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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Neuroinformatics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fninf.2023.1271059/full |
| _version_ | 1797643251791953920 |
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| author | Luca Leonardo Bologna Antonino Tocco Roberto Smiriglia Armando Romani Felix Schürmann Michele Migliore |
| author_facet | Luca Leonardo Bologna Antonino Tocco Roberto Smiriglia Armando Romani Felix Schürmann Michele Migliore |
| author_sort | Luca Leonardo Bologna |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-11T14:12:02Z |
| format | Article |
| id | doaj.art-361d5965719540b2982aa5b2162406ff |
| institution | Directory Open Access Journal |
| issn | 1662-5196 |
| language | English |
| last_indexed | 2024-03-11T14:12:02Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroinformatics |
| spelling | doaj.art-361d5965719540b2982aa5b2162406ff2023-11-01T17:34:47ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962023-11-011710.3389/fninf.2023.12710591271059Online interoperable resources for building hippocampal neuron models via the Hippocampus HubLuca Leonardo Bologna0Antonino Tocco1Roberto Smiriglia2Armando Romani3Felix Schürmann4Michele Migliore5Institute of Biophysics, National Research Council, Palermo, ItalyInstitute of Biophysics, National Research Council, Palermo, ItalyInstitute of Biophysics, National Research Council, Palermo, ItalyBlue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, SwitzerlandBlue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, SwitzerlandInstitute of Biophysics, National Research Council, Palermo, ItalyTo 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.https://www.frontiersin.org/articles/10.3389/fninf.2023.1271059/fullhippocampusresearch hubdata-driven brain modelsonline resourcesEBRAINS |
| spellingShingle | Luca Leonardo Bologna Antonino Tocco Roberto Smiriglia Armando Romani Felix Schürmann Michele Migliore Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub Frontiers in Neuroinformatics hippocampus research hub data-driven brain models online resources EBRAINS |
| 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 | hippocampus research hub data-driven brain models online resources EBRAINS |
| url | https://www.frontiersin.org/articles/10.3389/fninf.2023.1271059/full |
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