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Library-based numerical reduction of the Hodgkin–Huxley neuron for network simulation

Yi Sun, Douglas Zhou, Aaditya V. Rangan, David Cai
2009 Journal of Computational Neuroscience  
We present an efficient library-based numerical method for simulating the Hodgkin-Huxley (HH) neuronal networks.  ...  By using the library method, we can evolve the HH networks using time steps one order of magnitude larger than the typical time steps used for resolving the trajectories without the library, while achieving  ...  Acknowledgements The work was supported by NSF grant DMS-0506396 and a grant from the Swartz foundation.  ... 
doi:10.1007/s10827-009-0151-9 pmid:19401809 fatcat:2sjtrpppxnd35hkk3tvtmuzdfm

Predicting Spike Features of Hodgkin-Huxley-Type Neurons With Simple Artificial Neural Network

Tian Wang, Ye Wang, Jiamin Shen, Lei Wang, Lihong Cao
2022 Frontiers in Computational Neuroscience  
Hodgkin-Huxley (HH)-type model is the most famous computational model for simulating neural activity.  ...  The combination of SPM and FPM may offer a possible way to simulate the action potentials of biological neurons with high accuracy and efficiency.  ...  AUTHOR CONTRIBUTIONS LC designed the study. YW, TW, JS, and LW proposed the analysis. YW, TW, LW, and LC wrote the paper. All authors contributed to the article and approved the submitted version.  ... 
doi:10.3389/fncom.2021.800875 pmid:35197835 pmcid:PMC8859780 fatcat:5cr7vqbfsvewvnxzwwpnpogiru

NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML [article]

Justas Birgiolas, Vergil Haynes, Padraig Gleeson, Richard C Gerkin, Suzanne W. Dietrich, Sharon M. Crook
2021 bioRxiv   pre-print
Search capabilities of the database, together with web-based, programmable online interfaces, allow the community of researchers to rapidly assess stored model electrophysiology, morphology, and computational  ...  suitable models for reuse.  ...  Acknowledgements We would like to acknowledge Angus Silver and all of the current and previous NeuroML Editors for NeuroML language development (  ... 
doi:10.1101/2021.09.11.459920 fatcat:j5tet7u75zc5ppfrno73gjlruq

From Knights Corner to Landing: A Case Study Based on a Hodgkin-Huxley Neuron Simulator [chapter]

George Chatzikonstantis, Diego Jiménez, Esteban Meneses, Christos Strydis, Harry Sidiropoulos, Dimitrios Soudris
2017 Lecture Notes in Computer Science  
Our neuron simulator of choice features a Hodgkin-Huxley-based (HH) model which has been ported on both generations of Xeon Phi platforms and aggressively draws on both platforms' computational assets.  ...  The field of computational neuroscience has been developing a demand for physiologically plausible neuron models, that feature increased complexity and thus, require greater computational power.  ...  The neurons are based on an elaborate, realistic model of the human neuron, derived from the work of Hodgkin and Huxley [ ].  ... 
doi:10.1007/978-3-319-67630-2_27 fatcat:yldedjclafbz5gjibp3fwj4onq

Mean-field description and propagation of chaos in networks of Hodgkin-Huxley and FitzHugh-Nagumo neurons

Javier Baladron, Diego Fasoli, Olivier Faugeras, Jonathan Touboul
2012 Journal of Mathematical Neuroscience  
The neurons belong to a fixed number of populations and are represented either by the Hodgkin-Huxley model or by one of its simplified version, the FitzHugh-Nagumo model.  ...  We derive the mean-field equations arising as the limit of a network of interacting spiking neurons, as the number of neurons goes to infinity.  ...  Acknowledgements This work was partially supported by the ERC grant #227747 NerVi, the FACETS-ITN Marie-Curie Initial Training Network #237955 and the IP project BrainScaleS #269921.  ... 
doi:10.1186/2190-8567-2-10 pmid:22657695 pmcid:PMC3497713 fatcat:fvl2shci5fbanmkhbkxhagexha

ModSpec: An open, flexible specification framework for multi-domain device modelling

David Amsallem, Jaijeet Roychowdhury
2011 2011 IEEE/ACM International Conference on Computer-Aided Design (ICCAD)  
We illustrate the use of ModSpec for modelling semiconductor, photovoltaic, fluidic and neuronal devices and systems.  ...  The format is open, general and easy to use, and is supported by toolchains that translate and automatically differentiate models, set up equations for systems of interacting devices, and provide simulation  ...  This illustrates the nonlinear nature of the Hodgkin-Huxley model.  ... 
doi:10.1109/iccad.2011.6105356 dblp:conf/iccad/AmsallemR11 fatcat:55v2xziy6nd65jyyrzo33o3rpi

Simulation of networks of spiking neurons: A review of tools and strategies [article]

R. Brette, M. Rudolph, T. Carnevale, M. Hines, D. Beeman, J. M. Bower, M. Diesmann, A. Morrison, P. H. Goodman, F. C. Harris Jr., M. Zirpe, T. Natschlager, D. Pecevski (+8 others)
2007 arXiv   pre-print
Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based  ...  We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented.  ...  We are also grateful for the feedback and suggestions from users that have led to improvements of the simulators reviewed here.  ... 
arXiv:q-bio/0611089v2 fatcat:wc22vb75zrb6xj66ngffn6gjuy

Software for Brain Network Simulations: A Comparative Study

Ruben A. Tikidji-Hamburyan, Vikram Narayana, Zeki Bozkus, Tarek A. El-Ghazawi
2017 Frontiers in Neuroinformatics  
However, all simulators tend to expand the supported range of models by providing a universal environment for the computational study of individual neurons and brain networks.  ...  Numerical simulations of brain networks are a critical part of our efforts in understanding brain functions under pathological and normal conditions.  ...  The network consisted of 400 classical Hodgkin-Huxley (HH) (Hodgkin and Huxley, 1952) neurons with double-exponential synapses.  ... 
doi:10.3389/fninf.2017.00046 pmid:28775687 pmcid:PMC5517781 fatcat:a4dp346hizeflim4dulfeoe74q

Is realistic neuronal modeling realistic?

Mara Almog, Alon Korngreen
2016 Journal of Neurophysiology  
Here we discuss the oxymoronic, realistic modeling of single neurons.  ...  A model should not be a facsimile of reality; it is an aid for understanding it.  ...  ACKNOWLEDGMENTS The authors thank Dr. Izhar Bar-Gad for helpful comments and suggestions. The authors thank Ziv Almog for graphical design, and Meir-Simchah Panzer for editorial services.  ... 
doi:10.1152/jn.00360.2016 pmid:27535372 pmcid:PMC5102320 fatcat:yajnckhmivbuxje7licsootn6y

KInNeSS: A Modular Framework for Computational Neuroscience

Massimiliano Versace, Heather Ames, Jasmin Léveillé, Bret Fortenberry, Anatoli Gorchetchnikov
2008 Neuroinformatics  
Making use of very detailed neurophysiological, anatomical, and behavioral data to build biologicallyrealistic computational models of animal behavior is often a difficult task.  ...  Mike Hasselmo, Dash Sai Gaddam, and Jesse Palma for numerous valuable discussions and suggestions for this paper.  ...  Acknowledgements This work was supported by the Center of Excellence for Learning in Education, Science and Technology (NSF SBE-0354378).  ... 
doi:10.1007/s12021-008-9021-2 pmid:18695948 fatcat:coreidauxnawxplu3tjecsxi6i

Temporal constrained objects for modelling neuronal dynamics

Manjusha Nair, Jinesh Manchan Kannimoola, Bharat Jayaraman, Bipin Nair, Shyam Diwakar
2018 PeerJ Computer Science  
Computation in this paradigm is a process of constraint satisfaction within a time-based simulation.  ...  is necessary for modelling and simulation of large brain circuits.  ...  There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj-cs.159 pmid:33816812 pmcid:PMC7924700 fatcat:562afavawrbbdmcoaccoeq5m2m

Biologically Relevant Dynamical Behaviors Realized in an Ultra-Compact Neuron Model

Pablo Stoliar, Olivier Schneegans, Marcelo J. Rozenberg
2020 Frontiers in Neuroscience  
We also demonstrate that numerical simulations can faithfully represent the variety of spiking behavior and can be used for further exploration of dynamical behaviors.  ...  These behaviors may be useful to construct neural networks that can capture complex brain dynamics or may also be useful for artificial intelligence applications.  ...  AUTHOR CONTRIBUTIONS All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.  ... 
doi:10.3389/fnins.2020.00421 pmid:32595437 pmcid:PMC7247826 fatcat:7dqjwnderbfghlmwaokdtxef4m

Code Generation: A Strategy for Neural Network Simulators

Dan F. M. Goodman
2010 Neuroinformatics  
We demonstrate a technique for the design of neural network simulation software, runtime code generation.  ...  This technique can be used to give the user complete flexibility in specifying the mathematical model for their simulation in a high level way, along with the speed of code written in a low level language  ...  Acknowledgements The author would like to thank Romain Brette, Cyrille Rossant and Bertrand Fontaine for their work on Brian, testing of code generation, and helpful comments on the manuscript.  ... 
doi:10.1007/s12021-010-9082-x pmid:20857234 fatcat:vzkx3zwhnnf73dkt3robfdc45a

Neural Modeling with GENESIS [chapter]

James M. Bower, David Beeman
1998 The Book of GENESIS  
However, these Hodgkin-Huxley forms of voltage activated channels are an important ingredient of many more complex neuronal models.  ...  Most model tuning involves manipulation of the Hodgkin-Huxley parameters governing ionic channels.  ... 
doi:10.1007/978-1-4612-1634-6_3 fatcat:yhgdint5xjaczd3il7pwdwvhoy

Neural Modeling with GENESIS [chapter]

James M. Bower, David Beeman
1995 The Book of GENESIS  
However, these Hodgkin-Huxley forms of voltage activated channels are an important ingredient of many more complex neuronal models.  ...  Most model tuning involves manipulation of the Hodgkin-Huxley parameters governing ionic channels.  ... 
doi:10.1007/978-1-4684-0189-9_3 fatcat:gphpcvflnvb7dmnrb45pmgtxta
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