- SPOC - lists.galaxyproject.org

[SPOC 🖖🏾] Monthly meeting tomorrow and new meeting time!!
by Pavankumar Videm 04 Mar '26

04 Mar '26

Dear Galaxy Single-cell & sPatial Omics Community (SPOC) 🖖🏾! We are meeting tomorrow 5th March at 15:00 CET / 14:00 BST. *Attention!* Please note that we are adjusting our monthly meeting time. Previously, we used variable meeting times to accommodate participants across the US, Europe, and Australia. However, as our most consistent attendance currently comes from the European community, we have decided to prioritize a fixed time slot that is more accessible for this group. New meeting time: First Thursday of every month. Central Europe (CET/CEST): 15:00 / 3pm London (GMT/BST/UTC): 14:00 / 2pm If you are joining us from outside these zones, we still very much value your input! Please let us know if this new time creates a significant barrier for you. * * *Actions!* 📝<https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…>Check out/add to our meeting agenda <https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> 🗓️ Subscribe to new SPOC Calendar <https://calendar.google.com/calendar/u/0?cid=eeb0e40092fc3f41268e20da017f16…> and please delete any old SPOC calendar events 🗓️ SPOC iCalendar <https://calendar.google.com/calendar/ical/eeb0e40092fc3f41268e20da017f16012…> *Join Zoom Meeting* https://uni-freiburg.zoom-x.de/j/66133521539?pwd=Qdy68HeI786NHyUHDvYtiXlXqb… Meeting ID: 661 3352 1539 Passcode: XZ3i8jp2j Best, Pavan Videm Galaxy Single cell and spatial omics Community of Practice (SPOC🖖🏾) -- Dr. Pavankumar Videm (he/him) Chair for Bioinformatics Department of Computer Science University of Freiburg Georges-Koehler-Allee 079 D-79110 Freiburg, Germany Tel: (+49) 761 203 54132 Email:videmp@informatik.uni-freiburg.de European Galaxy Team https://galaxyproject.org/eu/ https://usegalaxy.eu

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Meeting tomorrow at 09:00 CET
by Pavankumar Videm 02 Feb '26

02 Feb '26

Hello 🖖🏾SPOC! Single-cell & sPatial Omics Community of practice We are meeting this week! Tomorrow 3rd of February at CET 9:00 / BST 8:00 Please check the agenda/meeting notes here: https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf… Join Zoom Meeting https://us02web.zoom.us/j/87443808126?pwd=QjZ3TEJmSVBpdHgrQUQwOGkraFM2UT09 Meeting ID: 874 4380 8126 Passcode: nerdsunite Actions! ✅ Please update the click-up board <https://app.clickup.com/9015477668/v/b/5-90152810734-2> with progress on the listed items. ✅ Please update the meeting notes with points to discuss Next meeting 🗓️SPOC Google Calendar <https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ct…> 🗓️SPOC Outlook Calendar (Embed) <https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/…> 📝Meeting Notes doc <https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> Cheers, Pavan -- Dr. Pavankumar Videm (he/him) Chair for Bioinformatics Department of Computer Science University of Freiburg Georges-Koehler-Allee 079 D-79110 Freiburg, Germany Tel: (+49) 761 203 54132 Email:videmp@informatik.uni-freiburg.de European Galaxy Team https://galaxyproject.org/eu/ https://usegalaxy.eu

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No SPOC community meeting this month
by Pavankumar Videm 03 Dec '25

03 Dec '25

Dear all, As some of us traveling (hacking on spatial analysis tools, workflows and tutorials at German BioHackathon), we will NOT have any community meeting this month. We will also take this break to restructure the meeting times. You will a separate email about the new meeting times. Let us meet again in the new year. Cheers, Pavan SPOC *🖖* * * -- Dr. Pavankumar Videm (he/him) Chair for Bioinformatics Department of Computer Science University of Freiburg Georges-Koehler-Allee 079 D-79110 Freiburg, Germany Tel: (+49) 761 203 54132 Email:videmp@informatik.uni-freiburg.de European Galaxy Team https://galaxyproject.org/eu/ https://usegalaxy.eu

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⌚Meeting Tomorrow
by Pavankumar Videm 04 Aug '25

04 Aug '25

Hello 🖖🏾SPOC! Single-cell & sPatial Omics Community of practice We are meeting this week! Tomorrow 5th of August at BST 8:00 / CEST 9:00 This time, we wil go through the click-up board <https://app.clickup.com/9015477668/v/b/5-90152810734-2> and discuss the progress of SPOC resources. Actions! ✅ Please update the click-up board <https://app.clickup.com/9015477668/v/b/5-90152810734-2> with progress on the listed items. ✅ As European Galaxy days is coming up, think about some ideas for co-fest. Next meeting 👋🏾Tuesday 5th of August 🗓️SPOC Google Calendar <https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ct…> 🗓️SPOC Outlook Calendar (Embed) <https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/…> 📝Meeting Notes doc <https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> Join Zoom Meeting https://us02web.zoom.us/j/87443808126?pwd=QjZ3TEJmSVBpdHgrQUQwOGkraFM2UT09 Meeting ID: 874 4380 8126 Passcode: nerdsunite Cheers, Pavan -- Dr. Pavankumar Videm (he/him) Chair for Bioinformatics Department of Computer Science University of Freiburg Georges-Koehler-Allee 079 D-79110 Freiburg, Germany Tel: (+49) 761 203 54132 Email:videmp@informatik.uni-freiburg.de European Galaxy Team https://galaxyproject.org/eu/ https://usegalaxy.eu

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⌚Meeting Tomorrow
by Pavankumar Videm 05 May '25

05 May '25

Hello 🖖🏾SPOC! /Single-cell & sPatial Omics Community of practice/ We are meeting this week!Tomorrow 6th of May at BST 8:00 / CEST 9:00 This week, you have opportunity of seeking help on any Galaxy single-cell related issues. *Actions!* ✅ Please add your requests or challenges that you are currently facing in the agenda document <https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…>. Either enter it in *Help calls from current work?* item or a separate item in the table. *Next meeting* 👋🏾Tuesday 6th of May <https://arewemeetingyet.com/London/2025-05-06/08:00/SPOC-ster> 🗓️SPOC Google Calendar <https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ct…> 🗓️SPOC Outlook Calendar (Embed) <https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/…> 📝Meeting Notes doc <https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> *Join Zoom Meeting* https://us02web.zoom.us/j/87443808126?pwd=QjZ3TEJmSVBpdHgrQUQwOGkraFM2UT09 <https://us02web.zoom.us/j/87443808126?pwd=QjZ3TEJmSVBpdHgrQUQwOGkraFM2UT09> Meeting ID: 874 4380 8126 Passcode: nerdsunite Cheers, Pavan -- Dr. Pavankumar Videm (he/him) Chair for Bioinformatics Department of Computer Science University of Freiburg Georges-Koehler-Allee 079 D-79110 Freiburg, Germany Tel: (+49) 761 203 54132 Email:videmp@informatik.uni-freiburg.de European Galaxy Team https://galaxyproject.org/eu/ https://usegalaxy.eu

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📝Notes from April meeting
by Pavankumar Videm 09 Apr '25

09 Apr '25

** *Hello Galaxy 🖖🏾SPOC!* * Single-cell & sPatial Omics Community of practice We had our ‘project updates’ meeting on 8th April, so a big thank you to the people sharing their achievements in the last months! 🎉 We are setting up the stage for the upcoming Galaxy Training Academy. 🖖🏾SPOC is adding two additional tutorials to the single-cell track. Thanks to Marisa for recording the Seurat PBMC3k Clustering tutorial and Diana for updating and recording the Pseudobulk DE analysis tutorial. 🎉 We now have a new group called “WORKFLOWS” on our 🖖🏾SPOC clickup board to track single-cell workflows on IWC <https://github.com/galaxyproject/iwc/tree/main/workflows/scRNAseq>. Check the 📝Meeting Notes doc <https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…>for full details from our last meeting! Actions ✅Update our Click-Up Site <https://app.clickup.com/9015477668/v/b/5-90152810734-2>! with what you’re working on, even if you can’t/didn’t make the meetings ✅ Check the previous SPOC CoFest setup <https://docs.google.com/document/d/1GRAY_uE3dtyaGlKR7rqCXgjrJQUkgch-eyc7Asi…>and tasks <https://docs.google.com/spreadsheets/d/17BsRGk_PwYdcSlhhfr4BgpDkS4cyZg8-qhv…>and let us know if you would volunteer to chair the next one after the GTA. ** *⭐️Sign up for the Galaxy Training Academy here: https://forms.gle/hDA7rfHALLkb4LNC8 <https://forms.gle/hDA7rfHALLkb4LNC8>* ** Next meeting 👋🏾Tuesday 6th of May <https://arewemeetingyet.com/London/2025-05-06/08:00/SPOC-ster> 🗓️SPOC Google Calendar <https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ct…> 🗓️SPOC Outlook Calendar (Embed) <https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/…> * *Cheers! * * * -- Dr. Pavankumar Videm (he/him) Chair for Bioinformatics Department of Computer Science University of Freiburg Georges-Koehler-Allee 079 D-79110 Freiburg, Germany Tel: (+49) 761 203 54132 Email:videmp@informatik.uni-freiburg.de European Galaxy Team https://galaxyproject.org/eu/ https://usegalaxy.eu

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⌚️Meeting this week!
by Wendi.Bacon [She/Her] 07 Apr '25

07 Apr '25

Hello 🖖🏾SPOC! Single-cell & sPatial Omics Community of practice We are meeting this week! Actions! ✅Please update our Click-Up Site<https://app.clickup.com/9015477668/v/b/5-90152810734-2> with what you’ve been up to in the Galaxy single cell world, whether you can attend the meeting or not! ⭐Check out/add to our meeting agenda<https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> Next meeting 👋🏾Tuesday 8th of April<https://arewemeetingyet.com/London/2025-04-08/13:00/SPOC-ster> 🗓️SPOC Google Calendar<https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ct…> 🗓️SPOC Outlook Calendar (Embed)<https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/…> 📝Meeting Notes doc<https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> Join Zoom Meeting https://us02web.zoom.us/j/87443808126?pwd=QjZ3TEJmSVBpdHgrQUQwOGkraFM2UT09 Meeting ID: 874 4380 8126 Passcode: nerdsunite I’m sadly away on leave, so this may be my last email to you all as Pavan is now 🖖🏾SPOC chair! May you have an awesome meeting! Wendi [cid:image001.png@01DB945D.857E5500] [signature_134045891] [cidimage002.png(a)01D7311B.5DCF6570] Wendi Bacon (she/her) Senior Lecturer in Health Sciences<https://www.open.ac.uk/people/wb2845> School of Life, Health & Chemical Sciences | Faculty of STEM The Open University | Milton Keynes MK7 6AA | United Kingdom 🎓Explore the Galaxy single-cell training materials!<https://training.galaxyproject.org/training-material/topics/single-cell/> Galaxy Contributor<https://training.galaxyproject.org/training-material/hall-of-fame/nomadscie…> | Single-cell & sPatial Omics Community Chair<https://galaxyproject.org/community/sig/singlecell/> Community Board Chair<https://galaxyproject.org/community/governance/gcb/> | Executive Board<https://galaxyproject.org/community/governance/geb/> I sometimes work flexibly so if you have received an email from me outside of normal business hours, I’m sending it at a time that suits me. Please do not feel you have to read or reply until normal working hours.

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📝Notes from March meeting
by Wendi.Bacon [She/Her] 14 Mar '25

14 Mar '25

Hello Galaxy 🖖🏾SPOC! Single-cell & sPatial Omics Community of practice We had our ‘calls for help’ meeting today, so a big thank you for people stepping up to help each other! It was lovely to welcome so many new participants to our group! 🎉In particular, a big thank you to Pavan, who will be taking over as 🖖🏾SPOC chair from April as I step back from Galaxy and into a new role with Health Data Research - UK. It has been an honour and a privilege to get to chair this community, and I believe that once a 🖖🏾SPOC, always a 🖖🏾SPOC! Check the 📝Meeting Notes doc<https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> for full details from our last meeting! Actions ✅Update our Click-Up Site<https://app.clickup.com/9015477668/v/b/5-90152810734-2>! with what you’re working on, even if you can’t/didn’t make the meetings ⭐️Sign up for the Galaxy Training Academy here: https://forms.gle/hDA7rfHALLkb4LNC8 ✅Run an event? Give a presentation? Do literally anything with our community? Make sure to write a blog post! There’s a googleform widget to make this super fast!<https://training.galaxyproject.org/training-material/news/2024/01/29/simpli…> Tag it single-cell! 🔺Feedback for Galaxy Governance: Tool panel manual steps with every new tool & need for more regional variation in SPOC Next meeting 👋🏾Tuesday 8th of April<https://arewemeetingyet.com/London/2025-04-08/13:00/SPOC-ster> 🗓️SPOC Google Calendar<https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ct…> 🗓️SPOC Outlook Calendar (Embed)<https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/…> Cheers! [cid:image001.png@01DB945D.5A724830] [signature_3908208330] [cidimage002.png(a)01D7311B.5DCF6570] Wendi Bacon (she/her) Senior Lecturer in Health Sciences<https://www.open.ac.uk/people/wb2845> School of Life, Health & Chemical Sciences | Faculty of STEM The Open University | Milton Keynes MK7 6AA | United Kingdom 🎓Explore the Galaxy single-cell training materials!<https://training.galaxyproject.org/training-material/topics/single-cell/> Galaxy Contributor<https://training.galaxyproject.org/training-material/hall-of-fame/nomadscie…> | Single-cell & sPatial Omics Community Chair<https://galaxyproject.org/community/sig/singlecell/> Community Board Chair<https://galaxyproject.org/community/governance/gcb/> | Executive Board<https://galaxyproject.org/community/governance/geb/> I sometimes work flexibly so if you have received an email from me outside of normal business hours, I’m sending it at a time that suits me. Please do not feel you have to read or reply until normal working hours.

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⌚️Meeting this week!
by Wendi.Bacon [She/Her] 03 Feb '25

03 Feb '25

Hello 🖖🏾SPOC! Single-cell & sPatial Omics Community of practice We are meeting this week! Actions! ✅Please update our Click-Up Site<https://app.clickup.com/9015477668/v/b/5-90152810734-2> with what you’ve been up to in the Galaxy single cell world, whether you can attend the meeting or not! ⭐Check out/add to our meeting agenda<https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> Also a reminder: ⭐Check the numerous actions from the meeting agenda! ⭐Continue doing ace work for the Galaxy single & spatial community! Next meeting 👋🏾https://arewemeetingyet.com/London/2025-02-04/08:00/SPOCentines 🗓️SPOC Google Calendar<https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ct…> 🗓️SPOC Outlook Calendar (Embed)<https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/…> 📝Meeting Notes doc<https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> Join Zoom Meeting https://us02web.zoom.us/j/87443808126?pwd=QjZ3TEJmSVBpdHgrQUQwOGkraFM2UT09 Meeting ID: 874 4380 8126 Passcode: nerdsunite See you then! Wendi [cid:image001.png@01DB518D.81713440] [signature_342049381] [cidimage002.png(a)01D7311B.5DCF6570] Wendi Bacon (she/her) Senior Lecturer in Health Sciences<https://www.open.ac.uk/people/wb2845> School of Life, Health & Chemical Sciences | Faculty of STEM The Open University | Milton Keynes MK7 6AA | United Kingdom 🎓Explore the Galaxy single-cell training materials!<https://training.galaxyproject.org/training-material/topics/single-cell/> Galaxy Contributor<https://training.galaxyproject.org/training-material/hall-of-fame/nomadscie…> | Single-cell & sPatial Omics Community Chair<https://galaxyproject.org/community/sig/singlecell/> Community Board Chair<https://galaxyproject.org/community/governance/gcb/> | Executive Board<https://galaxyproject.org/community/governance/geb/> I sometimes work flexibly so if you have received an email from me outside of normal business hours, I’m sending it at a time that suits me. Please do not feel you have to read or reply until normal working hours.

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🥛 Mid-point Reminder
by Wendi.Bacon [She/Her] 13 Jan '25

13 Jan '25

Hello 🖖🏾SPOC! Single-cell & sPatial Omics Community of practice Welcome to 2025! This is your mid-meeting reminder, occurring halfway between meetings! Actions from Last Meeting ⭐️Add when you joined SPOC here<https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…>, and other missing metadata ⭐️Check (and later, share!) our annual blog post: PR is here<https://github.com/galaxyproject/training-material/pull/5655> and the final post will (eventually) be found here: https://training.galaxyproject.org/training-material/news/2024-12-18-spoc.h… ⭐️Up-vote (or action) this issue around data integration between hub & GTN: https://github.com/galaxyproject/galaxy-hub/issues/2809 ⭐️Think of any other ELIXIR All-Hands workshop ideas you might want help with, due mid-Jan ⭐️Add ideas/thoughts to this idea<https://docs.google.com/document/d/17jowIApvgNZ0nzXIf9ihW2xmdwpI3Zj3/edit?u…> on collectively building a single-cell learning community ⭐️Check single cell site and raise issues / ideas on its view / function on the galaxy-labs-engine repo: https://github.com/usegalaxy-au/galaxy-labs-engine. If anyone is interested in substantially contributing to that repo, please message there! I bet Cam would be delighted to have help! ⭐️Rollover from previous meeting: How do we automate that any single-cell tools in the toolshed get into (all) of our single-cell subdomains? Installed, and also placed in a reasonable subcategory? Pavan to start looking at this, but is going to require global teamwork. ClickUp card created<https://app.clickup.com/t/86c1cfv8j> ⭐️Write-a-thon writers - write! Want a full draft for January! Hopefully this is going well… 🔺Feedback for Galaxy Governance: Save Helena! WB posted to GCB on 18-December. To follow up after next GCB meeting and report back. ✅Update our Click-Up Site<https://app.clickup.com/9015477668/v/b/5-90152810734-2>! with what you’re working on, even if you can’t/didn’t make the meetings ✅Answer any unanswered queries on our Galaxy single-cell help forum<https://help.galaxyproject.org/tag/single-cell/l/latest> ✅Run an event? Give a presentation? Do literally anything with our community? Make sure to write a blog post! There’s a googleform widget to make this super fast!<https://training.galaxyproject.org/training-material/news/2024/01/29/simpli…> Tag it single-cell! ⭐Continue doing ace work for the Galaxy single & spatial community! Next meeting 👋🏾https://arewemeetingyet.com/London/2025-02-04/08:00/SPOCentines 🗓️SPOC Google Calendar<https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ct…> 🗓️SPOC Outlook Calendar (Embed)<https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/…> 📝Meeting Notes doc<https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtf…> See you then! Wendi [cid:image001.png@01DB518D.5F767940] [signature_3098058536] [cidimage002.png(a)01D7311B.5DCF6570] Wendi Bacon (she/her) Senior Lecturer in Health Sciences<https://www.open.ac.uk/people/wb2845> School of Life, Health & Chemical Sciences | Faculty of STEM The Open University | Milton Keynes MK7 6AA | United Kingdom 🎓Explore the Galaxy single-cell training materials!<https://training.galaxyproject.org/training-material/topics/single-cell/> Galaxy Contributor<https://training.galaxyproject.org/training-material/hall-of-fame/nomadscie…> | Single-cell & sPatial Omics Community Chair<https://galaxyproject.org/community/sig/singlecell/> Community Board Chair<https://galaxyproject.org/community/governance/gcb/> | Executive Board<https://galaxyproject.org/community/governance/geb/> I sometimes work flexibly so if you have received an email from me outside of normal business hours, I’m sending it at a time that suits me. Please do not feel you have to read or reply until normal working hours.

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