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    Padraig Gleeson
    @pgleeson
    The updated documentation for the Open Source Brain platform, for both versions 1 and 2, can be found here: https://docs.opensourcebrain.org
    FranciscoD_
    @ankursinha:fedora.im
    [m]
    looking to see if there's a way to pin messages on gitter or matrix ..
    doesn't look like it, added it to the topic in the meantime
    FranciscoD_
    @ankursinha:fedora.im
    [m]

    @pgleeson: for Figshare, do we want to limit ourselves to datasets only? At the moment, the way it's implemented is that resources like this one can be imported as a repository:

    https://figshare.com/articles/presentation/Presentation_1_NWB_Query_Engines_Tools_to_Search_Data_Stored_in_Neurodata_Without_Borders_Format_pdf/12962813

    It's only because we haven't made the regex specific enough to limit URLs with dataset in it.
    Padraig Gleeson
    @pgleeson
    @ankursinha:fedora.im I think it's fine to allow adding a Figshare repository like that. There may well be something in a repo with documents that could form the basis of a workspace, e.g. if it's a spreadsheet, or pdf containing tables, or even extracting plot values from figures in pdfs...
    1 reply
    Ankur Sinha (FranciscoD@fedora)
    @ankursinha:fedora.im
    [m]
    anhknguyen96: hiya, this is the right channel---are you able to post in here?
    anhknguyen96
    @anhknguyen96:matrix.org
    [m]
    Yes I think
    I created a channel that included you and Padraig, not sure why you didn't get the message there
    1 reply
    Ankur Sinha (FranciscoD@fedora)
    @ankursinha:fedora.im
    [m]
    Let's use the channel here for all our discussion, we should only resort to closed channels if there's something private we need to discuss. Otherwise it's better to "default to open".
    FranciscoD|homeserver
    @sanjay_ankur:matrix.org
    [m]
    This is me from the second account---I don't see a private message invitation there either, unfortunately :/
    anhknguyen96
    @anhknguyen96:matrix.org
    [m]
    :/ anyway, thanks
    Right now to view NWB files on NWBE, users have to paste a url to the file. Has the option of opening NWBE with an already downloaded NWB file been looked into?
    Ankur Sinha (FranciscoD@fedora)
    @ankursinha:fedora.im
    [m]
    It's been discussed, but I don't think we've made any progress on that front yet. The idea currently is that NWBE is used in the new Open Source Brain v2 platform. So you'd upload your NWB file as a resource to the workspace, and then open it using NWBE there
    I do seem to remember that one could access a NWB file from the local file system in NWBE, but I can't quite remember what the method was. I think one had to use a special file:///... URL, but I'll have to double-check that.
    anhknguyen96
    @anhknguyen96:matrix.org
    [m]
    For the task I'm working on, checking compatibility of (possibly) all files on dandi, NWBE having access to local file system would make a streamlined workflow
    1 reply
    Please check that, thank you :)
    I also have some ideas but I think that would require working with geppeto and/or java
    Ankur Sinha (FranciscoD@fedora)
    @ankursinha:fedora.im
    [m]
    But it cannot open files from other systems because that'll require it to first "upload" the file, and this has not yet been implemented
    So, you can't use the instance at nwbexplorer.opensourcebrain.org with local files. You'll have to run your own NWBE instance to be able to use files from your computer
    How are you testing for compatibility? Are you downloading each file and loading it manually in NWBE (is that the idea?)?
    anhknguyen96
    @anhknguyen96:matrix.org
    [m]
    Well that's the primitive idea, which is also a concern I raised because it seem unfeasible given the number of datasets we have. If compatibility means being able to viewed and interacted with on the NWBE, I don't know other way besides doing it on a file-by-file basis. The downloading part can be done systematically with datalad though.
    Ankur Sinha (FranciscoD@fedora)
    @ankursinha:fedora.im
    [m]
    Hrm, yeh. There are far too many files though, so we're going to have to think of a way to automate this---you doing it one by one is not going to scale (and it'll be very boring too..)
    anhknguyen96
    @anhknguyen96:matrix.org
    [m]
    Agreed...
    Ankur Sinha (FranciscoD@fedora)
    @ankursinha:fedora.im
    [m]
    So before a NWB file is valid for NWBE, it needs to be valid NWB, right?
    as in, NWBE will probably support a subset of the NWB standard---but the file should adhere to this standard and be valid according to pynwb?
    anhknguyen96
    @anhknguyen96:matrix.org
    [m]
    Yes
    Ankur Sinha (FranciscoD@fedora)
    @ankursinha:fedora.im
    [m]
    so what we could perhaps do is see what aspects of the NWB standard NWB supports, and then check against those?
    so:
    • first, check if file is valid against standard using pynwb
    • if it is, check against parts of NWB standard that NWBE should already support
    anhknguyen96
    @anhknguyen96:matrix.org
    [m]
    Ah makes sense
    Ankur Sinha (FranciscoD@fedora)
    @ankursinha:fedora.im
    [m]
    so instead of you manually uploading files to NWBE, we take a look at the code to see what bits of the NWB standard are being read/processed by NWBE?