microGalaxy September 2024

microgalaxy@lists.galaxyproject.org

2 participants
3 discussions

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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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

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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

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microGalaxy September 2024