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Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits.
Gleeson, Padraig; Cantarelli, Matteo; Marin, Boris; Quintana, Adrian; Earnshaw, Matt; Sadeh, Sadra; Piasini, Eugenio; Birgiolas, Justas; Cannon, Robert C; Cayco-Gajic, N Alex; Crook, Sharon; Davison, Andrew P; Dura-Bernal, Salvador; Ecker, András; Hines, Michael L; Idili, Giovanni; Lanore, Frederic; Larson, Stephen D; Lytton, William W; Majumdar, Amitava; McDougal, Robert A; Sivagnanam, Subhashini; Solinas, Sergio; Stanislovas, Rokas; van Albada, Sacha J; van Geit, Werner; Silver, R Angus
Journal Title
Neuron
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Term and Year
Publication Date
2019-06-11
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Publication Volume
103
Publication Issue
3
Publication Begin
395
Publication End
411.e5
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mmc5.pdf
Adobe PDF, 10.68 MB
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Abstract
Computational models are powerful tools for exploring the properties of complex biological systems. In neuroscience, data-driven models of neural circuits that span multiple scales are increasingly being used to understand brain function in health and disease. But their adoption and reuse has been limited by the specialist knowledge required to evaluate and use them. To address this, we have developed Open Source Brain, a platform for sharing, viewing, analyzing, and simulating standardized models from different brain regions and species. Model structure and parameters can be automatically visualized and their dynamical properties explored through browser-based simulations. Infrastructure and tools for collaborative interaction, development, and testing are also provided. We demonstrate how existing components can be reused by constructing new models of inhibition-stabilized cortical networks that match recent experimental results. These features of Open Source Brain improve the accessibility, transparency, and reproducibility of models and facilitate their reuse by the wider community.
Citation
Gleeson P, Cantarelli M, Marin B, Quintana A, Earnshaw M, Sadeh S, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic NA, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, Idili G, Lanore F, Larson SD, Lytton WW, Majumdar A, McDougal RA, Sivagnanam S, Solinas S, Stanislovas R, van Albada SJ, van Geit W, Silver RA. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Neuron. 2019 Aug 7;103(3):395-411.e5. doi: 10.1016/j.neuron.2019.05.019. Epub 2019 Jun 11. PMID: 31201122; PMCID: PMC6693896.