[Neuroinfo] INCF/OCNS Software WG: Dev session on Neurolib (23rd Feb)

Ankur Sinha sanjay.ankur at gmail.com
Thu Feb 18 11:07:32 CET 2021

Hello everyone,

Apologies for the cross-posts.

The INCF/OCNS Software Working Group (WG)[1] is happy to announce the
next "Dev session" on Neurolib[2] where Caglar Cakan will introduce the
software and then discuss its *development* pipeline.

The session will be held on Feb 23, 2021 at 1700 UTC[3]. Zoom link:

The aim of these sessions is to stimulate discussion of the development
practices and tools used by different teams to improve the software we
use while also improving our knowledge of these practices and tools.
We also hope to encourage more users of these tools to contribute to
their development to ensure their longevity.

The abstract of the talk is below:

neurolib is a computational framework for whole-brain modelling 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 behaviour 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.


If you develop software for neuroscience, we would love to hear about
your development pipeline. Please get in touch with the Software WG
either on INCF's Neurostars platform[4] or on our GitHub repository[5].

The WG is a community based group that is open to everyone at all levels
of their careers (academic or otherwise). Please introduce yourself to
the community on our channels to get involved.

[1] https://ocns.github.io/SoftwareWG/pages/about.html
[2] https://neurolib-dev.github.io/
[3] https://ocns.github.io/SoftwareWG/2021/02/12/dev-session-caglar-cakan-neurolib.html
[4] https://neurostars.org/t/ocns-infrastructure-software-tools-sig-meet-and-greet-initial-discussions/15560/114
[5] https://github.com/OCNS/SoftwareWG/issues

On behalf of the WG,

Ankur Sinha (He / Him / His)
Research Fellow at the Silver Lab | http://silverlab.org/
Department of Neuroscience, Physiology, & Pharmacology
University College London, London, UK
Time zone: Europe/London

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