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 communityAdoptionNetPyNE, a tool for data-driven multiscale modeling of brain circuits
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. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. ELife 2019, 8: e44494. PMID: 31025934, PMCID: PMC6534378, DOI: 10.7554/elife.44494.Peer-Reviewed Original ResearchConceptsInformation-theoretic measuresDeclarative languageImplementation codeGraphical interfaceNetPyNENetwork parametersTheoretic measuresNetwork modelNeuron networkStandardized formatUsersMillions of cellsConnectivity rulesExperimental datasetsNetworkRaster plotMultiscale network modelMultiple scalesDatasetToolModelersSpecificationModel parametersModelingVisualization
2016
Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON
Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schürmann F, Hines ML. Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Computation 2016, 28: 2063-2090. PMID: 27557104, PMCID: PMC5295685, DOI: 10.1162/neco_a_00876.Peer-Reviewed Original ResearchConceptsHigh-performance computersLarge networksData management approachNew simulation technologyNeuronal network simulationsTypes of networksSimulation run timeMore big dataNumber of nodesNeuroscience GatewayBig dataData storageNetwork simulationComputational neuroscienceSimulation technologyHybrid networkNEURON simulatorNetwork sizeRun timeNetworkSimulation setupSuch simulationsFire neuronsMajor research initiativeNodes