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Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub

To build biophysically detailed models of brain cells, circuits, and regions, a data-driven approach is increasingly being adopted. This helps to obtain a simulated activity that reproduces the experimentally recorded neural dynamics as faithfully as possible, and to turn the model into a useful fra...

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Autores principales: Bologna, Luca Leonardo, Tocco, Antonino, Smiriglia, Roberto, Romani, Armando, Schürmann, Felix, Migliore, Michele
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10646550/
https://www.ncbi.nlm.nih.gov/pubmed/38025966
http://dx.doi.org/10.3389/fninf.2023.1271059
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author Bologna, Luca Leonardo
Tocco, Antonino
Smiriglia, Roberto
Romani, Armando
Schürmann, Felix
Migliore, Michele
author_facet Bologna, Luca Leonardo
Tocco, Antonino
Smiriglia, Roberto
Romani, Armando
Schürmann, Felix
Migliore, Michele
author_sort Bologna, Luca Leonardo
collection PubMed
description To build biophysically detailed models of brain cells, circuits, and regions, a data-driven approach is increasingly being adopted. This helps to obtain a simulated activity that reproduces the experimentally recorded neural dynamics as faithfully as possible, and to turn the model into a useful framework for making predictions based on the principles governing the nature of neural cells. In such a context, the access to existing neural models and data outstandingly facilitates the work of computational neuroscientists and fosters its novelty, as the scientific community grows wider and neural models progressively increase in type, size, and number. Nonetheless, even when accessibility is guaranteed, data and models are rarely reused since it is difficult to retrieve, extract and/or understand relevant information and scientists are often required to download and modify individual files, perform neural data analysis, optimize model parameters, and run simulations, on their own and with their own resources. While focusing on the construction of biophysically and morphologically accurate models of hippocampal cells, we have created an online resource, the Build section of the Hippocampus Hub -a scientific portal for research on the hippocampus- that gathers data and models from different online open repositories and allows their collection as the first step of a single cell model building workflow. Interoperability of tools and data is the key feature of the work we are presenting. Through a simple click-and-collect procedure, like filling the shopping cart of an online store, researchers can intuitively select the files of interest (i.e., electrophysiological recordings, neural morphology, and model components), and get started with the construction of a data-driven hippocampal neuron model. Such a workflow importantly includes a model optimization process, which leverages high performance computing resources transparently granted to the users, and a framework for running simulations of the optimized model, both available through the EBRAINS Hodgkin-Huxley Neuron Builder online tool.
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spelling pubmed-106465502023-01-01 Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub Bologna, Luca Leonardo Tocco, Antonino Smiriglia, Roberto Romani, Armando Schürmann, Felix Migliore, Michele Front Neuroinform Neuroscience To build biophysically detailed models of brain cells, circuits, and regions, a data-driven approach is increasingly being adopted. This helps to obtain a simulated activity that reproduces the experimentally recorded neural dynamics as faithfully as possible, and to turn the model into a useful framework for making predictions based on the principles governing the nature of neural cells. In such a context, the access to existing neural models and data outstandingly facilitates the work of computational neuroscientists and fosters its novelty, as the scientific community grows wider and neural models progressively increase in type, size, and number. Nonetheless, even when accessibility is guaranteed, data and models are rarely reused since it is difficult to retrieve, extract and/or understand relevant information and scientists are often required to download and modify individual files, perform neural data analysis, optimize model parameters, and run simulations, on their own and with their own resources. While focusing on the construction of biophysically and morphologically accurate models of hippocampal cells, we have created an online resource, the Build section of the Hippocampus Hub -a scientific portal for research on the hippocampus- that gathers data and models from different online open repositories and allows their collection as the first step of a single cell model building workflow. Interoperability of tools and data is the key feature of the work we are presenting. Through a simple click-and-collect procedure, like filling the shopping cart of an online store, researchers can intuitively select the files of interest (i.e., electrophysiological recordings, neural morphology, and model components), and get started with the construction of a data-driven hippocampal neuron model. Such a workflow importantly includes a model optimization process, which leverages high performance computing resources transparently granted to the users, and a framework for running simulations of the optimized model, both available through the EBRAINS Hodgkin-Huxley Neuron Builder online tool. Frontiers Media S.A. 2023-11-01 /pmc/articles/PMC10646550/ /pubmed/38025966 http://dx.doi.org/10.3389/fninf.2023.1271059 Text en Copyright © 2023 Bologna, Tocco, Smiriglia, Romani, Schürmann and Migliore. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Neuroscience
Bologna, Luca Leonardo
Tocco, Antonino
Smiriglia, Roberto
Romani, Armando
Schürmann, Felix
Migliore, Michele
Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub
title Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub
title_full Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub
title_fullStr Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub
title_full_unstemmed Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub
title_short Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub
title_sort online interoperable resources for building hippocampal neuron models via the hippocampus hub
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10646550/
https://www.ncbi.nlm.nih.gov/pubmed/38025966
http://dx.doi.org/10.3389/fninf.2023.1271059
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