- microGalaxy - lists.galaxyproject.org

microGalaxy + BioDIGs technical meeting - Sept 16th at 1 pm UTC / 3 pm CEST / 9 am EDT
by Bérénice Batut 15 Sep '26

15 Sep '26

Hi all, We have a meeting planned tomorrow at 1 pm UTC / 3 pm CEST / 9 am EDT to coordinate efforts in tool and workflow development, with a focus on the BioDIGs project. If you want to join, the meeting will take place here: https://visio.numerique.gouv.fr/fdl-vphp-nvt. Best, Bérénice Batut (she/her) —— CNRS Laboratoire Microorganismes: Génome Environnement (LMGE), Aubière, France Institut Français de Bioinformatique (IFB)

1 0

test - ignore it
by Paul Zierep 11 Sep '26

11 Sep '26

sorry this is a test to check if I get my own mail - needed for us :), ignore it -- 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

microGalaxy Hackathon for tool development
by Paul Zierep 11 Sep '26

11 Sep '26

Dear microGalaxy community, Now that our community paper is accepted, we can try to focus more on things like tool maintenance. As discussed in our last meeting, many - also highly used - microGalaxy tools are outdated. This includes tools in IUC https://github.com/galaxyproject/tools-iuc/issues/8301. We therefore plan a hackathon to update those tools. The main idea is to block some time for everyone that allows this work and also coordinate a bit on who does what. Please check for a day that works for you: https://terminplaner.dfn.de/public/polls/cebe393c-4d64-4541-90a2-cc1dd56393… It’s perfectly fine if there is only a short US/AU/EU overlap - the day can still serve as a dedicated block of time that you can use for tool maintenance. 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

Invitation: Next microGalaxy meeting - September 9th
by Bérénice Batut 09 Sep '26

09 Sep '26

Dear all, I hope you are all doing fine! We are excited to invite you to the next microGalaxy meeting, while will be held online on Wednesday, September 9th, at 1 pm UTC / 3 pm CEST / 9 am EDT (see your timezone <https://arewemeetingyet.com/UTC/2026-09-09/13:00/microGalaxy>). Agenda: Community news and updates (from all of you!) A talk by Tyler and Natalie on BioDIGs <https://biodigs.org/#home>, a US collaborative project exploring the connections between the soil microbiome, the environment, and health (paper <https://www.nature.com/articles/s41588-025-02442-5>) Discussion on how we can align our efforts and avoid duplication. Meeting details: Meeting rolling minutes <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Visio <https://visio.numerique.gouv.fr/pst-nyrz-yui> Google calendar event <https://calendar.google.com/calendar/event?action=TEMPLATE&tmeid=MmcxZTdicj…> We’d love to see you there! Feel free to share this invitation with anyone who might be interested in joining our community. Looking forward to connecting with you all. Best, Bérénice & Paul

1 1

Feedback Request before February 25th: microGalaxy community Roadmap
by Bérénice Batut 20 Feb '26

20 Feb '26

Hi everyone, We've received the reviews for the Microbiology Galaxy Lab paper. One reviewer requested a clearer distinction between currently implemented features and planned developments, ideally in the form of a concise roadmap. We’ve drafted a roadmap for the microGalaxy community here <https://docs.google.com/document/d/1CjhPbWLw-rc6bs7EQT_U-Dy8EypaIyNmWcW_Mnf…> and plan to add it to the microGalaxy Hub page <https://galaxyproject.org/community/sig/microbial/> and the paper by next week. Given the tight timeline, we'd greatly appreciate your feedback on the roadmap by Wednesday, February 25th (as comments/suggestions in the document <https://docs.google.com/document/d/1CjhPbWLw-rc6bs7EQT_U-Dy8EypaIyNmWcW_Mnf…> or by opening the discussion here) Thanks for your help! Bérénice and Paul

1 0

Planning a Meeting on AMR Analyses in Galaxy
by Bérénice Batut 06 Jan '26

06 Jan '26

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 2

***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