2022
Modernizing the NEURON Simulator for Sustainability, Portability, and Performance
Awile O, Kumbhar P, Cornu N, Dura-Bernal S, King JG, Lupton O, Magkanaris I, McDougal RA, Newton AJH, Pereira F, Săvulescu A, Carnevale NT, Lytton WW, Hines ML, Schürmann F. Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. Frontiers In Neuroinformatics 2022, 16: 884046. PMID: 35832575, PMCID: PMC9272742, DOI: 10.3389/fninf.2022.884046.Peer-Reviewed Original ResearchComputer architectureDomain-specific languageCloud platformSoftware distributionScientific workflowsDeveloper baseSource compilerHardware platformTime compilationBuild systemSimulation engineContinuous integrationSimulation platformComputational neuroscienceNew usersNEURON simulatorSimulation performanceBiological modelingUsersPlatformArchitectureWorkflowBetter documentationBackendGPU
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 ResearchConceptsGraphical 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
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
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 interest
2015
ModelView 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 hundredsSharing