NWB integration

[bendichter]

Hey all,

What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since that repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo?

[dlevenstein]

Conversion to/from NWB would be very good/useful. IMO

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On Mar 4, 2018, at 4:41 PM, Ben Dichter ***@***.***> wrote: Hey all, What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since this repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[brendonw1]

Seconded, I like the idea. Don't know the details of course On Sun, Mar 4, 2018 at 3:16 PM, Dan Levenstein <[email protected]> wrote:

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Conversion to/from NWB would be very good/useful. IMO > On Mar 4, 2018, at 4:41 PM, Ben Dichter ***@***.***> wrote: > > Hey all, > > What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since this repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo? > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub, or mute the thread. > — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#153 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADXrTXum3nd2vN_JDEoQFvr8_QvrGCuBks5tbGfNgaJpZM4SbhAe> .

[samamckenzie]

This is a big priority for Gyuri. Can we set up a Skype meeting? Sam Whatever we can do to help On Mar 4, 2018 5:24 PM, "Brendon Watson" <[email protected]> wrote: Seconded, I like the idea. Don't know the details of course On Sun, Mar 4, 2018 at 3:16 PM, Dan Levenstein <[email protected]> wrote:

Conversion to/from NWB would be very good/useful. IMO > On Mar 4, 2018, at 4:41 PM, Ben Dichter ***@***.***> wrote: > > Hey all, > > What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since this repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for

you

all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo? > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub, or mute the thread. > — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#153 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/

ADXrTXum3nd2vN_JDEoQFvr8_QvrGCuBks5tbGfNgaJpZM4SbhAe>

.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#153 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ANnfgE0kRbdFEOx2CesLRXSMu0M-Wl9gks5tbGmLgaJpZM4SbhAe> .

[petersenpeter]

There has been a lot of talk about this and it would be a great addition.

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Den 4. mar. 2018 kl. 16.41 skrev Ben Dichter ***@***.***>: Hey all, What are your thoughts on integrating conversion to NWB as part of buzcode? So far I have been using pynwb for conversion to and from NWB since this repo is under more active development, however all of that code is python-based. There is another repo, matnwb, for converting data to NWB using matlab. The development of matnwb has not been as active an pynwb, however I realize it might be a smoother integration and transition for you all to use matlab to convert to NWB instead of python. Would there be interest in using matnwb to build conversion scripts directly to and from your buzcode format? What would you imagine as the ideal workflow/integration with the current buzcode repo? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[bendichter]

Thanks for your input, guys. It's helpful to know there is interest in the MATLAB side of NWB. I'm also in touch with with Vijay Iyer, the neuroscience liaison at Mathworks, who is curious about interest in the matnwb project, and I've let him know about your lab's interest in the project.

[bendichter]

Hey all, I just wanted to let you know that I've started to work out data conversion for your format in MATLAB using matnwb. It's not finished yet, but you can track my progress here: https://github.com/bendichter/to_nwb/blob/master/convert_yuta.m

[petersenpeter]

Great Ben 2018-03-29 13:01 GMT-04:00 Ben Dichter <[email protected]>:

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Hey all, I just wanted to let you know that I've started to work out data conversion for your format in MATLAB using matnwb. It's not finished yet, but you can track my progress here: https://github.com/bendichter/ to_nwb/blob/master/convert_yuta.m — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#153 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ANb8ucsqh9-c8P3LJNEVl477DWMRvtJBks5tjRNngaJpZM4SbhAe> .

[DavidTingley]

In preparation for the coming hackathon, we can upload goals and ideas here:
https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK05_2018_Berkeley/projects/Buzsakilab