotz

Tuesday: 18:00 - 19:00

Title: Galaxy-Pulsar network traffic visualization (room B)
Description: The network of Galaxy and Pulsar installations is growing steadily. For both operation oversight and dissemination purposes it is desirable to visualize the flow of jobs and data transfers as a map overlay; several isolated attempts to do so have been already done. The BoF goal is to discuss ideas what is the traffic to visualize, how to render it, what data are required to do so, and how these data can be gathered.
Organizers: Aleš Křenek, Miroslav Ruda
Title: The future of Galaxy in EOSC (room C)
Description: Galaxy is and has been used by at least 7 different EOSC projects. With the EuroScienceGateway project we could build up national Galaxy instances and a European wide Pulsar Network, EGI technologies could be integrated and Galaxy's is reaching 100.000 and more users in Europe. In this BoF we would like to discuss the releatonship between EOSC and Galaxy, how to reach more communities and what comes after the EuroScienceGateway proejct.
Organizers: Bjoern Gruening
Title: Galaxy Training Academy Organizational Meet-Up (room M1)
Description: Inspired by the huge success of Smörgåsbord, the Galaxy Training Academy will be held October 7th-11th, 2024. This global, online, and asynchronous event will have multiple training tracks from a variety of trainers throughout the Galaxy community. Whether you hope to attend, hope to host a training session, or just want to show your support, join us in this BoF session to offer your ideas and suggestions for the Galaxy Training Academy!
Organizer: Delphine Lariviere

Thursday: 17:30 - 19:00

Title: Galaxy Collaborative Writing Group (room C)
Description: Are you interested in collaborating on research papers? This gathering is an excellent opportunity for GCC2024 attendees to connect and explore potential research partnerships. This session will provide a platform to discuss potential topics, share resources, and establish partnerships for current and future research projects. Whether you're looking for collaborators with specific expertise or are open to exploring new ideas, this session aims to foster meaningful collaborations within the Galaxy community.
Organizer: Marisa Loach
Title: Galaxy for MS (G4MS) (room D)
Description: Discuss published mass spectrometry tools and workflows available in GTN. Discuss the need for new tools with emerging technologies and research areas. Proteomics research - current status and needs. Metabolomics research - current status and needs. How to continue with MS/proteomics/Metabolomics community calls.
Organizers: Johan Gustafsson, Pratik Jagtap, Melanie Föll, Helge Hecht
Title: Namaste: Galaxy Bharat (room M1)
Description: The session is to discuss about the progress and possibilities of UseGalaxy in Bharat i.e India. Who are interested to join in this boat and sail with us. How are we doing now? How to sustain until the funding is obtained? What are expectations/suggestions from other UseGalaxies while usegalaxy.in is coming up.
Organizer: Kiran K Telukunta
Title: Galaxy's release process (room M2)
Description: Discussion of the Galaxy Release process and any improvements we can make to it. Topics can include release cycle, timing, naming, release testing (scope, infrastructure, teams), release notes, announcements, and anything else you can think of!
Organizers: John Davis, Dannon Baker
Title: WF invocation UI feedback (room B)
Description: Galaxy UI has a set of new powerful features such as the WF invocation graph view. We would like to invite users to do a quick analysis that will be provided to them and collect their feedback.
Organizer: Anton Nekrutenko

Social Programme

Conference Dinner

The conference dinner will take place in the Augistinian Abbey at Mendel's square, the place where Gregor Mendel conducted his experiments. The price for a ticket is EUR70 excluding VAT. During the dinner, participants have free access to the Mendel Museum. Please remember to bring your conference badge to dinner.

Participants may join the guided tours of the abbey including Mendel's room and the library shortly before (staring 18:30 & 19:15) or after the dinner (starting 21:00).

The venue is a 15 minute walk from Hotel International down Pekařská on Mendlovo Naměstí. Alternatively, you can take trams 5 and 6 from Šilingrovo Naměstí to Mendlovo Naměstí.

Wednesday Afternoon

The social programme will take place on the afternoon of Wednesday the 26th and will give you an opportunity to explore the city and its sights with an experienced guide, rather than on your own. Please note that places for all activities are limited.

DayTimeEventLocation
Wednesday, Jun 2614:00Don's WalkDenisovy Sady
14:30Vila Tugendhat - Group 1Vila Tugendhat
15:00Vila Tugendhat - Group 2Vila Tugendhat
16:00Guided Walking TourMoravské Naměstí

City Tours

Join us on one of the guided tours offered as part of this years Galaxy Community Conference. Our first guided tour of the city titled "Brno Ringstrasse" with Don Sparling, founder of the Brno Expat Centre, is drawing a comparison to the architecture of Vienna and will show you the city from a unique perspective. Explore the main sights of the city centre in our guided tours organized by the Brno Tourist Information Centre, including the Old Town Hall, St Peter's Cathedral as well as the Freedom and Market Square.

Villa Tugendhat

Those interested in architecture will have the unique opportunity to visit the UNESCO World Heritage Villa Tugendhat in an exclusive guided tour for conference participants.

For more information on Villa Tugendhat, head to the travel page.

Additional ideas

Rock climbing hall

Hangar climbing playground is a state-of-the-art bouldering center designed in collaboration with world-class climber Adam Ondra. With over 1000 square meters of climbing area and more than 200 routes of varying difficulty, it offers an exciting experience for climbers of all levels.