eprintid: 10093154
rev_number: 14
eprint_status: archive
userid: 608
dir: disk0/10/09/31/54
datestamp: 2020-03-11 14:16:40
lastmod: 2021-10-28 22:39:15
status_changed: 2020-03-11 14:16:40
type: article
metadata_visibility: show
creators_name: Dai, K
creators_name: Hernando, J
creators_name: Billeh, YN
creators_name: Gratiy, SL
creators_name: Planas, J
creators_name: Davison, AP
creators_name: Dura-Bernal, S
creators_name: Gleeson, P
creators_name: Devresse, A
creators_name: Dichter, BK
creators_name: Gevaert, M
creators_name: King, JG
creators_name: Van Geit, WAH
creators_name: Povolotsky, AV
creators_name: Muller, E
creators_name: Courcol, J-D
creators_name: Arkhipov, A
title: The SONATA data format for efficient description of large-scale network models
ispublished: pub
divisions: UCL
divisions: B02
divisions: C08
divisions: D09
divisions: G02
keywords: Neurons, Simulation and modeling, Network analysis, Neural networks, Biophysics, Biophysical simulations, Synapses, Neuronal morphology
note: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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.
date: 2020-02-24
date_type: published
official_url: https://doi.org/10.1371/journal.pcbi.1007696
oa_status: green
full_text_type: pub
language: eng
primo: open
primo_central: open_green
verified: verified_manual
elements_id: 1770105
doi: 10.1371/journal.pcbi.1007696
pii: PCOMPBIOL-D-19-01605
lyricists_name: Gleeson, Patrick
lyricists_id: PGLEE72
actors_name: Kalinowski, Damian
actors_id: DKALI47
actors_role: owner
full_text_status: public
publication: PLOS Computational Biology
volume: 16
number: 2
article_number: e1007696
event_location: United States
citation:        Dai, K;    Hernando, J;    Billeh, YN;    Gratiy, SL;    Planas, J;    Davison, AP;    Dura-Bernal, S;                                         ... Arkhipov, A; + view all <#>        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, J-D;  Arkhipov, A;   - view fewer <#>    (2020)    The SONATA data format for efficient description of large-scale network models.                   PLOS Computational Biology , 16  (2)    , Article e1007696.  10.1371/journal.pcbi.1007696 <https://doi.org/10.1371/journal.pcbi.1007696>.       Green open access   
 
document_url: https://discovery.ucl.ac.uk/id/eprint/10093154/1/Gleeson_The%20SONATA%20data%20format%20for%20efficient%20description%20of%20large-scale%20network%20models_VoR.pdf