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OCNS / SoftwareWG

The primary housekeeping repository for the INCF/OCNS Software Working Group, and the sources for the web site.
https://ocns.github.io/SoftwareWG/
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Dev session: neurolib #5

Closed caglorithm closed 3 years ago

caglorithm commented 3 years ago

I'm proactively adding an issue for scheduling time/date for the session on neurolib.

sanjayankur31 commented 3 years ago

Thanks @caglorithm . Assigning to you too.

sanjayankur31 commented 3 years ago

We have Brian set up for 9th of Feb. Would the following weeks work for you?

sanjayankur31 commented 3 years ago

NeuroFedora is set up for the week after (16th Feb), and GeNN is set up for the first week of March. Would the third week of Feb, starting on 22nd Feb work for you @caglorithm ?

caglorithm commented 3 years ago

Thanks for setting up everything @sanjayankur31. Could you maybe tell me a bit about the format of the sessions? I couldn't participate in the meeting so I don't really know anything apart from the log that I've read. What's the primary goal of the session? Will it be tutorial-like? Did you already agree on know how long each session will be?

sanjayankur31 commented 3 years ago

The goal of the sessions is to share knowledge of how research tools are developed

So, these sessions are intended to discuss the development side of the project. Most of us intend to give a short demonstration of how the tool is to be used with, to start with---to show what it does and how etc. A short overview. Then we intend to move on to the development side of things---how the tool is developed, what the pipeline is, what the contributing guidelines are and so on. If there are some easy issues for beginners to work on, that'll be an added bonus, since it'll help the project get some new contributors.

We expect the sessions to be 1 hour long, but we haven't set an explicit limit.

caglorithm commented 3 years ago

@sanjayankur31, 22nd February is good for me. Looking forward!

sanjayankur31 commented 3 years ago

Sounds good. What time would you prefer? Does 1700 UTC work?

sanjayankur31 commented 3 years ago

Oh, also: could you give me a short abstract/summary for the talk to put up on the website etc.? (Like here)

caglorithm commented 3 years ago

Yes, 1700 UTC works for me!

On Thu, 11 Feb 2021, 19:11 Ankur Sinha, notifications@github.com wrote:

Sounds good. What time would you prefer? Does 1700 UTC work?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/OCNS/SoftwareWG/issues/5#issuecomment-777687107, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB3HKDHYPWA2VVJRIXTFHK3S6QMTLANCNFSM4WV556SQ .

caglorithm commented 3 years ago

Sure, here you go:

neurolib is a computational framework for whole-brain modeling written in Python. It provides a set of neural mass models that represent the average activity of a brain region on a mesoscopic scale. In a whole-brain network model, brain regions are connected with each other based on structural connectivity data, i.e. the connectome of the brain. neurolib can load structural and functional data sets, set up a whole-brain model, manage its parameters, simulate it, and organize its outputs for later analysis. The activity of each brain region can be converted into a simulated BOLD signal in order to calibrate the model to empirical data from functional magnetic resonance imaging (fMRI). Extensive model analysis is possible using a parameter exploration module, which allows to characterize the model's behavior given a set of changing parameters. An optimization module allows for fitting a model to multimodal empirical data using an evolutionary algorithm. Besides its included functionality, neurolib is designed to be extendable such that custom neural mass models can be implemented easily. neurolib offers a versatile platform for computational neuroscientists for prototyping models, managing large numerical experiments, studying the structure-function relationship of brain networks, and for in-silico optimization of whole-brain models.

sanjayankur31 commented 3 years ago

Thanks, I'll set it up on the website and ping you there before sending the announcement out.

One last thing: are there any accounts I can tag when I post the announcement on twitter etc? Either for the software or for you/the dev team?

caglorithm commented 3 years ago

Sure, my twitter handle is @caglorithm, the account of @neurolib-dev is still in its infancy, almost nothing happening there yet. Maybe you can just use both?

I have created a Zoom meeting, in case you would like to use it.

Topic: OCNS Dev sessions: neurolib
Time: Feb 22, 2021 18:00 Berlin / 17:00 UTC

Join Zoom Meeting
https://tu-berlin.zoom.us/j/68960683644?pwd=a2JTTS8xZXhwY0ZtQ0J0aktRVW52Zz09
sanjayankur31 commented 3 years ago

Thanks, I'll use this!

sanjayankur31 commented 3 years ago

I've put the post up now @caglorithm : https://ocns.github.io/SoftwareWG/2021/02/12/dev-session-caglar-cakan-neurolib.html

Could you take a look to see if everything there is OK? Also, for the Zoom call, are the security settings set correctly so that anyone with a Zoom account can join? (Here at UCL, the default was set to only allow other UCL Zoom accounts to join).

caglorithm commented 3 years ago

Perfect, thanks!

Users should be able to join the Zoom call without an account, according to the privacy regulations of the TU Berlin.

sanjayankur31 commented 3 years ago

Sounds good. I'll send out the announcement to the MLs tomorrow morning.

caglorithm commented 3 years ago

Hi @sanjayankur31, did you send out the invitation yet? I noticed that, the last 2 times, we met on Tuesday. Feb 22nd is a Monday, are you aware of that? Might be better to stay on the same week day, but I can do both! Please let me know what you think is better.

sanjayankur31 commented 3 years ago

No, I'm sending the mails out now.

Yeh, I knew it was Monday but as long as we'd announced it in advance I didn't think it'd make a difference---the sessions will be held whenever convenient for the speaker.

If you want we can move to the Tuesday: can you create a new zoom meeting and share the link? I'll update the website announcement etc. too.

sanjayankur31 commented 3 years ago

@caglorithm : double-checking: would the zoom link stay the same if we move to Tuesday, or would you have to create a new one?

caglorithm commented 3 years ago

@sanjayankur31 sorry for the delay, I had problems receiving mail notificaitons. I changed the date, the URL stayed the same!

Caglar Cakan is inviting you to a scheduled Zoom meeting on the TU Berlin zoom service.

Topic: OCNS Dev sessions: neurolib
Time: Feb 23, 2021 06:00 PM Amsterdam, Berlin, Rome, Stockholm, Vienna

Join Zoom Meeting
https://tu-berlin.zoom.us/j/68960683644?pwd=a2JTTS8xZXhwY0ZtQ0J0aktRVW52Zz09
sanjayankur31 commented 3 years ago

Thanks! I'll send it out first thing tomorrow morning.

-- Thanks,

Ankur

(Sent from mobile device)

On Wed, 17 Feb 2021, 19:09 Caglar Cakan, notifications@github.com wrote:

@sanjayankur31 https://github.com/sanjayankur31 sorry for the delay, I had problems receiving mail notificaitons. I changed the date, the URL stayed the same!

Caglar Cakan is inviting you to a scheduled Zoom meeting on the TU Berlin zoom service.

Topic: OCNS Dev sessions: neurolib Time: Feb 23, 2021 06:00 PM Amsterdam, Berlin, Rome, Stockholm, Vienna

Join Zoom Meetinghttps://tu-berlin.zoom.us/j/68960683644?pwd=a2JTTS8xZXhwY0ZtQ0J0aktRVW52Zz09

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/OCNS/SoftwareWG/issues/5#issuecomment-780783954, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAZBLY2NYVMYH4CZ56WIPLS7QH7XANCNFSM4WV556SQ .

sanjayankur31 commented 3 years ago

Announcement sent to mailing lists. Twitter announcement sent: https://twitter.com/sanjay_ankur/status/1362344544357011456?s=20

sanjayankur31 commented 3 years ago

Recordings are here now. Got to update the website post:

https://www.youtube.com/watch?v=ngvVtqiilVk

sanjayankur31 commented 3 years ago

Post updated to include video: https://ocns.github.io/SoftwareWG/2021/02/12/dev-session-caglar-cakan-neurolib.html

Closing.