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
2020
Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data
Neymotin SA, Daniels DS, Caldwell B, McDougal RA, Carnevale NT, Jas M, Moore CI, Hines ML, Hämäläinen M, Jones SR. Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data. ELife 2020, 9: e51214. PMID: 31967544, PMCID: PMC7018509, DOI: 10.7554/elife.51214.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsElectroencephalographyEvoked PotentialsHumansMagnetoencephalographyModels, NeurologicalNeocortexSoftwareUser-Computer InterfaceConceptsGraphical user interfaceNew software toolUser interfaceMEG/EEGSoftware toolsMEG/EEG dataTranslational neuroscience researchNew therapiesNeural originReliable markerDisease statesEEG dataBrain rhythmsNetwork originBrain activityHuman brain activityElectro-encephalographyInformation processingEEGUsersNeuroscience research
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
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience
McDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML. Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. Journal Of Computational Neuroscience 2016, 42: 1-10. PMID: 27629590, PMCID: PMC5279891, DOI: 10.1007/s10827-016-0623-7.Peer-Reviewed Original ResearchConceptsComputational neuroscience modelsHigh performance computationEssential modeling toolUser experienceData-based modelsPerformance computationModelDBGraphical toolUser-friendly databaseModeling toolsResearch topicNeuroscience modelsCollect dataNew challengesNeuron modelingConvenient venueMassive developmentComplex modelsNew technologiesLarge research groupsRunning modelFuture of neuroscienceUsersMultiple scalesModel of interestSimulation 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 modelsDepolarizationPathwayModelView for ModelDB: Online Presentation of Model Structure
McDougal RA, Morse TM, Hines ML, Shepherd GM. ModelView for ModelDB: Online Presentation of Model Structure. Neuroinformatics 2015, 13: 459-470. PMID: 25896640, PMCID: PMC4618280, DOI: 10.1007/s12021-015-9269-2.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsComputational BiologyDatabases as TopicHumansModels, NeurologicalNeuronsNonlinear DynamicsOnline SystemsStochastic ProcessesConceptsSource codeModel source codeComputational neuroscience modelsWeb applicationModel reuseUser interfaceVisualization algorithmsWeb presentationCode sharingGraphical viewModelDBContextual informationSearchable repositoryManual curationModel structureNeuroscience modelsOnline presentationCodeNecessary dataData analysisKey featuresUsersRepositoryStructures of hundredsSharingNeuronal 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
2013
Water-tight membranes from neuronal morphology files
McDougal RA, Hines ML, Lytton WW. Water-tight membranes from neuronal morphology files. Journal Of Neuroscience Methods 2013, 220: 167-178. PMID: 24091136, PMCID: PMC4197804, DOI: 10.1016/j.jneumeth.2013.09.011.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsCell MembraneImaging, Three-DimensionalModels, NeurologicalNeuronsWaterConceptsConstructive solid geometryFull shapeGeometry algorithmsSolid geometryElectrophysiology simulationsTriangular meshesMulti-scale modelSuch modelsReaction-diffusion simulationsElectrophysiological simulationsSimple interpretationGeometryAlgorithmSurface trianglesSimulationsList of pointsSpace constantsMorphology descriptionDistance calculationNeuronal geometryThree-dimensional shapeSmall objects