- microGalaxy - lists.galaxyproject.org

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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Evaluation of uses and needs for microbial data analysis in Galaxy - A survey
by Bérénice Batut 21 Mar '23

21 Mar '23

Hi all, We would like to learnmore about use caseswhere Galaxy was beneficial, and also the barriersthat prevent researchers from using Galaxy. The aim is to collectively find solutions to improve user experience and reduce barriers. To this end, we launch a short survey (open untilApril 20th) to reach out to and learn from the microbial research community: https://forms.gle/q8LizeoHCxjjQp559 We encourage anyone to fill out this survey who: * has used Galaxy for any kind of microbial focused research (e.g. metagenomics, metatranscriptomics, microbiome, bacterial isolates … ), or * conducts microbial research or is planning to do so, but has not yet used Galaxy, or is hindered by certain aspects of Galaxy from using it. You can find more information about this survey and how we plan to use it on the dedicated post here: https://galaxyproject.org/news/2023-03-21-microbial-survey Please feel free to share this survey with anyone around you, or in your communities (I pasted a template email/post below and attached a visual) Thank you for your help supporting better microbial data analysis in Galaxy! Best, Bérénice ---- *Template* Subject: Evaluation of uses and needs for microbial data analysis in Galaxy - A survey Dear <Community>, Galaxy is an open-access, web-based platform for data-intensive computational research. It is used in a variety of domains including microbial data analysis: for microbiome samples or bacterial isolates, long reads or short, shotgun or 16S, genomics, transcriptomics, or proteomics. microGalaxy <https://galaxyproject.org/projects/microbial/#microgalaxy-community>, a community of practice focused on microbial data analysis in Galaxy, would like to learnmore about use caseswhere Galaxy was beneficial, and also the barriersthat prevent researchers from using Galaxy. The aim is to collectively find solutions to improve user experience and reduce barriers. To this end, we launch a short survey (open untilApril 20th) to reach out to and learn from the microbial research community: https://forms.gle/q8LizeoHCxjjQp559 We encourage anyone to fill out this survey who: * has used Galaxy for any kind of microbial focused research (e.g. metagenomics, metatranscriptomics, microbiome, bacterial isolates … ), or * conducts microbial research or is planning to do so, but has not yet used Galaxy, or is hindered by certain aspects of Galaxy from using it. You can find more information about this survey and how we plan to use it on the dedicated post here: https://galaxyproject.org/news/2023-03-21-microbial-survey Please feel free to share this survey with anyone around you, or in your communities! Thank you for your help supporting better microbial data analysis in Galaxy! <Your name> On behalf of the microGalaxy community -- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

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Paper and Tool working group meetings
by Bérénice Batut 02 Mar '23

02 Mar '23

Dear all, During our meetings 2 weeks ago, we decided to start 2 working groups: 1 for tool and 1 for paper(s) If you want to participate to any of this working group, please *fill the following forms before the 2nd of March* to find the meeting date * Tool working group <https://doodle.com/meeting/participate/id/eXQvNnoa> * Paper working group <https://doodle.com/meeting/participate/id/ax6AKzqd> If none of the dates or hours fit for you and you want to participate, please let me know so I can try to find extra slots. Thank you! Best, Bérénice -- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

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Next meeting - February 9th
by Bérénice Batut 09 Feb '23

09 Feb '23

Dear all, I hope you are doing well! Here are some news about the microGalaxy community. *Next meeting**- February 9th * The next microGalaxy meeting will take place on *February 9th8:00-10:00am UTC *(check your timezone) <https://arewemeetingyet.com/UTC/2023-02-09/08:00/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) Daniela Brites from the Swiss Tropical and Public Health Institute will give a talk. *Other news* /List of tools in Galaxy:/ <https://docs.google.com/spreadsheets/d/1Nq_g-CPc8t_eC4M1NAS9XFJDflA7yE3b9hf…>//A curated list of tools available in Galaxy and their metadata automatically extracted from different GitHub repositories using a dedicated script <https://github.com/bebatut/galaxy_tool_extractor>. In addition, we have a wishlist that is manually created. /Page on the Hub about Microbial data analysis in Galaxy: /We started a draft <https://docs.google.com/document/d/1SsUi5ZOxWbkCpnw1IYmDR0WpRK0csVMHzYhuME5…> for a page on Hub to present the effort of the community regarding Microbial data analysis in Galaxy. The idea is to collect available tools, workflows, and training but also use cases/applications, projects, publications, etc. We would your help there. So *please review/expand it.* * * I hope to see you during the next meeting. Best, Bérénice -- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

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