Neurite: electrophysiological-mechanical coupling simulation framework (Garcia-Grajales et al 2015)

 Download zip file 
Help downloading and running models
Accession:168861
Neurite simulates the electrical signal propagation in myelinated and unmyelinated axons, and in dendritic trees under mechanical loading. Two different solvers are available (explicit and implicit) with sequential (CPU) and parallel (GPUs) versions
Reference:
1 . Garci­a-Grajales JA, Rucabado G, Garci­a-Dopico A, Pena JM, Jerusalem A (2015) Neurite, a Finite Difference Large Scale Parallel Program for the Simulation of Electrical Signal Propagation in Neurites under Mechanical Loading. PLoS One 10(2):e0116532 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Axon; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Myelinated neuron;
Channel(s): I Sodium; I Potassium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program;
Model Concept(s): Action Potential Initiation; Axonal Action Potentials; Action Potentials;
Implementer(s): Garcia-Grajales, Julian Andres ;
Search NeuronDB for information about:  I Sodium; I Potassium;
  
/
Neurite_Public
applications
bin
build
doc
inc
others
src
README.txt
license.txt
Makefile
                            
Neurite is a program with wich the simulations shown in the paper
J.A. Garcia-Grajales, G. Rucabado, A. Garcia-Dopico, J.M. Pena and
A. Jerusalem, "Neurite, a finite difference large scale parallel
program for the simulation of the electrical signal propagation in
neurites under mechanical loading", García-Grajales JA, Rucabado G,
García-Dopico A, Peña J-M, Jérusalem A (2015), PLoS ONE 10(2):
e0116532. doi:10.1371/journal.pone.0116532, have been carried out.

Neurite is a finite difference program that simulates the electrical
signal propagation in myelinated and unmyelinated axons, and in
dendritic trees under mechanical loading. The program has two
different solvers---explicit and implicit---that can be executed
sequentially with a CPU processor or in parallel with GPU
accelerators.

To compile the code in UNIX system, type "make" in the root directory
(see in the Makefile for more compiling options). To execute a
simulation, go in the applications folder and follow the Readme.

Garci­a-Grajales JA, Rucabado G, Garci­a-Dopico A, Pena JM, Jerusalem A (2015) Neurite, a Finite Difference Large Scale Parallel Program for the Simulation of Electrical Signal Propagation in Neurites under Mechanical Loading. PLoS One 10(2):e0116532[PubMed]

References and models cited by this paper

References and models that cite this paper

Alford PW, Dabiri BE, Goss JA, Hemphill MA, Brigham MD, Parker KK (2011) Blast-induced phenotypic switching in cerebral vasospasm. Proc Natl Acad Sci U S A 108:12705-10 [PubMed]

Ascoli GA (2006) Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat Rev Neurosci 7:318-24 [PubMed]

Babbs CF, Shi R (2013) Subtle paranodal injury slows impulse conduction in a mathematical model of myelinated axons. PLoS One 8:e67767-96 [PubMed]

Belu R (2007) Using finite difference methods instead of standard calculus in teaching physics. Annual ASEE Conference and Exposition.

Bhalla US, Bilitch DH, Bower JM (1992) Rallpacks: a set of benchmarks for neuronal simulators. Trends Neurosci 15:453-8 [PubMed]

Blight AR (1985) Computer simulation of action potentials and afterpotentials in mammalian myelinated axons: the case for a lower resistance myelin sheath. Neuroscience 15:13-31 [PubMed]

Blight AR, Someya S (1985) Depolarizing afterpotentials in myelinated axons of mammalian spinal cord. Neuroscience 15:1-12 [PubMed]

Boucher PA, Joos B, Morris CE (2012) Coupled left-shift of Nav channels: modeling the Na(+)-loading and dysfunctional excitability of damaged axons J Comput Neurosci. [Journal] [PubMed]

   Nodes of Ranvier with left-shifted Nav channels (Boucher et al. 2012) [Model]

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

Cernak I, Noble-Haeusslein LJ (2010) Traumatic brain injury: an overview of pathobiology with emphasis on military populations. J Cereb Blood Flow Metab 30:255-66 [PubMed]

Channelpedia (2014) Channelpedia http:--channelpedia.epfl.ch

Cloots RJ, van Dommelen JA, Kleiven S, Geers MG (2013) Multi-scale mechanics of traumatic brain injury: predicting axonal strains from head loads. Biomech Model Mechanobiol 12:137-50 [PubMed]

Connell S, Gao J, Chen J, Shi R (2011) Novel model to investigate blast injury in the central nervous system. J Neurotrauma 28:1229-36 [PubMed]

Dagum L, Menon R (1998) Openmp: An industry-standard api for shared-memory programming Ieee Computational Science Engineering 5:46-55

Dalton S, Bell N (2013) Cusp: A c++ templated sparse matrix library. http:--cusplibrary.github.io.

De_camargo R (2011) A multi-GPU algorithm for communication in neuronal network simulations HiPC International Conference :1-10

De_camargo R, Rozante L, Song S (2011) A multi-GPU algorithm for large-scale neuronal networks. Concurrency and Computation: Practice And Experience 23:556-572

Fidjeland AK, Gamez D, Shanahan MP, Lazdins E (2013) Three tools for the real-time simulation of embodied spiking neural networks using GPUs. Neuroinformatics 11:267-90 [PubMed]

FITZHUGH R (1962) Computation of impulse initiation and saltatory conduction in a myelinated nerve fiber. Biophys J 2:11-21 [PubMed]

Franze K, Guck J (2010) The biophysics of neuronal growth Reports on Progress in Physics 73:1-19

Goldman L, Albus JS (1968) Computation of impulse conduction in myelinated fibers; theoretical basis of the velocity-diameter relation. Biophys J 8:596-607 [PubMed]

Goldstein LE, Fisher AM, Tagge CA, Zhang XL, Velisek L, Sullivan JA, Upreti C, Kracht JM, Eri (2012) Chronic traumatic encephalopathy in blast-exposed military veterans and a blast neurotrauma mouse model. Sci Transl Med 4:134ra60-9

Gonzalez C, Couve A (2014) The axonal endoplasmic reticulum and protein trafficking: Cellular bootlegging south of the soma. Semin Cell Dev Biol 27:23-31

Gropp W, Lusk E, Doss N, Skjellum A (1996) A high-performance, portable implementation of the mpi message passing interface standard Parallel Computing 22:789-828

Hamori J, Silakov VL (1981) Myelinated perikarya and dendrites in lateral geniculate nucleus of adult cat following chronic cortical deafferentation. J Neurocytol 10:879-88 [PubMed]

Heinecke A, Klemm M, Bungartz HJ (2012) From gpgpu to many-core: Nvidia fermi and intel many integrated core architecture Computing In Science Engineering 14:78-83

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

Hines ML, Carnevale NT (2008) Translating network models to parallel hardware in NEURON J. Neurosci. Meth. 169:425-455 [Journal] [PubMed]

   Translating network models to parallel hardware in NEURON (Hines and Carnevale 2008) [Model]

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]

   Squid axon (Hodgkin, Huxley 1952) (LabAXON) [Model]
   Squid axon (Hodgkin, Huxley 1952) (NEURON) [Model]
   Squid axon (Hodgkin, Huxley 1952) (SNNAP) [Model]
   Squid axon (Hodgkin, Huxley 1952) used in (Chen et al 2010) (R language) [Model]
   Squid axon (Hodgkin, Huxley 1952) (SBML, XPP, other) [Model]

Hutchinson NA, Koles ZJ, Smith RS (1970) Conduction velocity in myelinated nerve fibres of Xenopus laevis. J Physiol 208:279-89 [PubMed]

Intel_software_network (2012) Math kernel library (mkl) http:--software.intel.com-en-us-articles- intel-mkl-

Ishizuka N, Cowan WM, Amaral DG (1995) A quantitative analysis of the dendritic organization of pyramidal cells in the rat hippocampus. J Comp Neurol 362:17-45 [PubMed]

   [47 reconstructed morphologies on NeuroMorpho.Org]

Jerusalem A, Dao M (2012) Continuum modeling of a neuronal cell under blast loading. Acta Biomater 8:3360-71 [PubMed]

Jerusalem A, García-Grajales JA, Merchan-Perez A, Peña JM (2014) A computational model coupling mechanics and electrophysiology in spinal cord injury. Biomech Model Mechanobiol 13:883-96 [PubMed]

Koch C (1999) Biophysics Of Computation: Information Processing in Single Neurons

Koles ZJ, Rasminsky M (1972) A computer simulation of conduction in demyelinated nerve fibres. J Physiol 227:351-64 [PubMed]

Kotaleski JH, Blackwell KT (2010) Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches. Nat Rev Neurosci 11:239-51 [PubMed]

Lax P, Richtmeyer R (1956) Survey of the stability of linear finite difference equations Communications On Pure Applied Mathematics 9:267-293

Lukarski D (2013) Paralution project http:--www.paralution.com

Marti­ D, Rinzel J (2013) Dynamics of feature categorization. Neural Comput 25:1-45 [PubMed]

McIntyre CC, Richardson AG, Grill WM (2002) Modeling the excitability of Mammalian nerve fibers: influence of afterpotentials on the recovery cycle. J Neurophysiol 87:995-1006 [Journal] [PubMed]

   Spinal Motor Neuron (McIntyre et al 2002) [Model]

McNeal DR (1976) Analysis of a model for excitation of myelinated nerve. IEEE Trans Biomed Eng 23:329-37 [PubMed]

Meek J, Hafmans TG, Han V, Bell CC, Grant K (2001) Myelinated dendrites in the mormyrid electrosensory lobe. J Comp Neurol 431:255-75 [PubMed]

Memelli H, Torben-Nielsen B, Kozloski J (2013) Self-referential forces are sufficient to explain different dendritic morphologies. Front Neuroinform 7:1-75 [PubMed]

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119 [Journal] [PubMed]

   Parallel network simulations with NEURON (Migliore et al 2006) [Model]

Minkovich K, Thibeault C, Nogin A, Cho Y, Et_al (2014) HRLSim: a high performance spiking neural network simulator for GPGPU clusters. Ieee Transaction On Neural Networks And Learning Systems 25:316-331

Moore JW, Joyner RW, Brill MH, Waxman SD, Najar-Joa M (1978) Simulations of conduction in uniform myelinated fibers. Relative sensitivity to changes in nodal and internodal parameters. Biophys J 21:147-60 [Journal] [PubMed]

   Conduction in uniform myelinated axons (Moore et al 1978) [Model]

Nickolls J, Buck I, Garland M, Skadron K (2008) Scalable parallel programming with cuda Queue 6:40-53

nVidia (2012) CUBLAS Library User Guide http:--docs.nvidia.com-cuda- cublas-index.html

Ouyang H, Galle B, Li J, Nauman E, Shi R (2008) Biomechanics of spinal cord injury: a multimodal investigation using ex vivo guinea pig spinal cord white matter. J Neurotrauma 25:19-29 [PubMed]

Ouyang H, Sun W, Fu Y, Li J, Cheng JX, Nauman E, Shi R (2010) Compression induces acute demyelination and potassium channel exposure in spinal cord. J Neurotrauma 27:1109-20 [PubMed]

Peng H, Ruan Z, Long F, Simpson JH, Myers EW (2010) V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat Biotechnol 28:348-53

Peter SJ, Mofrad MR (2012) Computational modeling of axonal microtubule bundles under tension. Biophys J 102:749-57 [PubMed]

Richardson AG, McIntyre CC, Grill WM (2000) Modelling the effects of electric fields on nerve fibres: influence of the myelin sheath. Med Biol Eng Comput 38:438-46 [PubMed]

Rimon R, Roos BE, Kampman R, Hyyppa S, Ranta P, Myllyla V (1979) Monoamine metabolite levels in cerebrospinal fluid and brain atrophy in lobotomized schizophrenic patients. Ann Clin Res 11:25-9

Schauf CL, Davis FA (1974) Impulse conduction in multiple sclerosis: a theoretical basis for modification by temperature and pharmacological agents. J Neurol Neurosurg Psychiatry 37:152-61 [PubMed]

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

Shi R, Whitebone J (2006) Conduction deficits and membrane disruption of spinal cord axons as a function of magnitude and rate of strain. J Neurophysiol 95:3384-90 [PubMed]

Stephanova DI, Chobanova M (1997) Action potentials and ionic currents through paranodally demyelinated human motor nerve fibres: computer simulations. Biol Cybern 76:311-4

Walker D (1994) The design of a standard message-passing interface for distributed-memory concurrent computers. Parallel Computing 20:657-673

Wang JA, Lin W, Morris T, Banderali U, Juranka PF, Morris CE (2009) Membrane trauma and Na+ leak from Nav1.6 channels. Am J Physiol Cell Physiol 297:C823-34 [Journal] [PubMed]

Waxman SG, Brill MH (1978) Conduction through demyelinated plaques in multiple sclerosis: computer simulations of facilitation by short internodes. J Neurol Neurosurg Psychiatry 41:408-16 [PubMed]

Wokcik G, Kaminski W (2007) Liquid state machine and its separation ability as function of electrical parameters of cell. Neurocomputing 70:2593-2597

(63 refs)