The SONATA data format for efficient description of large-scale network models.
Average rating
Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Star rating
Your vote was cast
Thank you for your feedback
Thank you for your feedback
Author
Dai, KaelHernando, Juan
Billeh, Yazan N
Gratiy, Sergey L
Planas, Judit
Davison, Andrew P
Dura-Bernal, Salvador
Gleeson, Padraig
Devresse, Adrien
Dichter, Benjamin K
Gevaert, Michael
King, James G
Van Geit, Werner A H
Povolotsky, Arseny V
Muller, Eilif
Courcol, Jean-Denis
Arkhipov, Anton
Journal title
PLoS computational biologyDate Published
2020-02-24Publication Volume
16Publication Issue
2Publication Begin page
e1007696
Metadata
Show full item recordAbstract
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.Citation
Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Dichter BK, Gevaert M, King JG, Van Geit WAH, Povolotsky AV, Muller E, Courcol JD, Arkhipov A. The SONATA data format for efficient description of large-scale network models. PLoS Comput Biol. 2020 Feb 24;16(2):e1007696. doi: 10.1371/journal.pcbi.1007696. PMID: 32092054; PMCID: PMC7058350.DOI
10.1371/journal.pcbi.1007696ae974a485f413a2113503eed53cd6c53
10.1371/journal.pcbi.1007696
Scopus Count
Collections
The following license files are associated with this item:
- Creative Commons
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivatives 4.0 International
Related articles
- NSDF: Neuroscience Simulation Data Format.
- Authors: Ray S, Chintaluri C, Bhalla US, Wójcik DK
- Issue date: 2016 Apr
- NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
- Authors: Dura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW
- Issue date: 2019 Apr 26
- The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology.
- Authors: Hucka M, Finney A, Sauro HM, Bolouri H, Doyle J, Kitano H
- Issue date: 2002
- Computational neuroscience and neuroinformatics: Recent progress and resources.
- Authors: Nayak L, Dasgupta A, Das R, Ghosh K, De RK
- Issue date: 2018 Dec
- Towards reproducible descriptions of neuronal network models.
- Authors: Nordlie E, Gewaltig MO, Plesser HE
- Issue date: 2009 Aug