- microGalaxy - lists.galaxyproject.org

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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Technical Manuscript submitted to NAR
by Paul Zierep 14 Dec '23

14 Dec '23

Dear all members and friends on the microGalaxy Community. Bérénice, Engy and me just submitted the one-page summary for the technical manuscript to the NAR web server issue. Thank you all for your contribution and support ! It is very convincing, and we are confident, that it will be accepted. If accepted, we got one month to write the actual manuscript. Therefore, we should meet early in January to discuss the structure, figures, and responsibilities. You can still become an author if you would like to contribute. Please fill out the doodle https://doodle.com/meeting/participate/id/eEZYkLga, and I will set a meeting after the Christmas break, preferably early in January. Also, thank you all very much for contributing your workflows! For the manuscript, those must be listed on the microGalaxy subdomain, so if you have not done so, we ask again to please make them visible by importing them to usegalaxy.eu, usegalaxy.org, or usegalaxy.org.au; make them public and tag them with #microgalaxy, so they will be displayed on the dedicated subdomain: https://microgalaxy.usegalaxy.eu/ Thank for all for your help, have a great and relaxed Christmas, and looking forward to meeting you next year! 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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12 Dec '23

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NAR tool paper submission and next meeting
by Paul Zierep 07 Dec '23

07 Dec '23

Hi all, I hope you are doing well. As stated in the last announcement, we plan to write a NAR web server issue which will give an overview of the resources (tools, workflow, training, etc) available for microbial data analysis in Galaxy. We wrote a first draft of the one-page summary and cover letter for the NAR web server issue, which needs to be submitted by December 15th. We would highly welcome feedback and comments on this, so please feel free to contact me if you could help and contribute, and I will add you to the document. Thank you !! all for the great selection of workflows and tutorials you provided in the sheet: https://docs.google.com/spreadsheets/d/11Z1yXtS4GTER3QCyAIRqWupr5e43YFFKeMk… Feel free to add more workflows or tutorials (not only on the GTN) you worked on that are related to microbial data, we will try to collect as many as we can until submission. Please also help to make them visible by importing them to usegalaxy.eu, usegalaxy.org, or usegalaxy.org.au; make them public and tag them with #microgalaxy, so they will be displayed on the dedicated subdomain: https://microgalaxy.usegalaxy.eu/ The same tag can be used for GTN tutorials. Assuming that we will be allowed to submit the paper; I would propose to meet early next year to discuss who wants to contribute and how to divide the work. Please fill out the doodle to find a good time for the next meeting https://doodle.com/bp/paulzierep/next-microgalaxy-paper-wg. Thanks for your help, and looking forward to meeting you next year! 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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