- microGalaxy - lists.galaxyproject.org

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 03 Nov '24

03 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 03 Nov '24

03 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 15 Oct '24

15 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

microGalaxy technical paper - Updates & Meetings on November, 15th
by Bérénice Batut 14 Oct '24

14 Oct '24

Hi all, I hope you are all doing fine! Below is a summary of the key points discussed in our recent meeting: 1. Manuscript for Nature Microbiology: https://docs.google.com/document/d/1jFOzIm8aE0XBM2PTaQqO3JzAsd8WW16qXDPgFzR… Adaptation of Scope: The manuscript will be more user-oriented, focusing on the microbiology aspect and be written for Nature Microbiology. Most technical details will be included in the Supplementary materials. Please read, add suggestions and comments Use Cases: We would like to add published use cases (including preprints) in the manuscript within the tools, workflows, and training Result sections. Any use cases mentioned should be included in the Use Case table (in Supplementary) Overview Figure (Fig 1): Please provide comments and suggestions for changes in the manuscript. You can use Excalidraw or sketch manually to draft your ideas. Supplementary Materials: Comments and suggestions on tables (related platforms, training events) and figures should be added as comments in the manuscript. 2. Coordination: Assign yourself to the tasks you wish to work on and tick them off upon completion: https://docs.google.com/document/d/1TCGcooxVo_4FfPUdB7xv5n01UfkIIYz0z8Ydo1G… 3. Upcoming Hackathon: A one-day hackathon to add workflows to IWC is scheduled for November. Further details will be shared in a separate invitation email. 4. Lab/Subdomain: Please comment on the provided sketch: Excalidraw Sketch <https://excalidraw.com/#room=14e15dbbc2aea9d3696e,TCWhNxBPAQIgcUPS4WGBfA>. 5. Timeline: Workflow hackathon in November. Deadline for tasks: end of November (to be confirmed). 6. Next Meeting: The next meeting is scheduled for November 15th with 2 meetings (to accommodate different timezones): November 15th at 8am UTC / 5pm AEST / 9am CET (your timezone <https://arewemeetingyet.com/UTC/2024-15-11/08:00/microGalaxy-paper>) - Zoom <https://cnrs.zoom.us/j/93673899365?pwd=em88V8iKPaX3wvODKB8FvRcNSJHEbp.1> - Notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> November 15th at 3pm UTC / 4pm CET / 10am EDT (your timezone <https://arewemeetingyet.com/UTC/2024-11-15/15:00/microGalaxy-paper>) - Zoom <https://cnrs.zoom.us/j/99154648776?pwd=vj3fQ8BQdVmax5g12sbwApdEF5gxgD.1> - Notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> Calendar with all meetings <https://calendar.google.com/calendar/u/0/embed?src=npu7puk75n6p0u4aapv5t21u…> Anyone interested in participating in the paper is more than welcome! I hope to see you around Best, Bérénice

2 1

microGalaxy technical paper - Updates & Meetings on October, 8th
by Bérénice Batut 07 Oct '24

07 Oct '24

Hi all, I hope you are all doing fine! In the last meetings, we discussed tasks and also the scope/target audience of the paper we are writing. We aim for the paper to be useful for a wide range of people, including our users (i.e. microbiologists) We decided to make the paper more understandable by reducing the technicalities in the main text and moving details to the Supplementary. We will also target a microbiology journal. So there are a lot of things to do for the paper. To keep an updated overview of the tasks, we created a Google doc for coordination with all tasks we identified <https://docs.google.com/document/d/1TCGcooxVo_4FfPUdB7xv5n01UfkIIYz0z8Ydo1G…>. Feel free to Take care of some tasks, Comment on the tasks, Add new (sub)tasks And before our next meetings, we would need your help with the following tasks: Fill in the Platform table: https://docs.google.com/spreadsheets/d/1KxWoVRvuusMiKvs0ELiKHjbbQBBshdntSW1… Check the Training event table (if your events are there) and add any missing events: https://docs.google.com/spreadsheets/d/1Eejqmb4CJQnyy51ayLMOgTPf5mHArKlCtSY… microGalaxy - Training events 2019-2024 docs.google.com Our next meetings will be October 8th with 2 meetings (to accommodate different timezones): October 8th at 7am UTC / 5pm AEST / 9am CEST (your timezone <https://arewemeetingyet.com/UTC/2024-09-16/07:00/microGalaxy-paper>) - Zoom <https://cnrs.zoom.us/j/93258404935?pwd=qMSHlltNrIWMhoFIVD0quN6P9AMrhr.1> - Notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> October 8th at 2pm UTC / 4pm CEST / 10am EDT (your timezone <https://arewemeetingyet.com/UTC/2024-09-16/14:00/microGalaxy-paper>) - Zoom <https://cnrs.zoom.us/j/93258404935?pwd=qMSHlltNrIWMhoFIVD0quN6P9AMrhr.1> - Notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> Calendar with all meetings <https://calendar.google.com/calendar/u/0/embed?src=npu7puk75n6p0u4aapv5t21u…> Anyone interested in participating in the paper is more than welcome! I hope to see you around Best, Bérénice

1 1

microGalaxy paper writing - Who is interested in contributing actively?
by Bérénice Batut 16 Sep '24

16 Sep '24

Hi all, In the paper WG meeting yesterday, we discussed about the 2 papers we would like to write in the next months You can find below a quick description about the aims and timelines for both and more details in the paper WG notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…>. If you are interested in contributing actively in any or both papers, let us know either by answering this email or adding your name in the paper WG notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> on page 2 and 3 We will after that organise separate meetings for each paper. Best, Bérénice User-oriented paper What? (Opinion) paper showing that Galaxy is used for microbial data analysis and how with overview of publications using Galaxy, result of survey, use cases Where? Open-access user oriented journal (e.g. BMC Microbiology) When? November - December 2023 Process the survey and use cases Clarify the paper outline Beginning of 2024: write the manuscript Technical paper What? A technical paper presenting resources/infrastructure (tools, workflows, training, etc) available for microbial data analysis in Galaxy Where? NAR webserver <https://academic.oup.com/nar/pages/submission_webserver> When? Deadlines for NAR webserver Submission of one-page summary by December, 20th Submission of full manuscript 3 weeks after the date of the approval email or 31 January Timeline November - December: Collect tools, workflows, database and training available in Galaxy Write a 1st draft of the paper Write the summary Make a nice looking subdomain microgalaxy.usegalaxy.eu with links to workflows and training and selection of tools January Finalize the draft Submit the manuscript

3 2

microGalaxy technical paper - Meetings on September, 16th
by Bérénice Batut 12 Sep '24

12 Sep '24

Hi all, I hope you are all doing fine! After the meetings on July 25th, we decided to submit the paper as a Software Paper for Plos Computational Biology before the end of the year. Engy reformated the manuscript <https://docs.google.com/document/d/1s-xRPcclHsuQNLiElZyD9hkzrgMLqi6V/edit?u…> to fit the journal guidelines. Feel free to work on it to add content there! During the meetings, we identified several tasks everyone could work on To keep an updated overview of the tasks, we created a Google doc for coordination with the tasks we identified <https://docs.google.com/document/d/1TCGcooxVo_4FfPUdB7xv5n01UfkIIYz0z8Ydo1G…> Feel free to comment on the tasks, add new (sub)tasks, and assign yourself to tasks you are interested in (even if others are already assigned)especially To coordinate our efforts, we will meet on September 16th with 2 meetings (to accommodate different timezones): September 16th at 7am UTC / 5pm AEST / 9am CEST (your timezone <https://arewemeetingyet.com/UTC/2024-09-16/07:00/microGalaxy-paper>) - Zoom <https://cnrs.zoom.us/j/94378827695?pwd=hwcfDAQzHDRFjNjQw1PtQfxsoZjNUX.1> - Notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> September 16th at 2pm UTC / 4pm CEST / 10am EDT (your timezone <https://arewemeetingyet.com/UTC/2024-09-16/14:00/microGalaxy-paper>) - Zoom <https://cnrs.zoom.us/j/97130510993?pwd=oiznXwPnyj3GUc8yBPfSKrCi64IeTS.1> - Notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> Calendar with all meetings <https://calendar.google.com/calendar/u/0/embed?src=npu7puk75n6p0u4aapv5t21u…> Anyone interested in participating in the paper is more than welcome! I hope to see you around Feel free to share the details about these meetings and this community with anyone that may be interested :) Best, Bérénice

2 3

microGalaxy technical paper - Meetings on July 25th
by Bérénice Batut 03 Jul '24

03 Jul '24

Hi all, I hope you are all doing fine! It was nice to meet some of you at GCC. By the end of the year, we would like to submit the technical paper we have been working on over the last year. To organize that, the Paper working group <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> (calendar with all meetings <https://calendar.google.com/calendar/u/0/embed?src=npu7puk75n6p0u4aapv5t21u…>) will meet on July 25th with 2 meetings (to accommodate different timezones): July 25th at 7am UTC / 5pm AEST / 9am CEST (your timezone) - Zoom <https://cnrs.zoom.us/j/92224823565?pwd=goIjlyaJ5wtr5c4vK34VKeHuoFJFdJ.1> - Notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> July 25th at 2pm UTC / 4pm CEST / 10am EDT (your timezone) - Zoom <https://cnrs.zoom.us/j/93013986530?pwd=N2gyRSbuJf0jLPIWf655Nnj85xhaYY.1> - Notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> We will discuss the technical paper <https://docs.google.com/document/d/1s-xRPcclHsuQNLiElZyD9hkzrgMLqi6V/edit>, the work we have been doing over the last months, and the timeline for submitting it this year. Anyone interested in participating in the paper is more than welcome! I hope to see you around Feel free to share the details about these meetings and this community with anyone that may be interested :) Best, Bérénice

1 0