Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    fgiacomoni
    @franckgiacomoni_twitter
    Hello @/all, the W4M team is thinking about this organization - @lecorguille, Gildas should come back soon with our plan.
    Gildas Le Corguillé
    @lecorguille
    Here it’s: https://github.com/workflow4metabolomics/tools-metabolomics
    So indeed, there is still only the xcms tools (I rename the xcms one and add the iuc ci) but I plan to transfert the camera ones quickly.
    The other w4m repos will join this one gradually.
    M Bernt
    @bernt-matthias
    Hey there. We just finished the genform tool and wonder where to open the PR... Is the W4M fine for everybody?
    Gildas Le Corguillé
    @lecorguille
    Still ok for us.
    Ralf Weber
    @RJMW
    Where is the current repo? Fine with me.
    M Bernt
    @bernt-matthias
    Already done :) .. will just finish the test cases then the PR is ready
    Gildas Le Corguillé
    @lecorguille

    Can you broadcast this event on your different networks, please:

    The French Institute of Bioinformatics (IFB, Elixir-FR) and the Infrastructure for Metabolomics and Fluxomics (MetaboHUB) organize in collaboration with the Université libre de Bruxelles the next Workflow4Experimenters International Course (W4E2020).
    Venue: Brussels, Belgium

    Analyze your own data with Galaxy and the Workflow4metabolomics e-infrastructure! The next Workflow4Experimenters international course (W4E2020) will take place in Brussels (February 3 to February 7, 2020). During this one-week course (entirely in English), you will learn how to use Galaxy and the W4M infrastructure to analyze your own LC-MS, GC-MS, or NMR data set. Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring.

    Invited speakers: Dr S. Marr (Leibniz Institute of Plant Biochemistry, Germany), Dr R. Weber (Phenome Centre Birmingham, United Kingdom), Dr N. Poupin (Unité Toxalim, INRA Toulouse, France)

    Registrations: https://workflow4metabolomics.org/w4e2020
    Contact: contact@workflow4metabolomics.org

    The deadline for pre-registration has been postponed to November 03rd.

    Ralf Weber
    @RJMW
    Yes - will do
    M Bernt
    @bernt-matthias
    I'm just about to add some datatypes required for OpenMS: galaxyproject/galaxy#8109. Comments and wishes are very welcome
    Thomas N Lawson
    @Tomnl
    Hi all, I was hoping someone might be able to help with some issues with MetFrag and SIRIUS CSI:FingerID on usegalaxy.eu
    Thomas N Lawson
    @Tomnl
    MetFrag is giving the following error computational-metabolomics/metfrag-galaxy#25 . It seems that to get CDK to work - a folder needs to be created within the user directory (in the case of usegalaxy.eu this location is /opt/galaxy/.jnati/)
    Also SIRIUS CSI:FingerID is taking a long time to finish tasks (which take a much shorter time locally). This is perhaps down to the resources given. Is there any way to check how much resources is given to a tool on usegalaxy.eu?
    Simon Bray
    @simonbray
    I guess CDK is creating a cache for some reason - hopefully there's some way to disable this as tools aren't expected to create files outside of the job working directory.
    @ resources: if you click on 'View details' on a job there should be some information under the 'Job Metrics' section
    M Bernt
    @bernt-matthias
    Seems to try to write to home http://jni-inchi.sourceforge.net/faq.html
    Simon Bray
    @simonbray
    it's also possible to increase the resources allocated to a certain tools, I believe this is defined on this page: https://github.com/usegalaxy-eu/infrastructure-playbook/blob/master/files/galaxy/dynamic_rules/usegalaxy/tool_destinations.yaml
    Thomas N Lawson
    @Tomnl
    @ resources: Is that only visible after the job has finished?
    Simon Bray
    @simonbray
    I think so yes
    Thomas N Lawson
    @Tomnl
    OK thanks - I will leave SIRIUS for the weekend to see if it finishes. But if it doesn't finish I might change the resources to match what we use at Birmingham - and see if it runs at a similar speed
    Regarding jni-inchi writing to home. Is it possible to change the location of "home" in a conda enviroment?...
    ... probably not. It might be possible to include the relevant files in the build though
    M Bernt
    @bernt-matthias
    I thing you need to set the tool's profile to some recent galaxy version. than each job gets a HOME as far as I know
    Thomas N Lawson
    @Tomnl
    Does that mean adding something like "<tool profile="19.09" ...>" into the Galaxy tool XML?
    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
    hechth
    @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
    hechth
    @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.