December 2023 - microGalaxy - lists.galaxyproject.org

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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Technical Manuscript submitted to NAR
by Paul Zierep 15 Dec '23

15 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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by talhaaqeelwk＠gmail.com 12 Dec '23

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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