October 2024 - microGalaxy - lists.galaxyproject.org

microGalaxy mailing list
by Valerie Schiml 16 Oct '24

16 Oct '24

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

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[November 21st] microGalaxy Meets IWC - A Hackathon for microbial data analysis workflow FAIRification
by Bérénice Batut 16 Oct '24

16 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

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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

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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

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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

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