- microGalaxy - lists.galaxyproject.org

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

1 2

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

1 0

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

1 2

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

1 2

Workshop for pathogen detection from sequencing data using Galaxy - February 2nd, 2023
by Bérénice Batut 04 Jan '23

04 Jan '23

Hi all, First of all, happy new year! We organize a practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy * Date: February 2nd, 2023 * Location: FHNW, Switzerland & online * Free * Info & Registration : https://galaxyproject.org/events/2023-02-02-foodborne-pathogen-detection-wo… Feel free to share the information with anyone that would be interested. Best, -- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

1 0

Draft for a page on Hub, tool list, next meeting and more news
by Bérénice Batut 17 Oct '22

17 Oct '22

Dear all, I hope you are doing well! Here are some news about the microGalaxy community. *Previous meeting - October 5th during European Galaxy Days* During our last meeting 2 weeks ago (see notes <https://docs.google.com/document/d/13VjcUjStuIp7bK29e74k8Nqb7N4lmVcg1ioArEW…>), we discussed: * We would like to create a page on the Galaxy Hub collecting tools, workflows, projects, etc and present the microGalaxy community o We created a draft for such page on Google doc <https://docs.google.com/document/d/1SsUi5ZOxWbkCpnw1IYmDR0WpRK0csVMHzYhuME5…> o We would like *your feedback on the structure* o *Could you also add some details about your projects and nice papers using Galaxy for microbial data analysis? * * The Hub page could be a starting point for a possible paper to show / advertise microb* analyses are possible in Galaxy, and also define a vision for the next years o *If you are interested in leading this effort, please let us know* * * *Next meeting - February **9, 2023, 9-11am CEST* The next microGalaxy meeting will take place on *February 9, 2023, 9-11am CEST***(check your timing) <https://arewemeetingyet.com/Berlin/2023-02-09/09:00/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) If you are *interested in giving a talk*, please either contact me or add your name in the table on the first page of the minutes. Best, Bérénice -- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

1 0

Next meeting - BoF at EGD - October 5th + Subscribe to the mailing list (last call)
by Bérénice Batut 30 Sep '22

30 Sep '22

Dear all, I hope you are doing well! Here are some news about the microGalaxy community. *Next meeting**- October 5th during European Galaxy Days * The next microGalaxy meeting will take place on *October 5th(likely 4 or 5 pm CEST, to confirm*) as an hybrid BoF during European Galaxy Days <https://galaxyproject.org/events/2022-10-egd/> * 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) Aaron will give a talk about IRIDA and we would like to talk about next steps for the community (page on the Hub, paper?, hackathon). *Mailing list* We have now a mailing list for microGalaxy (microgalaxy(a)lists.galaxyproject.org) I will in the future only use the mailing list. So if you want to be kept informed, please subscribe here: https://lists.galaxyproject.org/lists/microgalaxy.lists.galaxyproject.org/ <https://lists.galaxyproject.org/lists/microgalaxy.lists.galaxyproject.org/>: Best, Bérénice -- Bérénice Batut (she/her) Researcher University of Freiburg de.NBI / ELIXIR-DE https://research.bebatut.fr

1 2

Next meeting - BoF at GCC - July 17th, 5:15pm CDT
by Bérénice Batut 13 Jul '22

13 Jul '22

Dear all, I hope you are doing well! Here are some news about the microGalaxy community. *Next meeting**- July 17th during GCC * The next microGalaxy meeting will take place in few days (*July 17th <https://arewemeetingyet.com/Chicago/2022-07-17/17:15/microGalaxy>, 5:15pm CDT*) during GCC as a BoF <https://gcc2022.sched.com/event/c7bbada233915ab512408f73d7749679> * 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) I hope I will see some of you there. I do not expect anyone from EMEA (middle of the night). *Next meetings** * As we discussed last time, we would like to change the timing for the next meetings by alternating every time between timing fitting for EMEA & AMER and timing fitting for EMEA & APAC. My suggestion would be * 2-4pm European time (EMEA, AMER) * 9-11am European time (EMEA, APAC) How does the time look like for you? Would you have other proposition? Normally the next meeting should be September 9th. But we shifted our June meeting by a month to align with GCC. What do you think about shifting our next meetings by a month too? *Mailing list* We have now a mailing list for microGalaxy (microgalaxy(a)lists.galaxyproject.org) You can subscribe here: https://lists.galaxyproject.org/lists/microgalaxy.lists.galaxyproject.org/ <https://lists.galaxyproject.org/lists/microgalaxy.lists.galaxyproject.org/> Best, Bérénice

1 0

Mailing list + Next meeting - March 10th, 2-4pm CET
by Bérénice Batut 09 Mar '22

09 Mar '22

Dear all, I hope you are doing well! Here are some news about the microGalaxy community. *Mailing list* We have now a mailing list for microGalaxy (microgalaxy(a)lists.galaxyproject.org) You can subscribe here: https://lists.galaxyproject.org/lists/microgalaxy.lists.galaxyproject.org/ <https://lists.galaxyproject.org/lists/microgalaxy.lists.galaxyproject.org/> *Next meeting** * The next microGalaxy meeting will take place on *March**10th, 2-4pm CET* <https://arewemeetingyet.com/Berlin/2022-03-10/14:00/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) Currently at the agenda, we have 2 confirmed talks by Pratik and Engy and maybe a 3rd one, and also time for discussion :) The next meetings will happen every 3 months, on 2nd Thursday, 2-4pm European time (possible to modify) (Google calendar with all planned meetings <https://calendar.google.com/calendar/u/1?cid=bnB1N3B1azc1bjZwMHU0YWFwdjV0Mj…>). If you would like to give a talk about your project(s), tools, workflows, data, training, or anything else in a next meeting, please add yourself to the table on the 1st page of of the meeting rolling minutes <https://docs.google.com/document/d/13VjcUjStuIp7bK29e74k8Nqb7N4lmVcg1ioArEW…>. 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

1 1

[µGalaxy] microGalaxy mailing list
by Valerie Schiml 09 Dec '21

09 Dec '21

Hi, Please have me in your mailing list: valerie.schiml(a)nmbu.no<mailto:valerie.schiml@nmbu.no> Best Valerie

1 0