2022
Modernizing the NEURON Simulator for Sustainability, Portability, and Performance
Awile O, Kumbhar P, Cornu N, Dura-Bernal S, King JG, Lupton O, Magkanaris I, McDougal RA, Newton AJH, Pereira F, Săvulescu A, Carnevale NT, Lytton WW, Hines ML, Schürmann F. Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. Frontiers In Neuroinformatics 2022, 16: 884046. PMID: 35832575, PMCID: PMC9272742, DOI: 10.3389/fninf.2022.884046.Peer-Reviewed Original ResearchComputer architectureDomain-specific languageCloud platformSoftware distributionScientific workflowsDeveloper baseSource compilerHardware platformTime compilationBuild systemSimulation engineContinuous integrationSimulation platformComputational neuroscienceNew usersNEURON simulatorSimulation performanceBiological modelingUsersPlatformArchitectureWorkflowBetter documentationBackendGPU
2019
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits
Gleeson P, Cantarelli M, Marin B, Quintana A, Earnshaw M, Sadeh S, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic NA, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, Idili G, Lanore F, Larson SD, Lytton WW, Majumdar A, McDougal RA, Sivagnanam S, Solinas S, Stanislovas R, van Albada SJ, van Geit W, Silver RA. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Neuron 2019, 103: 395-411.e5. PMID: 31201122, PMCID: PMC6693896, DOI: 10.1016/j.neuron.2019.05.019.Peer-Reviewed Original ResearchConceptsData-driven modelsReproducibility of modelsCollaborative interactionsCollaborative resourceExperimental resultsComputational modelAnalyzingReuseStandardized modelModel structureSpecialist knowledgeMultiple scalesComplex biological systemsSharingVisualizingToolInfrastructureNetworkNew modelPlatformPowerful toolSimulatingModelWider communityAdoption