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Connectivity concepts in neuronal network modeling

Senk, Johanna ; Kriener, Birgit ; Djurfeldt, Mikael ; Voges, Nicole ; Jiang, Han-Jia ; Schüttler, Lisa ; Gramelsberger, Gabriele ; Diesmann, Markus ; Plesser, Hans E ; van Albada, Sacha J Toro, Roberto

PLoS computational biology, 2022-09, Vol.18 (9), p.e1010086-e1010086 [Periódico revisado por pares]

San Francisco: Public Library of Science

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Título:
Connectivity concepts in neuronal network modeling
Autor: Senk, Johanna ; Kriener, Birgit ; Djurfeldt, Mikael ; Voges, Nicole ; Jiang, Han-Jia ; Schüttler, Lisa ; Gramelsberger, Gabriele ; Diesmann, Markus ; Plesser, Hans E ; van Albada, Sacha J
Toro, Roberto
Assuntos: Analysis ; Anatomy ; Biology and Life Sciences ; Brain architecture ; Brain research ; Cognitive science ; Computational neuroscience ; Computer and Information Sciences ; Descriptions ; Engineering and Technology ; Interfaces ; Mathematical analysis ; Mathematical models ; Medicine and Health Sciences ; Metric space ; Nervous system ; Neural circuitry ; Neural networks ; Neurons ; Neuroscience ; Neurosciences ; Physical Sciences ; Reviews ; Simulation ; Software ; Specification and description languages ; Synthetic training devices
É parte de: PLoS computational biology, 2022-09, Vol.18 (9), p.e1010086-e1010086
Notas: ObjectType-Article-2
SourceType-Scholarly Journals-1
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content type line 23
ObjectType-Review-1
The authors have declared that no competing interests exist.
Descrição: Sustainable research on computational models of neuronal networks requires published models to be understandable, reproducible, and extendable. Missing details or ambiguities about mathematical concepts and assumptions, algorithmic implementations, or parameterizations hinder progress. Such flaws are unfortunately frequent and one reason is a lack of readily applicable standards and tools for model description. Our work aims to advance complete and concise descriptions of network connectivity but also to guide the implementation of connection routines in simulation software and neuromorphic hardware systems. We first review models made available by the computational neuroscience community in the repositories ModelDB and Open Source Brain, and investigate the corresponding connectivity structures and their descriptions in both manuscript and code. The review comprises the connectivity of networks with diverse levels of neuroanatomical detail and exposes how connectivity is abstracted in existing description languages and simulator interfaces. We find that a substantial proportion of the published descriptions of connectivity is ambiguous. Based on this review, we derive a set of connectivity concepts for deterministically and probabilistically connected networks and also address networks embedded in metric space. Beside these mathematical and textual guidelines, we propose a unified graphical notation for network diagrams to facilitate an intuitive understanding of network properties. Examples of representative network models demonstrate the practical use of the ideas. We hope that the proposed standardizations will contribute to unambiguous descriptions and reproducible implementations of neuronal network connectivity in computational neuroscience.
Editor: San Francisco: Public Library of Science
Idioma: Inglês;Norueguês

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Connectivity concepts in neuronal network modeling

Senk, Johanna ; Kriener, Birgit ; Djurfeldt, Mikael ; Voges, Nicole ; Jiang, Han-Jia ; Schüttler, Lisa ; Gramelsberger, Gabriele ; Diesmann, Markus ; Plesser, Hans E ; van Albada, Sacha J Toro, Roberto

San Francisco: Public Library of Science

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