2023
Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories
Cudone E, Lower A, McDougal R. Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories. PLOS Computational Biology 2023, 19: e1011548. PMID: 37824576, PMCID: PMC10597496, DOI: 10.1371/journal.pcbi.1011548.Peer-Reviewed Original ResearchConceptsInitial conditionsDifferential equation modelMore biological detailUnknown initial conditionsLarge network modelsDifferential equationsMore computational resourcesCell state variablesData-driven modelingState variablesNeuron statesLarge systemsComputational resourcesModel time constantsModeling assumptionsModel statesEquationsNetwork modelModeling frameworkBiological detailsDetailed simulationsAdditional realismCellular biophysicsModerate numberInput history
2022
Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks
McDougal RA, Conte C, Eggleston L, Newton AJH, Galijasevic H. Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks. Frontiers In Neuroinformatics 2022, 16: 847108. PMID: 35655652, PMCID: PMC9152282, DOI: 10.3389/fninf.2022.847108.Peer-Reviewed Original ResearchFinite volume method simulationIrregular 3D geometryMethod simulationsDouglas-GunnDimensional simulationsHigh-dimensional simulationsWave curvatureEfficient simulationSimulationsParallel algorithmCylinderModels of neuronsNetwork modelNEURON simulatorReconstruction algorithmRegion of interestAccelerated versionConnected cylindersReaction diffusionReaction-diffusion kineticsElectrophysiological simulationsAlgorithmKinetics
2019
NetPyNE, 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