- microGalaxy - lists.galaxyproject.org

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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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 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

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Meeting in 25 Minutes
by Paul Zierep 30 May '24

30 May '24

Dear all, this is a quick reminder about our microGalaxy Meeting in 30 minutes: [Meeting rolling minutes]( https://docs.google.com/document/d/13VjcUjStuIp7bK29e74k8Nqb7N4lmVcg1ioArEW… ) [Zoom]( https://us02web.zoom.us/j/82453101719?pwd=NlJudHk1c0xqSC83eXM4bTM1YWJ2UT09) (Meeting ID: 824 5310 1719; Passcode: micro) 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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Community meeting - May 30th, 2pm UTC
by Bérénice Batut 15 May '24

15 May '24

Dear all, I hope you are all doing fine! Here is some news about the microGalaxy community. Next Community meeting We are supposed to have a community meeting tomorrow at 3pm UTC. Paul and I are under the water lately with some proposals and other work until the end of the week and we forgot to advertize it. We will move the Community meeting to Thursday, May 30 at 2 pm UTC / 4 pm CEST / 10am EDT (your timezone <https://arewemeetingyet.com/UTC/2024-05-30/14:00/microGalaxy>). Meeting rolling minutes <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> Zoom <https://us02web.zoom.us/j/82453101719?pwd=NlJudHk1c0xqSC83eXM4bTM1YWJ2UT09> (Meeting ID: 824 5310 1719; Passcode: micro) During this meeting, we will mostly catch up with news from the community, share the outcomes of the hackathon we did in March, plan for GCC, and talk about the next months. 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 & Paul

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GCC - Abstract for poster about microGalaxy
by Bérénice Batut 04 Apr '24

04 Apr '24

Hi all, I hope you are doing well. We started a draft for an abstract for a poster at GCC on our community, microGalaxy https://docs.google.com/document/d/1b-ZspQMWnEpZJzuoAs6TJQExW66xhpzIQHrENpC… GCC 2024 - microGalaxy docs.google.com If you want to be involved there, please have a look at this abstract, make suggestions, and add yourself as author before April, 11th. I will submit it on April 12th. Thank you! Best, Bérénice

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Online Hackathon - March 11-15, 2024 - Improving the annotation of Galaxy resources for microbial data analysis and beyond
by Bérénice Batut 11 Mar '24

11 Mar '24

Hi all, We organize an Online Hackathon in March to improve the annotation of Galaxy resources for microbial data analysis and beyond: https://galaxyproject.org/events/2024-03-11-hackathon-galaxy-resources-anno… Objectives The objective of this hackathon is to improve the annotation of the Galaxy resources (tools, training, workflows) for microbial data analysis by: • Linking microbial Galaxy tools <https://galaxyproject.github.io/galaxy_tool_metadata_extractor/microgalaxy/> to bio.tools <http://bio.tools/> to obtain EDAM ontology annotation <https://edamontology.org/page> • Improving bio.tools annotations • Annotating existing microbial-related tutorials <https://training.galaxyproject.org/training-material/search2?query=microgal…> with EDAM terms • Reflecting on the addition of EDAM terms to workflows • Reflecting on missing terms in the EDAM ontology for microbial data analyses • Brainstorming about a way to connect tool annotations to improve training and workflow annotations All this work will be beneficial to structure the tools, workflows, and training we have to display them on the microGalaxy landing page <https://microgalaxy.usegalaxy.eu/>, structure the Galaxy tool panel, and create figures and tables for the technical paper <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> we are working on. General information • Date: March 11th - 15th 2024 (full week) • Location: Online with a • a Zoom room, open the whole week • 2 daily stand-ups to accommodate different time zones • Several brainstorming meetings • microGalaxy Matrix chat <https://matrix.to/#/%23galaxyproject_microGalaxy:gitter.im> for communication • Time: full day, 9/10am 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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Community meeting - Feburary 8th, 9am CET
by Paul Zierep 01 Feb '24

01 Feb '24

Dear all, I hope you are all doing fine! Here are some news about the microGalaxy community. *Next Community meeting* Next week, we will have a *Community meeting*, on *Thursday 8th October at 9am CET* (your timezone <https://arewemeetingyet.com/UTC/2024-02-08/08:00/microGalaxy>). - Meeting rolling minutes <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> - Zoom <https://us02web.zoom.us/j/82453101719?pwd=NlJudHk1c0xqSC83eXM4bTM1YWJ2UT09> (Meeting ID: 824 5310 1719; Passcode: micro) During this meeting, we will mostly catch up with news from the community and talk about the next months. Unfortunately, we could not organize a dedicated speaker, but we had an idea that could be very useful for our planned publications and the overall organization of the community tools. To improve the annotation of microbial-related tools, we would like to organize an event where we as a community link bio.tools entries to the galaxy wrappers in order to improve their EDAM terms. We will explain the details and how everybody can participate during this call. 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, 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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