2024
Expression of model ion channel currents generated using neuron in silico software in real time using dynamic clamp
Acharya S, Panama B, Korbel L, Nilsson L, Hines M, Carnevale N, Bett G, Rasmusson R, Nowak M. Expression of model ion channel currents generated using neuron in silico software in real time using dynamic clamp. Biophysical Journal 2024, 123: 532a-533a. DOI: 10.1016/j.bpj.2023.11.3218.Peer-Reviewed Original Research
2023
Input of expressed hERG current into a complex neuron in silico cardiac atrial cell: Implications for cardiotoxicity screening
Nowak M, Korbel L, Kane A, Panama B, Hines M, Carnevale N, Bett G, Rasmusson R. Input of expressed hERG current into a complex neuron in silico cardiac atrial cell: Implications for cardiotoxicity screening. Biophysical Journal 2023, 122: 382a. DOI: 10.1016/j.bpj.2022.11.2097.Peer-Reviewed Original Research
2022
NEURON Simulation Environment
Hines M, Carnevale T, McDougal R. NEURON Simulation Environment. 2022, 2355-2361. DOI: 10.1007/978-1-0716-1006-0_795.Peer-Reviewed Original ResearchNumerical Integration Methods
Hines M, Carnevale T. Numerical Integration Methods. 2022, 2487-2496. DOI: 10.1007/978-1-0716-1006-0_242.Peer-Reviewed Original ResearchModelDB
McDougal R, Wang R, Morse T, Migliore M, Marenco L, Carnevale T, Hines M, Shepherd G. ModelDB. 2022, 2053-2056. DOI: 10.1007/978-1-0716-1006-0_158.Peer-Reviewed Original ResearchSenseLab: Integration of Multidisciplinary Neuroscience Data
Shepherd G, Morse T, Marenco L, Cheung K, Carnevale T, Migliore M, McDougal R, Hines M, Miller P. SenseLab: Integration of Multidisciplinary Neuroscience Data. 2022, 3069-3072. DOI: 10.1007/978-1-0716-1006-0_497.Peer-Reviewed Original ResearchInterfacing a real-time dynamic clamp system with neuron simulation software in living cells
Nowak M, Korbel L, Kane A, Panama B, Hines M, Carnevale N, Bett G, Rasmusson R. Interfacing a real-time dynamic clamp system with neuron simulation software in living cells. Biophysical Journal 2022, 121: 391a. DOI: 10.1016/j.bpj.2021.11.818.Peer-Reviewed Original Research
2020
An Optimizing Multi-platform Source-to-source Compiler Framework for the NEURON MODeling Language
Kumbhar P, Awile O, Keegan L, Alonso J, King J, Hines M, Schürmann F. An Optimizing Multi-platform Source-to-source Compiler Framework for the NEURON MODeling Language. Lecture Notes In Computer Science 2020, 12137: 45-58. PMCID: PMC7302241, DOI: 10.1007/978-3-030-50371-0_4.Peer-Reviewed Original ResearchDomain-specific languageDomain-specific optimizationsSource compiler frameworkCode generation frameworkTarget code generationUser modelCompiler frameworkModeling languageCode generationMultiple SIMDModern hardwareTarget architectureParallel simulationGeneration frameworkOverall speedupEfficient codeUser communityOptimized kernelsSpeedupAlgebraic simplificationSoftwareFrameworkCodeProduction simulationKernelFully-Asynchronous Fully-Implicit Variable-Order Variable-Timestep Simulation of Neural Networks
Magalhães B, Hines M, Sterling T, Schürmann F. Fully-Asynchronous Fully-Implicit Variable-Order Variable-Timestep Simulation of Neural Networks. Lecture Notes In Computer Science 2020, 12141: 94-108. PMCID: PMC7302593, DOI: 10.1007/978-3-030-50426-7_8.Peer-Reviewed Original Research
2019
NEURON Simulation Environment
Hines M, Carnevale T, McDougal R. NEURON Simulation Environment. 2019, 1-7. DOI: 10.1007/978-1-4614-7320-6_795-2.Peer-Reviewed Original ResearchFully-Asynchronous Cache-Efficient Simulation of Detailed Neural Networks
Magalhães B, Sterling T, Hines M, Schürmann F. Fully-Asynchronous Cache-Efficient Simulation of Detailed Neural Networks. Lecture Notes In Computer Science 2019, 11538: 421-434. DOI: 10.1007/978-3-030-22744-9_33.Peer-Reviewed Original ResearchRuntime systemNeural networkScientific applicationsLarge-scale scientific applicationsAsynchronous runtime systemHPX runtime systemParalleX execution modelOverlap of computationLinear data structuresBetter cache localityCompute architecturesExecution modelParallel executionCore kernelsData structureCache localitySynchronous executionMemory spaceCache levelsNode levelBenchmark resultsExecutionLower timeNumber of timestepsNetworkExploiting Flow Graph of System of ODEs to Accelerate the Simulation of Biologically-Detailed Neural Networks
Magalhães B, Hines M, Sterling T, Schürmann F. Exploiting Flow Graph of System of ODEs to Accelerate the Simulation of Biologically-Detailed Neural Networks. 2019, 00: 176-187. DOI: 10.1109/ipdps.2019.00028.Peer-Reviewed Original ResearchCompute nodesScientific use casesHPX runtime systemParalleX execution modelSingle compute nodeLarge-scale benchmarksGranularity of parallelismCompute architecturesRuntime systemAsynchronous executionExecution modelUse casesData implementationParallel simulatorNeural networkScientific applicationsFlow graphDifferent architecturesStrong scalingCore requirementsConcurrent outputArchitectureFlow dependencyParallelismLarge systemsPerformance Analysis of Computational Neuroscience Software NEURON on Knights Corner Many Core Processors
Kumbhar P, Sivagnanam S, Yoshimoto K, Hines M, Carnevale T, Majumdar A. Performance Analysis of Computational Neuroscience Software NEURON on Knights Corner Many Core Processors. Communications In Computer And Information Science 2019, 964: 67-76. DOI: 10.1007/978-981-13-7729-7_5.Peer-Reviewed Original ResearchCore processorsKnights CornerMessage Passing Interface (MPI) libraryHigh performance resourcesLoad imbalance issueHigh-performance computingKnights Landing processorPerformance computingInterface libraryLoad balanceDifferent size problemsSimulation environmentParallel performancePerformance resourcesImbalance issueProcessorsLarge modelsSize problemsPerformance analysisHigh performanceNeuroscience communityPerformance of neuronsNetwork of neuronsComputingParallelization
2016
25th Annual Computational Neuroscience Meeting: CNS-2016
Sharpee T, Destexhe A, Kawato M, Sekulić V, Skinner F, Wójcik D, Chintaluri C, Cserpán D, Somogyvári Z, Kim J, Kilpatrick Z, Bennett M, Josić K, Elices I, Arroyo D, Levi R, Rodriguez F, Varona P, Hwang E, Kim B, Han H, Kim T, McKenna J, Brown R, McCarley R, Choi J, Rankin J, Popp P, Rinzel J, Tabas A, Rupp A, Balaguer-Ballester E, Maturana M, Grayden D, Cloherty S, Kameneva T, Ibbotson M, Meffin H, Koren V, Lochmann T, Dragoi V, Obermayer K, Psarrou M, Schilstra M, Davey N, Torben-Nielsen B, Steuber V, Ju H, Yu J, Hines M, Chen L, Yu Y, Kim J, Leahy W, Shlizerman E, Birgiolas J, Gerkin R, Crook S, Viriyopase A, Memmesheimer R, Gielen S, Dabaghian Y, DeVito J, Perotti L, Kim A, Fenk L, Cheng C, Maimon G, Zhao C, Widmer Y, Sprecher S, Senn W, Halnes G, Mäki-Marttunen T, Keller D, Pettersen K, Andreassen O, Einevoll G, Yamada Y, Steyn-Ross M, Alistair Steyn-Ross D, Mejias J, Murray J, Kennedy H, Wang X, Kruscha A, Grewe J, Benda J, Lindner B, Badel L, Ohta K, Tsuchimoto Y, Kazama H, Kahng B, Tam N, Pollonini L, Zouridakis G, Soh J, Kim D, Yoo M, Palmer S, Culmone V, Bojak I, Ferrario A, Merrison-Hort R, Borisyuk R, Kim C, Tezuka T, Joo P, Rho Y, Burton S, Bard Ermentrout G, Jeong J, Urban N, Marsalek P, Kim H, Moon S, Lee D, Lee S, Lee J, Molkov Y, Hamade K, Teka W, Barnett W, Kim T, Markin S, Rybak I, Forro C, Dermutz H, Demkó L, Vörös J, Babichev A, Huang H, Verduzco-Flores S, Dos Santos F, Andras P, Metzner C, Schweikard A, Zurowski B, Roach J, Sander L, Zochowski M, Skilling Q, Ognjanovski N, Aton S, Zochowski M, Wang S, Ouyang G, Guang J, Zhang M, Michael Wong K, Zhou C, Robinson P, Sanz-Leon P, Drysdale P, Fung F, Abeysuriya R, Rennie C, Zhao X, Choe Y, Yang H, Mi Y, Lin X, Wu S, Liedtke J, Schottdorf M, Wolf F, Yamamura Y, Wickens J, Rumbell T, Ramsey J, Reyes A, Draguljić D, Hof P, Luebke J, Weaver C, He H, Yang X, Ma H, Xu Z, Wang Y, Baek K, Morris L, Kundu P, Voon V, Agnes E, Vogels T, Podlaski W, Giese M, Kuravi P, Vogels R, Seeholzer A, Podlaski W, Ranjan R, Vogels T, Torres J, Baroni F, Latorre R, Gips B, Lowet E, Roberts M, de Weerd P, Jensen O, van der Eerden J, Goodarzinick A, Niry M, Valizadeh A, Pariz A, Parsi S, Warburton J, Marucci L, Tamagnini F, Brown J, Tsaneva-Atanasova K, Kleberg F, Triesch J, Moezzi B, Iannella N, Schaworonkow N, Plogmacher L, Goldsworthy M, Hordacre B, McDonnell M, Ridding M, Zapotocky M, Smit D, Fouquet C, Trembleau A, Dasgupta S, Nishikawa I, Aihara K, Toyoizumi T, Robb D, Mellen N, Toporikova N, Tang R, Tang Y, Liang G, Kiser S, Howard J, Goncharenko J, Voronenko S, Ahamed T, Stephens G, Yger P, Lefebvre B, Spampinato G, Esposito E, et Olivier Marre M, Choi H, Song M, Chung S, Lee D, Sompolinsky H, Phillips R, Smith J, Chatzikalymniou A, Ferguson K, Alex Cayco Gajic N, Clopath C, Angus Silver R, Gleeson P, Marin B, Sadeh S, Quintana A, Cantarelli M, Dura-Bernal S, Lytton W, Davison A, Li L, Zhang W, Wang D, Song Y, Park S, Choi I, Shin H, Choi H, Pasupathy A, Shea-Brown E, Huh D, Sejnowski T, Vogt S, Kumar A, Schmidt R, Van Wert S, Schiff S, Veale R, Scheutz M, Lee S, Gallinaro J, Rotter S, Rubchinsky L, Cheung C, Ratnadurai-Giridharan S, Shomali S, Ahmadabadi M, Shimazaki H, Nader Rasuli S, Zhao X, Rasch M, Wilting J, Priesemann V, Levina A, Rudelt L, Lizier J, Spinney R, Rubinov M, Wibral M, Bak J, Pillow J, Zaho Y, Park I, Kang J, Park H, Jang J, Paik S, Choi W, Lee C, Song M, Lee H, Park Y, Yilmaz E, Baysal V, Ozer M, Saska D, Nowotny T, Chan H, Diamond A, Herrmann C, Murray M, Ionta S, Hutt A, Lefebvre J, Weidel P, Duarte R, Morrison A, Lee J, Iyer R, Mihalas S, Koch C, Petrovici M, Leng L, Breitwieser O, Stöckel D, Bytschok I, Martel R, Bill J, Schemmel J, Meier K, Esler T, Burkitt A, Kerr R, Tahayori B, Nolte M, Reimann M, Muller E, Markram H, Parziale A, Senatore R, Marcelli A, Skiker K, Maouene M, Neymotin S, Seidenstein A, Lakatos P, Sanger T, Menzies R, McLauchlan C, van Albada S, Kedziora D, Neymotin S, Kerr C, Suter B, Shepherd G, Ryu J, Lee S, Lee J, Lee H, Lim D, Wang J, Lee H, Jung N, Anh Quang L, Maeng S, Lee T, Lee J, Park C, Ahn S, Moon J, Choi Y, Kim J, Jun S, Lee S, Lee H, Jo S, Jun E, Yu S, Goetze F, Lai P, Kim S, Kwag J, Jang H, Filipović M, Reig R, Aertsen A, Silberberg G, Bachmann C, Buttler S, Jacobs H, Dillen K, Fink G, Kukolja J, Kepple D, Giaffar H, Rinberg D, Shea S, Koulakov A, Bahuguna J, Tetzlaff T, Kotaleski J, Kunze T, Peterson A, Knösche T, Kim M, Kim H, Park J, Yeon J, Kim S, Kang J, Lee C, Spiegler A, Petkoski S, Palva M, Jirsa V, Saggio M, Siep S, Stacey W, Bernar C, Choung O, Jeong Y, Lee Y, Kim S, Jeong M, Lee J, Kwon J, Kralik J, Jahng J, Hwang D, Kwon J, Park S, Kim S, Kim H, Kim P, Yoon S, Lim S, Park C, Miller T, Clements K, Ahn S, Ji E, Issa F, Baek J, Oba S, Yoshimoto J, Doya K, Ishii S, Mosqueiro T, Strube-Bloss M, Smith B, Huerta R, Hadrava M, Hlinka J, Bos H, Helias M, Welzig C, Harper Z, Kim W, Shin I, Baek H, Han S, Richter R, Vitay J, Beuth F, Hamker F, Toppin K, Guo Y, Graham B, Kale P, Gollo L, Stern M, Abbott L, Fedorov L, Giese M, Ardestani M, Faraji M, Preuschoff K, Gerstner W, van Gendt M, Briaire J, Kalkman R, Frijns J, Lee W, Frangou S, Fulcher B, Tran P, Fornito A, Gliske S, Lim E, Holman K, Fink C, Kim J, Mu S, Briggman K, Sebastian Seung H, the EyeWirers, Wegener D, Bohnenkamp L, Ernst U, Devor A, Dale A, Lines G, Edwards A, Tveito A, Hagen E, Senk J, Diesmann M, Schmidt M, Bakker R, Shen K, Bezgin G, Hilgetag C, van Albada S, Sun H, Sourina O, Huang G, Klanner F, Denk C, Glomb K, Ponce-Alvarez A, Gilson M, Ritter P, Deco G, Witek M, Clarke E, Hansen M, Wallentin M, Kringelbach M, Vuust P, Klingbeil G, De Schutter E, Chen W, Zang Y, Hong S, Takashima A, Zamora C, Gallimore A, Goldschmidt D, Manoonpong P, Karoly P, Freestone D, Soundry D, Kuhlmann L, Paninski L, Cook M, Lee J, Fishman Y, Cohen Y, Roberts J, Cocchi L, Sweeney Y, Lee S, Jung W, Kim Y, Jung Y, Song Y, Chavane F, Soman K, Muralidharan V, Srinivasa Chakravarthy V, Shivkumar S, Mandali A, Pragathi Priyadharsini B, Mehta H, Davey C, Brinkman B, Kekona T, Rieke F, Buice M, De Pittà M, Berry H, Brunel N, Breakspear M, Marsat G, Drew J, Chapman P, Daly K, Bradle S, Seo S, Su J, Kavalali E, Blackwell J, Shiau L, Buhry L, Basnayake K, Lee S, Levy B, Baker C, Leleu T, Philips R, Chhabria K. 25th Annual Computational Neuroscience Meeting: CNS-2016. BMC Neuroscience 2016, 17: 54. PMID: 27534393, PMCID: PMC5001212, DOI: 10.1186/s12868-016-0283-6.Peer-Reviewed Original ResearchRetinal ganglion cellsGanglion cellsBasal gangliaSynaptic connectivityElectrical stimulationNeural activityGamma oscillationsIctal-like epileptiform activityNeuronal ion channel functionBrain networksDistribution of inhibitoryParvalbumin-positive neuronsBrain structure abnormalitiesEffects of riluzoleParkinsonian basal gangliaShort-term synaptic plasticityHigh-frequency neuronsField potentialsLong-term depressionRole of cerebellumPrimary visual cortexDependent protein kinase II activityAdaptation of neuronsTime-periodic coupling strengthResting-state activityLeveraging a Cluster-Booster Architecture for Brain-Scale Simulations
Kumbhar P, Hines M, Ovcharenko A, Mallon D, King J, Sainz F, Schürmann F, Delalondre F. Leveraging a Cluster-Booster Architecture for Brain-Scale Simulations. Lecture Notes In Computer Science 2016, 9697: 363-380. DOI: 10.1007/978-3-319-41321-1_19.Peer-Reviewed Original ResearchCluster-Booster architectureComplex scientific workflowsBrain-scale simulationsIntel MIC platformIntel Xeon Phi coprocessorXeon Phi coprocessorType of architectureSupercomputing architecturesScalable partScientific workflowsIntel MICStampede supercomputerCompute EngineCompute kernelsMIC platformData structureDevelopment workflowImplementation detailsScientific applicationsArchitecture performanceCore simulatorArchitectureEntry platformDeep platformPlatformERROR ANALYSIS AND QUANTIFICATION IN NEURON SIMULATIONS
Casalegno F, Cremonesi F, Yates S, Hines M, Schürmann F, Delalondre F. ERROR ANALYSIS AND QUANTIFICATION IN NEURON SIMULATIONS. 2016, 1366-1380. DOI: 10.7712/100016.1892.7366.Peer-Reviewed Original Research
2015
Parallelizing large networks using NEURON-Python
Seidenstein A, McDougal R, Hines M, Lytton W. Parallelizing large networks using NEURON-Python. BMC Neuroscience 2015, 16: p151. PMCID: PMC4697477, DOI: 10.1186/1471-2202-16-s1-p151.Peer-Reviewed Original ResearchNTW-MT
Lin Z, Tropper C, Patoary M, McDougal R, Lytton W, Hines M. NTW-MT. 2015, 157-167. DOI: 10.1145/2769458.2769459.Peer-Reviewed Original ResearchNumerical Integration Methods
Hines M, Carnevale T. Numerical Integration Methods. 2015, 2115-2124. DOI: 10.1007/978-1-4614-6675-8_242.Peer-Reviewed Original ResearchNEURON Simulation Environment
Hines M, Carnevale T. NEURON Simulation Environment. 2015, 2012-2017. DOI: 10.1007/978-1-4614-6675-8_795.Books