ConGen-A Simulator-Agnostic Visual Language for Definition and Generation of Connectivity in Large and Multiscale Neural Networks.

Patrick Herbers,Sandra Diaz-Pier,Pablo Toharia,Alexander Peyser,Oscar D Robles,Abigail Morrison,Iago Calvo,Luis Pastor,Susana Mata,Wouter Klijn

doi:10.3389/fninf.2021.766697

Abstract

An open challenge on the road to unraveling the brain's multilevel organization is establishing techniques to research connectivity and dynamics at different scales in time and space, as well as the links between them. This work focuses on the design of a framework that facilitates the generation of multiscale connectivity in large neural networks using a symbolic visual language capable of representing the model at different structural levels—ConGen. This symbolic language allows researchers to create and visually analyze the generated networks independently of the simulator to be used, since the visual model is translated into a simulator-independent language. The simplicity of the front end visual representation, together with the simulator independence provided by the back end translation, combine into a framework to enhance collaboration among scientists with expertise at different scales of abstraction and from different fields. On the basis of two use cases, we introduce the features and possibilities of our proposed visual language and associated workflow. We demonstrate that ConGen enables the creation, editing, and visualization of multiscale biological neural networks and provides a whole workflow to produce simulation scripts from the visual representation of the model.

Highlights

The brain has a multilevel organization, with anatomical and dynamic features spanning orders of magnitudes
We will describe first two use cases which are used to demonstrate the functionality of ConGen while addressing specific needs from the neuroscience community
The model has been used to address a variety of scientific questions and is able to show spiking dynamics similar to those observed in real cortical tissue. We chose this model to test the whole functionality of ConGen, from visual language definition to simulation

Summary

Introduction

The brain has a multilevel organization, with anatomical and dynamic features spanning orders of magnitudes. Connectivity is an essential aspect defining the functionality at all organizational scales of the brain (Sporns et al, 2005). The 21st century has seen multiple interdisciplinary research initiatives initiated to address this important topic (Collins and Prabhakar, 2013; Markram et al, 2015); despite advances and ConGen—Visual Connectivity Generation efforts toward standardization in this field (Gadde et al, 2012; Gorgolewski et al, 2016), there is no consistent way to represent, visualize, explore, and generate connectivity for simulation or analysis across different scales. A central method in such investigations is numerical simulation of the brain. By exploiting high performance computing we are able to simulate large scale networks as well as those which represent the brain at different scales simultaneously. The absence of methods to create, and explore complex connectivity in these types of networks limits investigations in the relationships between connectivity and function

Methods

Results

Discussion

Conclusion