2022
Multiscale Computer Modeling of Spreading Depolarization in Brain Slices
Kelley C, Newton AJH, Hrabetova S, McDougal RA, Lytton WW. Multiscale Computer Modeling of Spreading Depolarization in Brain Slices. ENeuro 2022, 9: eneuro.0082-22.2022. PMID: 35927026, PMCID: PMC9410770, DOI: 10.1523/eneuro.0082-22.2022.Peer-Reviewed Original ResearchConceptsBrain slicesNeuronal spike rateGreater neuronal densityExtracellular spaceEffects of hypoxiaNeuronal densityNeurologic conditionsNeuronal depolarizationNeuronal silenceNeuronal volumeRelative hypoxiaSD velocityPathologic cycleECS volumeECS shrinkageSD speedMore dendritesSpike rateSDConcentration homeostasisNeuronsDepolarizationHypoxiaSlicesMultiscale computer modeling
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 ResearchMeSH KeywordsBrainComputational BiologyComputer SimulationHumansInternetModels, NeurologicalNeural Networks, ComputerNeuronsOnline SystemsConceptsData-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
2017
Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron
Patoary M, Tropper C, McDougal RA, Lin Z, Lytton WW. Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2017, 16: 1007-1019. PMID: 28961124, PMCID: PMC5869087, DOI: 10.1109/tcbb.2017.2756930.Peer-Reviewed Original ResearchConceptsStochastic reaction-diffusion systemsDeterministic modelWave modelReaction-diffusion systemStochastic discrete event simulationStochastic modelDeterministic simulationDiscrete event simulationParallel simulationCalcium wave modelBuffer modelEvent simulationDiscrete event simulation environmentSimulationsContinuous simulationNontrivial differencesDynamicsModelSimulation environmentRare eventSystem
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 ResearchMeSH KeywordsAction PotentialsBrainComputer SimulationHumansModels, NeurologicalNeural Networks, ComputerNeuronsConceptsHigh-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
2015
Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex
Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW. Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex. Neuroscience 2015, 316: 344-366. PMID: 26746357, PMCID: PMC4724569, DOI: 10.1016/j.neuroscience.2015.12.043.Peer-Reviewed Original ResearchConceptsHCN channelsExcitation/inhibition balancePersistent activityMetabotropic glutamate receptorsCalcium regulationNeuronal persistent activityEndoplasmic reticulum storesIonotropic inputsGABAB receptorsGlutamate receptorsInhibition balanceMultiple pathwaysCell excitabilityCortical layersMembrane depolarizationCompartmental neuronsInositol triphosphateIP3 receptorReceptorsNeuronsActivationMolecular eventsNeocortical modelsDepolarizationPathwayNeuronal Calcium Wave Propagation Varies with Changes in Endoplasmic Reticulum Parameters: A Computer Model
Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW. Neuronal Calcium Wave Propagation Varies with Changes in Endoplasmic Reticulum Parameters: A Computer Model. Neural Computation 2015, 27: 898-924. PMID: 25734493, PMCID: PMC4386758, DOI: 10.1162/neco_a_00712.Peer-Reviewed Original Research