Chat room for users/developers of the Open Source Brain platforms. Please find the updated documentation at https://docs.opensourcebrain.org.
The updated documentation for the Open Source Brain platform, for both versions 1 and 2, can be found here: https://docs.opensourcebrain.org
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
@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:
It's only because we haven't made the regex specific enough to limit URLs with
dataset in it.
@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...
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I created a channel that included you and Padraig, not sure why you didn't get the message there
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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".
This is me from the second account---I don't see a private message invitation there either, unfortunately :/
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?
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.
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
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Please check that, thank you :)
I also have some ideas but I think that would require working with geppeto and/or java
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?)?
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.
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..)
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?
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
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?
This should be automatable. And of course, we can pick a few files here and there to verify that the results from this automated validation do reflect what NWBE is able to load
I'm afraid this will require you to dive into the NWB code a little. I did look into it a year ago, so I remember a little of how it works.
Do you want to go through it yourself and then we can discuss it at a meeting and see what we know about it together?
Your starting point will be here:
https://github.com/MetaCell/nwb-explorer/tree/master/nwb_explorer/nwb_model_interpreter
here's a quick summary of how it works:
- it loads NWB using PyNWB and creates a "nwb model"
- the UI bits are javascript etc., and know how to work with a particular model, called the "geppetto model" (because the tool is called geppetto)
- to show an NWB file in the UI, it maps bits of the "nwb model" to the "geppetto model".
So as long as the file can be converted to the "nwb model", it will be converted to the "geppetto model" and shown in the UI elements
awesome, ping us here whenver you need to---I usually keep my element app open so I should get notifications etc.