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