- microGalaxy - lists.galaxyproject.org

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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Engineer position in Galaxy workflows development for -omics data analysis in antibiotic resistance - France
by Bérénice Batut 07 Dec '23

07 Dec '23

Hi all, The French Institute for Bioinformatics (Institut Français de Bioinformatique) is looking for Engineer position in Galaxy workflows development for -omics data analysis in antibiotic resistance: More information there: https://www.sfbi.fr/emplois/offre/202311241133-cdd-engineer-position-in-wor… Feel free to spread about it to anyone that might be interested. Thanks, Bérénice --- Bérénice Batut (she/her) Researcher https://research.bebatut.fr

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Tell us about your workflows and tutorial - Before November 20th
by Bérénice Batut 09 Nov '23

09 Nov '23

Hi all, I hope you are doing well. As some of you know, we plan to write a paper for the NAR webserver issue which will give an overview of the resources (tools, workflow, training, etc) available for microbial data analysis in Galaxy. We started to work on the tool aspect and generated an interactive table listing 200+ tools: http://galaxyproject.github.io/galaxy_tool_extractor/microgalaxy/ Now, we would like to have an overview of the workflows and also tutorials available. For that, we started a spreadsheet: https://docs.google.com/spreadsheets/d/11Z1yXtS4GTER3QCyAIRqWupr5e43YFFKeMk… It would be great if you could add before November 20th in the spreadsheet any workflows or tutorial (not only on the GTN) you worked on that are related to microbial data Once we have them, we will make the workflows available on usegalaxy.eu, tag them with #microgalaxy so they will be displayed on the dedicated subdomain: https://microgalaxy.usegalaxy.eu/ If your workflow is available on usegalaxy.eu, usegalaxy.org, or usegalaxy.org.au, please add the #microgalaxy tag to it and they will be automatically visible in the subdomain And we will do the same for the tutorials. We will then start writing the manuscript and submit the 1 page by December 15th. Thanks for your help there, Best, Bérénice --- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

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microGalaxy paper WG meeting in <1 hour
by Bérénice Batut 18 Oct '23

18 Oct '23

Dear all, We plan to write 2 papers related to microbial data analysis in Galaxy. Interested to learn more about that and/or to contribute? Join our meeting in <1 hour (Zoom <https://us02web.zoom.us/j/82453101719?pwd=NlJudHk1c0xqSC83eXM4bTM1YWJ2UT09>, notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…>), check the notes, and/or let me know :) Best, Bérénice --- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

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Community meeting - October 4th & Paper WG meeting - September 26th
by Bérénice Batut 25 Sep '23

25 Sep '23

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 as part of the European Galaxy Days <https://galaxyproject.org/events/2023-10-egd>, on Wednesday 4th October at 4:30pm CEST (your timezone <https://arewemeetingyet.com/Berlin/2023-10-04/16:30/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. Working group meetings (calendar with all meetings <https://calendar.google.com/calendar/u/0/embed?src=npu7puk75n6p0u4aapv5t21u…>) Tomorrow, Tuesday 26th September, 3pm CEST (your timezone <https://arewemeetingyet.com/UTC/2023-09-26/13:00/microGalaxy>), we will have the Paper working group <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> meeting. We will talk about the user paper writing, in particular the use cases, the next steps, etc. 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 --- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

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Next community meeting
by Bérénice Batut 06 Jul '23

06 Jul '23

Hi all, The microGalaxy community will meet online next Monday (10th) at 5:30pm Brisbane time (9:30am CEST) as part of the Galaxy Community Conference. Anyone (even if not participating in GCC) is welcome to join it Zoom <https://us02web.zoom.us/j/82453101719?pwd=NlJudHk1c0xqSC83eXM4bTM1YWJ2UT09> Meeting rolling minutes <https://docs.google.com/document/d/13VjcUjStuIp7bK29e74k8Nqb7N4lmVcg1ioArEW…> I hope to see you around! Best, Bérénice --- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

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Next paper working group
by Paul Zierep 11 May '23

11 May '23

Hi all, The next microGalaxy Working group meeting for the Paper working group <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> will take place June 13th, 1pm UTC Main Topics: - First impression of the survey (59 Answers) - Template for the people who want to join the community-oriented paper - Ideas for the community-oriented paper We hope to see you around! -- 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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Next community meeting and other news
by Bérénice Batut 02 May '23

02 May '23

Hi all, Here are some news about the microGalaxy community of practice ** *The next microGalaxy community meeting will take place on May 4th 3-5pm UTC*(check yourtimezone) <https://arewemeetingyet.com/UTC/2023-05-04/15:00/microGalaxy> * 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) * * *Working group meetings*(calendar with all meetings <https://calendar.google.com/calendar/embed?src=npu7puk75n6p0u4aapv5t21uj8%4…>) * Paper working group <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…>: May 2nd, 1pm UTC (survey, user-oriented paper) * Tool working group <https://docs.google.com/document/d/14LJLyVgT29m63iovCww7nMDmfRAqOicedzxHu3a…>: April 6th, 7am UTC (survey, BioHackathon proposal) * * *Survey* We launched a*survey*to reach out to, and learn from, the microbial research community, about*use cases*where Galaxy was beneficial, and also the barriers*that prevent researchers from using Galaxy*. with the aim is to collectively*find solutions*to improve user experience and reduce barriers:https://forms.gle/q8LizeoHCxjjQp559 <https://forms.gle/q8LizeoHCxjjQp559> *Please fill the survey and share it around you and your communities.* You can find more information about this survey and how we plan to use the information collected on the dedicated post here:https://galaxyproject.org/news/2023-03-21-microbial-survey <https://galaxyproject.org/news/2023-03-21-microbial-survey> I hope to see you around! Best, Bérénie -- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

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