ArticlePLoS computational biology2020
The SONATA data format for efficient description of large-scale network models.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- eFEL: electrophysiology feature extraction library.Bioinformatics (Oxford, England) · 2026Article
- Deep-learning-assisted simulation of a cortical circuit: integrating anatomy, physiology and function.bioRxiv : the preprint server for biology · 2026Article
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- NEURONpyxl: fast, flexible, Python-integrated simulation of biophysical neural networks with complex plastic synapses.Frontiers in computational neuroscience · 2026Article
- Container-based framework for large-scale spiking network simulation.Frontiers in neuroscience · 2026Article
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- The Virtual Brain Ontology: A Digital Knowledge Framework for Reproducible Brain Network Modeling.bioRxiv : the preprint server for biology · 2025Article
- Building on models-a perspective for computational neuroscience.Cerebral cortex (New York, N.Y. : 1991) · 2025Article
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- BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models.PLoS computational biology · 2025Article
- Heterogeneous and higher-order cortical connectivity undergirds efficient, robust, and reliable neural codes.iScience · 2025Article
- Self-organized and self-sustained ensemble activity patterns in simulation of mouse primary motor cortex.bioRxiv : the preprint server for biology · 2025Article
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- A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations.Network neuroscience (Cambridge, Mass.) · 2025Article
- Large-Scale Mechanistic Models of Brain Circuits with Biophysically and Morphologically Detailed Neurons.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Review
- Interdisciplinary and Collaborative Training in Neuroscience: Insights from the Human Brain Project Education Programme.Neuroinformatics · 2024Article
- A Perspective on Neuroscience Data Standardization with Neurodata Without Borders.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Article
- A FAIR, open-source virtual reality platform for dendritic spine analysis.Patterns (New York, N.Y.) · 2024Article
- Article
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Authors and funding
17 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.