The SONATA data format for efficient description of large-scale network models

Kael Dai, Juan Hernando, Yazan N Billeh, Sergey L Gratiy, Judit Planas, Andrew P Davison, Salvador Dura-Bernal, Padraig Gleeson, Adrien Devresse, Benjamin K Dichter, Michael Gevaert, James G King, Werner A H Van Geit, Arseny V Povolotsky, Eilif Muller, Jean-Denis Courcol and Anton Arkhipov

PLOS Computational Biology, 2020, vol. 16, issue 2, 1-24

Abstract: Increasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation, as well as sharing of such large-scale models, a broadly applicable, flexible, and high-performance data format is necessary. To address this need, we have developed the Scalable Open Network Architecture TemplAte (SONATA) data format. It is designed for memory and computational efficiency and works across multiple platforms. The format represents neuronal circuits and simulation inputs and outputs via standardized files and provides much flexibility for adding new conventions or extensions. SONATA is used in multiple modeling and visualization tools, and we also provide reference Application Programming Interfaces and model examples to catalyze further adoption. SONATA format is free and open for the community to use and build upon with the goal of enabling efficient model building, sharing, and reproducibility.Author summary: Neuroscience is experiencing a rapid growth of data streams characterizing composition, connectivity, and activity of brain networks in ever increasing details. Data-driven modeling will be essential to integrate these multimodal and complex data into predictive simulations to advance our understanding of brain function and mechanisms. To enable efficient development and sharing of such large-scale models utilizing diverse data types, we have developed the Scalable Open Network Architecture TemplAte (SONATA) data format. The format represents neuronal circuits and simulation inputs and outputs via standardized files and provides much flexibility for adding new conventions or extensions. SONATA is already supported by several popular tools for model building, simulations, and visualization. It is free and open for everyone to use and build upon and will enable increased efficiency, reproducibility, and scientific exchange in the community.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1007696

DOI: 10.1371/journal.pcbi.1007696

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