References and models cited by this paper

References and models that cite this paper

Achard P, De Schutter E (2006) Complex parameter landscape for a complex neuron model. PLoS Comput Biol 2:e94 [Journal] [PubMed]

Al-fares M, Loukissas A, Vahdat A (2008) A scalable, commodity data center network architecture SIGCOMM ’08: Proceedings of the ACM SIGCOMM 2008 Conference on Data Communication :62-74

Almasi G, Heidelberger P, Archer CJ, Martorell X, Erway CC, Moreira JE, Steinmacher-burow B, (2005) Optimization of MPI collective communication on BlueGene-L systems Proc. 19th annual international conference on Supercomputing :253-262

Anastassiou CA, Perin R, Markram H, Koch C (2011) Ephaptic coupling of cortical neurons. Nat Neurosci 14:217-23 [Journal] [PubMed]

Ascoli GA, Atkeson JC (2005) Incorporating anatomically realistic cellular-level connectivity in neural network models of the rat hippocampus. Biosystems 79:173-81 [Journal] [PubMed]

Ascoli GA, Donohue DE, Halavi M (2007) NeuroMorpho.Org: a central resource for neuronal morphologies. J Neurosci 27:9247-51 [Journal] [PubMed]

Bower JM, Beeman D (1998) The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System

Braitenberg V, Schuz A (1998) Cortex Statistics and Geometry of Neuronal Connectivity 2nd ed

Brette R, Rudolph M, Carnevale T, Hines M, Beeman D, Bower JM, Diesmann M, Morrison A, Goodman PH, Harris FC, Zirpe M, Natschläger T, Pecevski D, Ermentrout B, Djurfeldt M, Lansner A, Rochel O, Vieville T, Muller E, Davison AP, El Boustani S, Destexhe A (2007) Simulation of networks of spiking neurons: a review of tools and strategies. J Comput Neurosci 23:349-98 [Journal] [PubMed]

Bruce GH, Peaceman DW, Rachford HH, Rice JD (1953) Calculations of unsteady-state gas flow through porous media Trans Am Inst Mining Metallurgical Petroleum Eng 198:52-79

Chklovskii DB (2004) Synaptic connectivity and neuronal morphology: two sides of the same coin. Neuron 43:609-17 [Journal] [PubMed]

Church AJ, Andrew RD (2005) Spreading depression expands traumatic injury in neocortical brain slices. J Neurotrauma 22:277-90 [Journal] [PubMed]

Cooley JW, Dodge FA (1966) Digital computer solutions for excitation and propagation of the nerve impulse. Biophys J 6:583-99 [Journal] [PubMed]

De Schutter E, Bower JM (1994) An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. J Neurophysiol 71:375-400 [Journal] [PubMed]

De Schutter E, Bower JM (1994) An active membrane model of the cerebellar Purkinje cell II. Simulation of synaptic responses. J Neurophysiol 71:401-19 [Journal] [PubMed]

De Schutter E, Bower JM (1994) Simulated responses of cerebellar Purkinje cells are independent of the dendritic location of granule cell synaptic inputs. Proc Natl Acad Sci U S A 91:4736-40 [PubMed]

Destexhe A, Mainen Z, Sejnowski TJ (1994) An efficient method for computing synaptic conductances based on a kinetic model of receptor binding Neural Comput 6:14-18 [Journal]

Destexhe A, Mainen ZF, Sejnowski TJ (1998) Kinetic models of synaptic transmission Methods In Neuronal Modeling, Koch C:Segev I, ed. pp.1

Druckmann S, Banitt Y, Gidon A, Schürmann F, Markram H, Segev I (2007) A novel multiple objective optimization framework for constraining conductance-based neuron models by experimental data. Front Neurosci 1:7-18 [Journal] [PubMed]

Druckmann S, Berger TK, Hill S, Schürmann F, Markram H, Segev I (2008) Evaluating automated parameter constraining procedures of neuron models by experimental and surrogate data. Biol Cybern 99:371-9 [Journal] [PubMed]

Eisenstein M (2009) Neural circuits: Putting neurons on the map. Nature 461:1149-52 [Journal] [PubMed]

Evers JF, Schmitt S, Sibila M, Duch C (2005) Progress in functional neuroanatomy: precise automatic geometric reconstruction of neuronal morphology from confocal image stacks. J Neurophysiol 93:2331-42 [Journal] [PubMed]

Goddard NH, Hood G (1998) Large-scale simulation using parallel genesis The Book of GENESIS, 2nd Edn, Bower JM:Beeman D, ed. pp.349

Hines M (1984) Efficient computation of branched nerve equations. Int J Biomed Comput 15:69-76 [PubMed]

Hines M (1993) NEURON--a program for simulation of nerve equations. Neural Systems: Analysis And Modeling, Eeckman F, ed. pp.127

Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hines ML, Eichner H, Schürmann F (2008) Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors. J Comput Neurosci 25:203-10 [Journal] [PubMed]

Hines ML, Markram H, Schürmann F (2008) Fully implicit parallel simulation of single neurons. J Comput Neurosci 25:439-48 [Journal] [PubMed]

HODGKIN AL, HUXLEY AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500-44 [Journal] [PubMed]

Hong K, Nishiyama M (2010) From guidance signals to movement: signaling molecules governing growth cone turning. Neuroscientist 16:65-78 [Journal] [PubMed]

King JG, Hines M, Hill S, Goodman PH, Markram H, Schürmann F (2009) A Component-Based Extension Framework for Large-Scale Parallel Simulations in NEURON. Front Neuroinform 3:10 [Journal] [PubMed]

Kozloski J (2011) Automated reconstruction of neural tissue and the role of large-scale simulation. Neuroinformatics 9:133-42 [Journal] [PubMed]

Kozloski J, Eleftheriou M, Fitch B, Peck C (2009) Interoperable Model Graph Simulator for High-Performance Computing IBM Technical Report RC24811

Kozloski J, Sfyrakis K, Hill S, Schurmann F, Peck C, Markram H (2008) Identifying, tabulating, and analyzing contacts between branched neuron morphologies Ibm J Res Dev 52:43-55

Krichmar JL, Nasuto SJ, Scorcioni R, Washington SD, Ascoli GA (2002) Effects of dendritic morphology on CA3 pyramidal cell electrophysiology: a simulation study. Brain Res 941:11-28 [PubMed]

Kumar S, Heidelberger P, Chen D, Hines M (2010) Optimization of applications with non-blocking neighborhood collectives via multisends on the blue gene/p supercomputer Proceedings IEEE International Parallel & Distributed Processing (IPDPS) Symposium, Atlanta, GA :1-11

Markram H (2006) The blue brain project. Nat Rev Neurosci 7:153-60 [Journal] [PubMed]

Mathy A, Ho SS, Davie JT, Duguid IC, Clark BA, Häusser M (2009) Encoding of oscillations by axonal bursts in inferior olive neurons. Neuron 62:388-99 [Journal] [PubMed]

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel network simulations with NEURON. J Comput Neurosci 21:119-29 [Journal] [PubMed]

Morrison A, Mehring C, Geisel T, Aertsen AD, Diesmann M (2005) Advancing the boundaries of high-connectivity network simulation with distributed computing. Neural Comput 17:1776-801 [Journal] [PubMed]

Parnas I, Segev I (1979) A mathematical model for conduction of action potentials along bifurcating axons. J Physiol 295:323-43 [PubMed]

Rempe MJ, Chopp DL (2006) Predictor-corrector algorithm for reaction-diffusion equations associated with neural activity on branched structures Siam Journal Of Scientific Computing 28:2139-2161

Rempe MJ, Spruston N, Kath WL, Chopp DL (2008) Compartmental neural simulations with spatial adaptivity. J Comput Neurosci 25:465-80 [Journal] [PubMed]

Schmitz D, Schuchmann S, Fisahn A, Draguhn A, Buhl EH, Petrasch-Parwez E, Dermietzel R, Heinemann U, Traub RD (2001) Axo-axonal coupling. a novel mechanism for ultrafast neuronal communication. Neuron 31:831-40 [PubMed]

Segev I, Fleshman JW, Burke RE (1998) Compartmental models of complex neurons Methods in Neuronal Modeling, Koch C:Segev I, ed. pp.93

Segev I, London M (2000) Untangling dendrites with quantitative models. Science 290:744-50 [PubMed]

Sosa C (2008) IBM System Blue Gene Solution: Blue Gene-P Application Development, 3rd Edn

Thomas LH (1949) Elliptic Problems in Linear Difference Equations Over a Network Watson Scientific Computing Laboratory Report

Traub RD, Contreras D, Cunningham MO, Murray H, LeBeau FE, Roopun A, Bibbig A, Wilent WB, Higley MJ, Whittington MA (2005) Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. J Neurophysiol 93:2194-232 [Journal] [PubMed]

Traub RD, Wong RK, Miles R, Michelson H (1991) A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances. J Neurophysiol 66:635-50 [Journal] [PubMed]

Wang Y, Gupta A, Toledo-Rodriguez M, Wu CZ, Markram H (2002) Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex. Cereb Cortex 12:395-410 [PubMed]

Magalhães B, Hines M, Sterling T, Schüermann F (2019) Exploiting Flow Graph of System of ODEs to Accelerate the Simulation of Biologically-Detailed Neural Networks 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) :176-187 [Journal]

Magalhães BR, Sterling T, Hines M, Schürmann F (2019) Fully-Asynchronous Cache-Efficient Simulation of Detailed Neural Networks Computational Science -- ICCS 2019, Rodrigues, João M. F. and Cardoso, Pedro J. S. and Monteiro, Jânio and Lam, Roberto and Krzhizhanovskaya, Valeria V. and Lees, Michael H. and Dongarra, Jack J. and Sloot, Peter M.A., ed. pp.421 [Journal]

Magalhães BRC, Sterling T, Hines M, Schürmann F (2019) Asynchronous Branch-Parallel Simulation of Detailed Neuron Models. Front Neuroinform 13:54 [Journal] [PubMed]