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    M Bernt
    @bernt-matthias
    18.01 or highrer
    Thomas N Lawson
    @Tomnl
    OK thanks
    M Bernt
    @bernt-matthias
    Apropos sirius .. this is also part of the OpenMS wrappers .. as I just noticed.
    Melanie C. Föll
    @foellmelanie
    Hi metabolomics folks, maybe you are interested in this online conference. It takes place every Friday, next week is compound ID and you can still submit your work for an one slide (poster) presentation: https://docs.google.com/forms/d/e/1FAIpQLSfo6-wzlXDGqHxVc7GI8asZXJN4uIFLtiR9vwpohynxnQFYEA/viewform
    Ralf Weber
    @RJMW
    @foellmelanie - sorry I am only now reading your message. Yes I can highly recommend these webinar series.
    korseby
    @korseby
    Hi all. We have just updated the MetFrag tool from the MSpurity suite. Can you update the tool? Can you also install the new metfrag-vis tool? Thanks and best wishes.
    Arthur Eschenlauer
    @eschen42
    @Tomnl Is there a relatively simple way to set up MOGI, especially to use UseGalaxy.eu? I have a client that would be interested in doing metabolomics with ISA and Galaxy, and MOGI seems like an attractive option.
    miaomiaozhou88
    @miaomiaozhou88
    Dear trainers, here at Avans University of Applied Sciences is planning to have a training session on metabolomics by using MALDI and LC-MS (XCMS) on galaxy. We found these great tutorials on the galaxy training portal, we would really love to invite one of you to give us a hand on this training session. The date would be 05-06 November 2020, the training will be online due to COVID restrictions. Would anyone be so kind to help out?
    BTW, avans university of applied sciences is located at Breda, the Netherlands :-)
    Carolin Huber
    @chufz
    Hi all, is there a Galaxy wrapper for the xcms- diffreport function including the plotting?
    Guitton Yann
    @yguitton
    Hi Carolin (@chufz ), in https://workflow4metabolomics.usegalaxy.fr/ we split the diffreport in 2 matrices variableMetadata where you'll find mz mzmin...npeaks columns and dataMatrix where you'll find intensity fro features. you can use the "Table Merge" wrapper if you want to get an equivalent of the diffreport. For ploting you mean EICs those can be generated by the CAMERA.annotate function and they will be saved in a zip folder or a PDF.Just a not the statistical part of diffreport have been removed from our table as we think that it's best to correct batch effect and normalise data before doing any kind of statistics. Hope it helps.
    Pratik Jagtap
    @pratikomics_twitter

    Summary of Galaxy Mass Spectrometry October 15th meeting.

    1) Metabolomics researchers - please respond to Doodle survey for a bi-monthly meeting: https://doodle.com/poll/rbemey7afzznf37g#calendar

    2) Vijay Nagampalli (Blankenberg Lab) presented on Mass Spectrometry research tools needs.

    3) Next Galaxy meetings –
    a) Proteomics 26th November 2020 and January 7th 2021 at 1 PM GMT
    b) Mass Spectrometry February 18th, 2021 at 1 PM GMT.

    4) Details of prior meetings at: http://z.umn.edu/celestialmasses

    5) Gitter channels:
    For Proteomics: https://gitter.im/GalaxyProteomics/Lobby
    For Metabolomics: https://gitter.im/usegalaxy-eu/metabolomics
    https://gitter.im/workflow4metabolomics/Lobby

    Melanie C. Föll
    @foellmelanie
    Hi @/all Galaxy metabolomics researcher,
    I am starting to organize a bimonthly Galaxy metabolomics meeting and have a doodle open until Friday to find a weekday and time that fits most: https://doodle.com/poll/rbemey7afzznf37g#table.
    The idea behind these informal meetings, is to bring together all Galaxy metabolomics researchers, including users and developers to have an easier exchange of needs, ideas, discuss scientific results and find new collaborators and general synergies in the community. I plan to start the meetings in December, run it until GCC and then decide if the format needs adjusting or can be continued as it started.
    Please spread the word to everyone interested.
    Thanks,
    Melanie
    Melanie C. Föll
    @foellmelanie
    Hi, I would like to invite you @/all to the first Galaxy metabolomics call on Thursday. A bit more information is here: https://galaxyproject.eu/event/2020-11-24-metabolomics/ To obtain the zoom link write me via mail or gitter or subscribe to the mailing list. Hope to see many of you in the call. Best, Melanie
    M Bernt
    @bernt-matthias
    @foellmelanie do you plan to record the meeting? I can't make it.
    Melanie C. Föll
    @foellmelanie
    I am sorry that you can't make it. I am not planning to record it, but we'll take some notes and maybe the presenters agree to share their slides in this channel or via the new mailing list.
    Melanie C. Föll
    @foellmelanie

    Copy of Email that was send to the new Galaxy metabolomics mailing list:

    Dear Galaxy Metabolomics researchers,
    Thank you for joining the call today.

    We created a new google drive folder: https://drive.google.com/drive/folders/1aZWbLDluwZo65owthJ4yMWiHlnoooqv1
    in which you’ll find two subfolders. The meeting notes and slides of today are in the “call” folder and the other folder “Minisymposium” contains a document for the planned Minisymposium.
    In case you missed today’s call, feel free to sign in your name, interests and needs into the “profile” section of the meeting notes document.

    We agreed on holding a Minisymposium in January/February at European morning times (9 am to 12pm) to get to know each other better and give everyone a chance to present their research.
    Everyone interested in joining the Minisymposium please fill in your availability in the doodle link until 18th December:
    https://doodle.com/poll/3d9k9xif7d5mfxft?utm_source=poll&utm_medium=link
    Please also fill in your details into the spreadsheet until 18th December for joining (don’t fill in column with talk title) and presenting (fill in talk title in column) at the Minisymposium: https://docs.google.com/spreadsheets/d/1PiWVL_V01n6jNEkFC5roWFDxIBffZ3FUnvCV3sFGpeE/edit?usp=sharing

    Please feel free to share all the content with interested colleagues and invite them to join or present at the Minisymposium.

    Best wishes,
    Melanie & Bea

    M Bernt
    @bernt-matthias
    thanks for the update @foellmelanie
    Helge Hecht
    @hechth
    Hi everyone - any update on the Symposium?
    Melanie C. Föll
    @foellmelanie
    Hi all, sorry for the late notice. The Mini-Symposium will happen on Friday 29th January from 9 - 12 CET via zoom. More information will follow soon.
    we might have a few last minute presentation slots open so if anyone is interested please let me know ASAP
    Helge Hecht
    @hechth
    Hi Melanie, Thank you for the update!
    Melanie C. Föll
    @foellmelanie
    Hi all, in case you registered for the Galaxy Metabolomics Mini-Symposium on Friday you should have received an email with the zoom link. More information about the event here:
    https://usegalaxy-eu.github.io/event/2021-1-25-Metabolomics-Mini-Symposium/plain.html
    Martin Cech
    @martenson
    For anyone else that forgot, today's call was cancelled during the symposium, next one is in April. :)
    Melanie C. Föll
    @foellmelanie
    Actually we decided to continue with a bi-monthly rhythm after the symposium. The next dates are March 11, May 6 (originally announced as May 13, but this is a holiday in Germany from where we had a lot of participation)
    Martin Cech
    @martenson
    Thanks for the update, it seems my calendar is a mess.
    Beatriz Serrano-Solano
    @beatrizserrano
    Hi all, just in case you are not aware of it, you might find this course interesting
    M Bernt
    @bernt-matthias

    The IWC (Intergalactic Workflow Commission) has recently made some progress:

    • we have now automated testing of submitted workflows (with planemo)
    • and we also have automatic deployment (which allows easier installation on Galaxy instances)

    IWC would be happy about submissions of workflows. So if you have finished workflows open a PR over here: https://github.com/galaxyproject/iwc

    Gildas Le Corguillé
    @lecorguille
    Do you plan to add automatically the ones already available within the GTN materials?
    Martin Cech
    @martenson
    @lecorguille I assume IWC targets more "production-ready" workflows. I could be wrong though.
    M Bernt
    @bernt-matthias
    @lecorguille if they are production ready yes, but not automatically at the moment.
    Gildas Le Corguillé
    @lecorguille
    I guess that the one in the GTN are rather close to some production workflow. The reduction is mainly handle by the dataset. And by the way, you will always have some adaptation to do to suit your real data or study.
    Do you plan a link with https://workflowhub.eu/ ?
    Melanie C. Föll
    @foellmelanie

    I's time for another Galaxy metabolomics call. Please join us on May 6, 2 pm CET via the zoom https://us02web.zoom.us/j/83058868819?pwd=djB0RWtwSXUzZjJvbk5wcGJoWktTUT09

    Meeting ID: 830 5886 8819
    Passcode: 720575

    We'll have a guest speaker: Amrita Cheema, Georgetown University School of Medicine in Washington DC will present "Radiometabolomics: Identification of Metabolic Predictors of Radiation Late Effects". Amrita is involved in the ABRF Metabolomics Research Group (https://www.abrf.org/metabolomics-mrg- ) and I hope we can discuss with her also about training and standardization in metabolomics.

    Melanie C. Föll
    @foellmelanie
    it's actually central european summer time, so the meeting starts now
    Gildas Le Corguillé
    @lecorguille
    Have a nice meeting! Unfortunately I can’t join.
    Melanie C. Föll
    @foellmelanie
    We meet today to prepare CoFest, everyone interested is welcome to join: Thursday 1st July 12 pm CEST via Zoom:
    https://northeastern.zoom.us/j/99385202340?pwd=a0FWSW5XbVV6bkFrYXRoZDZOVjI5dz09
    Meeting-ID: 993 8520 2340
    Kenncode: 283064
    Next Meeting: during the Galaxy conference there will be a joint Galaxy metabolomics and proteomics meeting to discuss the current state and the future of the communities. Regardless of the Galaxy conference attendance the meeting is open to everyone interested: Wednesday July 7th 3.20pm CEST to 4.40pm:
    https://umn.zoom.us/j/98449669068?pwd=WlQwWW5mbGt5MlJCYzlNYjhTSFpvUT09 (ID: 98449669068, password: XE6UD7)
    Matt Padula
    @Matt_Padula_twitter
    From a Twitter post by Brett Phinney, I ended up here: https://metabolomics.blog/2021/07/slaw/. I have only read the blog post and have no data to test this pipeline out, but it might be worth looking at as an addition to Galaxy for metabolomics.
    Johan Gustafsson
    @supernord
    @foellmelanie - maybe this pipeline can be added to the list for cofest?
    Melanie C. Föll
    @foellmelanie
    It looks interesting indeed. For CoFest it seems too much work. In general we might first want to fill gaps in functionalities in Galaxy before we bring new options for existing functionalities?
    Maybe XCMS users can comment on how happy/unhappy they are with it in Galaxy, I assume several of the points they didn't like about it will not happen within Galaxy?
    Melanie C. Föll
    @foellmelanie

    Topic: Metabolomics call
    Time: Sep 9, 2021 02:00 PM Amsterdam, Berlin, Rome, Stockholm, Vienna

    Join Zoom Meeting
    https://us02web.zoom.us/j/85169523832?pwd=SllUcUVQNk01T1BYZEt6WlVtOHNOZz09

    Meeting ID: 851 6952 3832
    Passcode: 905720

    tp175
    @tp175
    Hi, I’m using metabolomics.usegalaxy.eu to run some analysis over a MetaboLights study (MTBLS169) and found an error re ‘xcms get a sampleMetadata file’ – when extracting file names, certain characters are replaced “,”, “-“ with “’.” which causes errors downstream. Please revise… thanks!
    Melanie C. Föll
    @foellmelanie
    During paper cuts today we are working on the 'Galaxy Metabolomics Tool Compendium', please let me know if you want to join and I will give further instructions.
    Guitton Yann
    @yguitton
    @tp175 Hi, I've you tried teh check_format tool? toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0 the option "Make syntactically valid sample and variable names" may do the job
    tp175
    @tp175
    Hi @yguitton – thanks for the suggestion, though the link seems to be broken “An error occurred while processing your request: no such method: checkFormat”. No problem, I solved this by making my own ‘sampleMetadata file’ – I just thought someone should be aware etc
    Melanie C. Föll
    @foellmelanie
    Hi all, I would like to invite you to tomorrows Galaxy metabolomics call (March 10, 2pm CET). Claire O’Donovan will speak about "Metabolights and it’s community". Zoom link: https://uni-freiburg.zoom.us/j/69841228126?pwd=TTdrUjFOcXVTTEV1em9VN203MHNIUT09
    Meeting-ID: 698 4122 8126
    Kenncode: 6BNZr6Tgc
    Guitton Yann
    @yguitton
    @PGbioinf Maybe already solved on your side (since 2021^^) But just to let you know that a new HMDB tool with updated access is available https://toolshed.g2.bx.psu.edu/view/fgiacomoni/hmdb_ms_search/d8e2ede293a6
    PGbioinf
    @PGbioinf
    @yguitton thank you so much for the update :-)