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Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system works or why certain phenomena are observed. Dat...

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Autores principales: Eriksson, Olivia, Bhalla, Upinder Singh, Blackwell, Kim T, Crook, Sharon M, Keller, Daniel, Kramer, Andrei, Linne, Marja-Leena, Saudargienė, Ausra, Wade, Rebecca C, Hellgren Kotaleski, Jeanette
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9259018/
https://www.ncbi.nlm.nih.gov/pubmed/35792600
http://dx.doi.org/10.7554/eLife.69013
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author Eriksson, Olivia
Bhalla, Upinder Singh
Blackwell, Kim T
Crook, Sharon M
Keller, Daniel
Kramer, Andrei
Linne, Marja-Leena
Saudargienė, Ausra
Wade, Rebecca C
Hellgren Kotaleski, Jeanette
author_facet Eriksson, Olivia
Bhalla, Upinder Singh
Blackwell, Kim T
Crook, Sharon M
Keller, Daniel
Kramer, Andrei
Linne, Marja-Leena
Saudargienė, Ausra
Wade, Rebecca C
Hellgren Kotaleski, Jeanette
author_sort Eriksson, Olivia
collection PubMed
description Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system works or why certain phenomena are observed. Data-driven modeling, on the other hand, follows a more unbiased approach, with model construction informed by the computationally intensive use of data. At the same time, researchers employ models at different biological scales and at different levels of abstraction. Combining these models while validating them against experimental data increases understanding of the multiscale brain. However, a lack of interoperability, transparency, and reusability of both models and the workflows used to construct them creates barriers for the integration of models representing different biological scales and built using different modeling philosophies. We argue that the same imperatives that drive resources and policy for data – such as the FAIR (Findable, Accessible, Interoperable, Reusable) principles – also support the integration of different modeling approaches. The FAIR principles require that data be shared in formats that are Findable, Accessible, Interoperable, and Reusable. Applying these principles to models and modeling workflows, as well as the data used to constrain and validate them, would allow researchers to find, reuse, question, validate, and extend published models, regardless of whether they are implemented phenomenologically or mechanistically, as a few equations or as a multiscale, hierarchical system. To illustrate these ideas, we use a classical synaptic plasticity model, the Bienenstock–Cooper–Munro rule, as an example due to its long history, different levels of abstraction, and implementation at many scales.
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spelling pubmed-92590182022-07-07 Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows Eriksson, Olivia Bhalla, Upinder Singh Blackwell, Kim T Crook, Sharon M Keller, Daniel Kramer, Andrei Linne, Marja-Leena Saudargienė, Ausra Wade, Rebecca C Hellgren Kotaleski, Jeanette eLife Computational and Systems Biology Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system works or why certain phenomena are observed. Data-driven modeling, on the other hand, follows a more unbiased approach, with model construction informed by the computationally intensive use of data. At the same time, researchers employ models at different biological scales and at different levels of abstraction. Combining these models while validating them against experimental data increases understanding of the multiscale brain. However, a lack of interoperability, transparency, and reusability of both models and the workflows used to construct them creates barriers for the integration of models representing different biological scales and built using different modeling philosophies. We argue that the same imperatives that drive resources and policy for data – such as the FAIR (Findable, Accessible, Interoperable, Reusable) principles – also support the integration of different modeling approaches. The FAIR principles require that data be shared in formats that are Findable, Accessible, Interoperable, and Reusable. Applying these principles to models and modeling workflows, as well as the data used to constrain and validate them, would allow researchers to find, reuse, question, validate, and extend published models, regardless of whether they are implemented phenomenologically or mechanistically, as a few equations or as a multiscale, hierarchical system. To illustrate these ideas, we use a classical synaptic plasticity model, the Bienenstock–Cooper–Munro rule, as an example due to its long history, different levels of abstraction, and implementation at many scales. eLife Sciences Publications, Ltd 2022-07-06 /pmc/articles/PMC9259018/ /pubmed/35792600 http://dx.doi.org/10.7554/eLife.69013 Text en © 2022, Eriksson et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Computational and Systems Biology
Eriksson, Olivia
Bhalla, Upinder Singh
Blackwell, Kim T
Crook, Sharon M
Keller, Daniel
Kramer, Andrei
Linne, Marja-Leena
Saudargienė, Ausra
Wade, Rebecca C
Hellgren Kotaleski, Jeanette
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows
title Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows
title_full Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows
title_fullStr Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows
title_full_unstemmed Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows
title_short Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows
title_sort combining hypothesis- and data-driven neuroscience modeling in fair workflows
topic Computational and Systems Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9259018/
https://www.ncbi.nlm.nih.gov/pubmed/35792600
http://dx.doi.org/10.7554/eLife.69013
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