- microGalaxy - lists.galaxyproject.org

Planning a Meeting on AMR Analyses in Galaxy
by Bérénice Batut 10 Dec '25

10 Dec '25

Hi everyone, During last week’s workflow meetings, many of you expressed interest in AMR (Antimicrobial Resistance) analyses. To partially address this, I’ve created a GitHub issue to track the tools we need to add or update in Galaxy: https://github.com/galaxyproject/tools-iuc/issues/7516 (feel free to comment to add missing tools) We already have several workflows available, but there’s room for improvement—especially to support different analyses. To move forward, let’s schedule a dedicated meeting in January to discuss these workflows and next steps. If you’re interested in participating, please fill out this poll by December 15th—even if none of the proposed slots work for you. This will help us gauge interest and find a suitable time for most: https://doodle.com/group-poll/participate/dLBKZOva. Thank you in advance for your participation! Bérénice

1 0

***UNCHECKED*** microGalaxy workflow meeting - December 5th, 2pm UTC / 3pm CET / 9am EST
by Bérénice Batut 02 Dec '25

02 Dec '25

Hi all, Thank you all for participating in the poll. Based on your responses, the microGalaxy workflow meeting is now scheduled for: 📅 Date: December 5, 2025 🕒 Time: 2:00 pm UTC (3:00 pm CET / 9:00 am EST) <https://arewemeetingyet.com/UTC/2025-12-05/14:00/microGalaxy> 📍 Location: Zoom <https://cnrs.zoom.us/j/98383584662?pwd=6o3ZKd47MBhKQJ2YbmYPtTdniz0Y0A.1> 📄 Agenda & Notes <https://docs.google.com/document/d/13VjcUjStuIp7bK29e74k8Nqb7N4lmVcg1ioArEW…>: Community news & updates Workflow discussions To prepare for the meeting, we’ve created a shared slide deck <https://docs.google.com/presentation/d/1x0-kY4FTscYTeQ8C2VApLZEgmdTNqgugjjX…> where each of you can add one slide per workflow using the provided template. Please add your workflows to the deck by December 3, 2025, so we can review them in advance. Looking forward to seeing you all online! Best, Bérénice

1 2

microGalaxy workflow meeting - Fill in poll before November 18th
by Bérénice Batut 13 Nov '25

13 Nov '25

Hi all, I hope this email finds you well. It’s been some time since our last microGalaxy community meeting. During the European Galaxy Days, Mina and I discussed, and we discovered that we’ve both been working on similar workflows independently. To avoid duplicating work, foster collaboration, and share insights, I’d like to propose that our next meeting focus on workflows. To accommodate everyone’s schedules, please fill out this poll <https://doodle.com/group-poll/participate/avJ4rp0a> by Tuesday, November 18th, to help us find a suitable time in early December: https://doodle.com/group-poll/participate/avJ4rp0a. Thank you. Best, Bérénice

1 0

microGalaxy Community Meeting - October 2, 2025, at 4:30 PM CEST / 2:30 PM UTC / 10:30 AM ET
by Bérénice Batut 09 Sep '25

09 Sep '25

Hi all, I hope this message finds you well! It’s been a while since our last microGalaxy community meeting, and we’re excited to share some updates about the Microbiology Galaxy Lab, microGalaxy paper, and more. The European Galaxy Days 2025 will take place in Freiburg, Germany, from October 1–3, 2025. We’ve secured a hybrid Birds of a Feather (BoF) session for our microGalaxy community meeting on October 2, 2025, at 4:30 PM CEST (2:30 PM UTC / 10:30 AM ET). 📅 Date: October 2, 2025 🕒 Time: 4:30–5:30 PM CEST <https://arewemeetingyet.com/UTC/2025-10-02/14:30/microGalaxy> (hybrid format) 📍 Location: In-person: Freiburg, Germany Online: Zoom <https://cnrs.zoom.us/j/94711724563?pwd=NDQrGtn0ESrPRwCoKXaJ8N4Vnyds9G.1> 📄 Agenda & Notes <https://docs.google.com/document/d/13VjcUjStuIp7bK29e74k8Nqb7N4lmVcg1ioArEW…>: Community news & updates Progress on the Microbiology Galaxy Lab and paper Open discussion: Tools, workflows, training, funding, etc Looking forward to seeing you in Freiburg or online. Let us know if you have questions or topics to add to the agenda. Best, Bérénice

1 0

Invitation to FAIRyMAGs Hackathon in Freiburg (06.10.2025 - 09.10.2025)
by Paul Zierep 27 Mar '25

27 Mar '25

Dear all, Following the fantastic news of our *Nature* paper submission, I’m excited to share another great event that might interest some of you! We are organizing a *hackathon in Freiburg* focused on *Metagenome-Assembled Genomes (MAGs) building workflows*: 🔗 Event details <https://galaxyproject.org/events/2025-10-06-fairy-ma-gs-hackathon/> This hackathon is open to *anyone working with MAGs*, regardless of their preferred workflow editor. If you’d like to join—or know someone who might be interested—please spread the word! Looking forward to a fantastic hackathon in October. Best, Paul -- Dr. Paul Zierep Chair for Bioinformatics Department of Computer Science University of Freiburg Georges-Koehler-Allee 079, Room 1005a, D-79110 Freiburg, Germany E-mail: zierep(a)informatik.uni-freiburg.de <erxleben(a)informatik.uni-freiburg.de> Tel. 0049 761 203 54129 European Galaxy Team https://galaxyproject.eu https://usegalaxy.eu

1 0

Updates from the microGalaxy Community: Paper, Workflow Hackathon & Write-a-thon
by Bérénice Batut 18 Nov '24

18 Nov '24

Hi everyone, I hope this email finds you well! I’m writing to share a few important updates from the microGalaxy community, including upcoming meetings, hackathons, and progress on our Nature Microbiology manuscript. 1. Manuscript <https://docs.google.com/document/d/1jFOzIm8aE0XBM2PTaQqO3JzAsd8WW16qXDPgFzR…> for Nature Microbiology Thank you all for the productive discussions during last Friday’s meetings! You can find the meeting notes here <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…>. Next Steps: Introduction: We aim to reshape the introduction <https://docs.google.com/document/d/1jFOzIm8aE0XBM2PTaQqO3JzAsd8WW16qXDPgFzR…> by highlighting key challenges in microbiology and tying them to our solutions. Graphical Abstract: Raphaëlle has started working on a nice draft <https://excalidraw.com/#json=Ix0NdYygNbjO8oVKRWqd4,lUms1KiKi0B1c1pDrHgqbw>, which might also serve as a figure for the introduction. Please review and expand on it as needed. Overview Figure: The first version <https://docs.google.com/document/d/1jFOzIm8aE0XBM2PTaQqO3JzAsd8WW16qXDPgFzR…> is ready! Your feedback is invaluable, so please share your thoughts in the manuscript <https://docs.google.com/document/d/1jFOzIm8aE0XBM2PTaQqO3JzAsd8WW16qXDPgFzR…>. Tools/Workflows/Subdomains: We're continuing to refine these (see point 2 below). Updates on the subdomain will be shared soon for your input. We are targeting submission—at least as a preprint—before Christmas. To Coordinate the Work: Next Meetings (November 29th): 8 AM UTC / 5 PM AEST / 9 AM CET <https://arewemeetingyet.com/UTC/2024-11-29/08:00/microGalaxy-paper>– Zoom Link <https://cnrs.zoom.us/j/93068549437?pwd=6lDAIN1TvFkSDbzrkA4jkxq3xWvNab.1> 3 PM UTC / 10 AM EST / 4 PM CET <https://arewemeetingyet.com/UTC/2024-11-29/15:00/microGalaxy-paper> – Zoom Link <https://cnrs.zoom.us/j/99703731107?pwd=ZbbV38ehNOcyrmSQbthiURYs34z4HP.1> Write-a-thon (December 10th): Details below in point 3. 2. microGalaxy Meets IWC: Hackathon for Workflow FAIRification Date: November 21st, 2024 Location: Online Time: Full day, 9/10 AM CET to open end The focus of this hackathon is to identify, prepare, integrate, and FAIRify microbial data analysis workflows in Galaxy for inclusion in the Intergalactic Workflow Commission (IWC). These workflows will also feature in the manuscript. This event is open to everyone! Many tasks do not require technical knowledge, except interacting with the Galaxy workflow editor or Galaxy histories. Format: Zoom room <https://cnrs.zoom.us/j/95387124571?pwd=KMw6DXoedea5swdlw5SWDiPeGfT5Jj.1> available throughout the day Two stand-ups (8 AM UTC / 5 PM AEST / 9 AM CET <https://arewemeetingyet.com/UTC/2024-11-21/08:00/microGalaxy-Workflow-Hacka…> & 3 PM UTC / 10 AM EST / 4 PM CET <https://arewemeetingyet.com/UTC/2024-11-21/15:00/microGalaxy-Workflow-Hacka…>) to accommodate multiple time zones MicroGalaxy Matrix chat for ongoing communication A Google doc <https://docs.google.com/document/d/1tXy3lMYDqpq6A08MLS52U7t9f41V1ByE4jAb6Ss…> and a tracking spreadsheet <https://docs.google.com/spreadsheets/d/154s6YnabgX5oEMpAgdu0kLTKIEl_Ydu8aMG…> with information, task descriptions, etc Your participation will make a significant difference, whether for a few hours or the whole day! 3. microGalaxy Write-a-thon Date: December 10th, 2024 Location: Online Time: Full day, 9/10 AM CET to open end This event is dedicated to finalizing the manuscript collaboratively, both synchronously and asynchronously. Format: Zoom room <https://cnrs.zoom.us/j/99513690948?pwd=zauQ7LRtQyU9XkJmOUH6pZEb2m4O6N.1> open all day Two stand-ups (8 AM UTC / 5 PM AEST / 9 AM CET <https://arewemeetingyet.com/UTC/2024-12-10/08:00/microGalaxy-write-a-thon> & 3 PM UTC / 10 AM EST / 4 PM CET <https://arewemeetingyet.com/UTC/2024-12-10/15:00/microGalaxy-write-a-thon>) for time zone flexibility MicroGalaxy Matrix chat for discussions A Google doc <https://docs.google.com/document/d/1SHN9IXkjmcyDylKDt0kiiwsRBR0Vvi3AFS9RjuP…> and [WIP] a tracking spreadsheet with information, task descriptions, etc We look forward to seeing many of you to finalize the paper! All events have been added to the microGalaxy Google calendar <https://calendar.google.com/calendar/embed?src=npu7puk75n6p0u4aapv5t21uj8@g…>. Thank you all for your contributions and dedication to the microGalaxy community. Let’s make great progress together in the coming weeks! Best, Bérénice

1 0

microGalaxy mailing list
by Valerie Schiml 04 Nov '24

04 Nov '24

Hi, Please have me in your mailing list: valerie.schiml(a)gmail.com<mailto:valerie.schiml@gmail.com> Best Valerie

2 1

Canceled event: microGalaxy technical paper - Meetings on J... @ mer. 3 juil. 2024 13:30 - 14:30 (UTC+2) (microgalaxy@lists.galaxyproject.org)
by Clea Siguret 04 Nov '24

04 Nov '24

This event has been canceled. [microGalaxy] microGalaxy technical paper - Meetings on July 25th mercredi 3 juil. 2024 ⋅ 13:30 – 14:30 Heure d’Europe centrale - Paris https://cnrs.zoom.us/j/92224823565?pwd=goIjlyaJ5wtr5c4vK34VKeHuoFJFdJ.1 Guests Clea Siguret - creator microgalaxy(a)lists.galaxyproject.org galo.goig(a)swisstph.ch pvanheusden(a)uwc.ac.za kimberlymetris(a)gmail.com berenice.batut(a)gmail.com d.brites(a)swisstph.ch nikosp41(a)certh.gr smehta(a)umn.edu saskiahiltemann(a)gmail.com Pierre MARIN bmirauta(a)gmail.com valerie.schiml(a)nmbu.no asimejamesoba(a)gmail.com fpsom(a)certh.gr pierre.amato(a)uca.fr bjoern.gruening(a)gmail.com evan.bolyen(a)nau.edu blanked2(a)ccf.org raphaelle.peguilhan(a)univ-pau.fr cumbof(a)ccf.org anthony.simard(a)nau.edu greg.caporaso(a)nau.edu pjagtap(a)umn.edu anshu(a)imtech.res.in nicola.soranzo(a)earlham.ac.uk ~~//~~ Invitation from Google Calendar: https://calendar.google.com/calendar/ You are receiving this email because you are an attendee on the event. To stop receiving future updates for this event, decline this event. Forwarding this invitation could allow any recipient to send a response to the organizer, be added to the guest list, invite others regardless of their own invitation status, or modify your RSVP. Learn more https://support.google.com/calendar/answer/37135#forwarding

2 1

[November 21st] microGalaxy Meets IWC - A Hackathon for microbial data analysis workflow FAIRification
by Bérénice Batut 31 Oct '24

31 Oct '24

Hi all, Join us for a one-day hackathon focused on integrating, refining, and FAIRifying microbial data analysis Galaxy workflows within the Intergalactic Workflow Commission (IWC), enhancing their accessibility and reusability for the microbiology community. https://galaxyproject.org/events/2024-03-11-hackathon-galaxy-resources-anno… Objectives The primary goal of this hackathon is to prepare, integrate, and FAIRify microbial data analysis Galaxy workflows within the Intergalactic Workflow Commission (IWC), ensuring they adhere to best practices for accessibility, interoperability, and reusability across the bioinformatics community. IWC acts as a central hub for Galaxy workflows, automatically listing them in major registries like Dockstore and WorkflowHub, while ensuring workflows are rigorously reviewed, tested, and updated with every new Galaxy release. Versioning, tool updates, and essential metadata enhance the findability and usability of each workflow. In short, the objectives of this hackathon are to: Annotate and apply best practices to microbial data analysis Galaxy workflows for consistency and reusability Implement robust tests to ensure workflow reliability and accuracy Successfully integrate key microbial data analysis Galaxy workflows into IWC, improving accessibility and usability Collaborate as a community to refine and improve workflows, ensuring they are peer-reviewed and meet high standards Make these peer-reviewed workflows accessible to the broader community through the future microGalaxy Lab This hackathon is open to participants from all communities, so join us to help shape the future of bioinformatics workflows! General information Date: November 21th 2024 (one day) Location: Online a Zoom room, open the whole day 2 daily stand-ups to accommodate different time zones microGalaxy Matrix chat for communication Time: full day, 9/10 am CET to open end Cost: Free Preliminary Schedule The schedule is quite flexible. There is no requirement to join the whole week. See the event page for more details about the planned schedule (stand-ups, brainstorming meetings): https://galaxyproject.org/events/2024-03-11-hackathon-galaxy-resources-anno…. Participation To participate, add your name, your affiliation, your availability during the week, and your email in the "Participation" section of the organizational GDoc so we can include you in further communication: https://docs.google.com/document/d/1B125dSKhB6AevnyShSi_zXIXUQd49tvNYfWHuyq… We hope to see a lot of you, even if it is just to say hi :) Best, Paul and Bérénice

4 4

Poster for GCC - input needed
by Paul Zierep 16 Oct '24

16 Oct '24

Dear microGalaxy Community, I am currently working on the poster for GCC. We want to print next week (19th of June). One thing I wanted to show are highlight workflows. If you have a *workflow that you think should be highlighted*, please let me know, or add it directly to the poster ( https://docs.google.com/presentation/d/1cUMofj-KfswDyeIl9iq2eLSRifDrcj83LGj… ). If you have any other comments or suggestions, also feel free to reach out or add it to the poster as well. Thank you and all the best, Paul -- Dr. Paul Zierep Chair for Bioinformatics Department of Computer Science University of Freiburg Georges-Koehler-Allee 079, Room 1005a, D-79110 Freiburg, Germany E-mail: zierep(a)informatik.uni-freiburg.de <erxleben(a)informatik.uni-freiburg.de> Tel. 0049 761 203 54129 European Galaxy Team https://galaxyproject.eu https://usegalaxy.eu

2 1