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
Conditions for Synaptic Specificity during the Maintenance Phase of Synaptic Plasticity
Huertas MA, Newton AJH, McDougal RA, Sacktor TC, Shouval HZ. Conditions for Synaptic Specificity during the Maintenance Phase of Synaptic Plasticity. ENeuro 2022, 9: eneuro.0064-22.2022. PMID: 35443991, PMCID: PMC9087736, DOI: 10.1523/eneuro.0064-22.2022.Peer-Reviewed Original 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 ResearchConceptsData-driven modelsReproducibility of modelsCollaborative interactionsCollaborative resourceExperimental resultsComputational modelAnalyzingReuseStandardized modelModel structureSpecialist knowledgeMultiple scalesComplex biological systemsSharingVisualizingToolInfrastructureNetworkNew modelPlatformPowerful toolSimulatingModelWider communityAdoption
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 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
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 ResearchConceptsSource 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 ResearchConceptsConstructive solid geometryFull shapeGeometry algorithmsSolid geometryElectrophysiology simulationsTriangular meshesMulti-scale modelSuch modelsReaction-diffusion simulationsElectrophysiological simulationsSimple interpretationGeometryAlgorithmSurface trianglesSimulationsList of pointsSpace constantsMorphology descriptionDistance calculationNeuronal geometryThree-dimensional shapeSmall objects