Comparison of DA-based Stochastic Algorithms (Pezo et al. 2014)

Bezanilla F, Perozo E, Stefani E. (1994). Gating of Shaker K+ channels: II. The components of gating currents and a model of channel activation. Biophysical journal. 66 [PubMed]

Bruce IC. (2007). Implementation issues in approximate methods for stochastic Hodgkin-Huxley models. Annals of biomedical engineering. 35 [PubMed]

• Implementation issues in approximate methods for stochastic Hodgkin-Huxley models (Bruce 2007) [Model]

Bruce IC. (2009). Evaluation of stochastic differential equation approximation of ion channel gating models. Annals of biomedical engineering. 37 [PubMed]

• Evaluation of stochastic diff. eq. approximation of ion channel gating models (Bruce 2009) [Model]

Colquhoun D, Hawkes AG. (1981). On the stochastic properties of single ion channels. Proceedings of the Royal Society of London. Series B, Biological sciences. 211 [PubMed]

Dangerfield CE, Kay D, Burrage K. (2012). Modeling ion channel dynamics through reflected stochastic differential equations Physical review. E, Statistical, nonlinear, and soft matter physics. 85 [PubMed]

• Reflected SDE Hodgkin-Huxley Model (Dangerfield et al. 2012) [Model]

Fox RF. (1997). Stochastic versions of the Hodgkin-Huxley equations. Biophysical journal. 72 [PubMed]

Fox RF, Lu Yn. (1994). Emergent collective behavior in large numbers of globally coupled independently stochastic ion channels. Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics. 49 [PubMed]

Gillespie DT. (2007). Stochastic simulation of chemical kinetics. Annual review of physical chemistry. 58 [PubMed]

Goldwyn JH, Imennov NS, Famulare M, Shea-Brown E. (2011). Stochastic differential equation models for ion channel noise in Hodgkin-Huxley neurons. Physical review. E, Statistical, nonlinear, and soft matter physics. 83 [PubMed]

• On stochastic diff. eq. models for ion channel noise in Hodgkin-Huxley neurons (Goldwyn et al. 2010) [Model]

Goldwyn JH, Shea-Brown E. (2011). The what and where of adding channel noise to the Hodgkin-Huxley equations. PLoS computational biology. 7 [PubMed]

• Stochastic versions of the Hodgkin-Huxley equations (Goldwyn, Shea-Brown 2011) [Model]
• Stochastic versions of the Hodgkin-Huxley equations (Goldwyn, Shea-Brown 2011) (pylab) [Model]

HODGKIN AL, HUXLEY AF. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. The Journal of physiology. 117 [PubMed]

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

Hines ML, Carnevale NT. (2001). NEURON: a tool for neuroscientists. The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry. 7 [PubMed]

• Spatial gridding and temporal accuracy in NEURON (Hines and Carnevale 2001) [Model]

Hines ML, Davison AP, Muller E. (2009). NEURON and Python. Frontiers in neuroinformatics. 3 [PubMed]

• NEURON + Python (Hines et al. 2009) [Model]

Horn R, Ding S, Gruber HJ. (2000). Immobilizing the moving parts of voltage-gated ion channels. The Journal of general physiology. 116 [PubMed]

Horrigan FT, Aldrich RW. (2002). Coupling between voltage sensor activation, Ca2+ binding and channel opening in large conductance (BK) potassium channels. The Journal of general physiology. 120 [PubMed]

Linaro D, Storace M, Giugliano M. (2011). Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation. PLoS computational biology. 7 [PubMed]

• Accurate and fast simulation of channel noise in conductance-based model neurons (Linaro et al 2011) [Model]

Mino H, Rubinstein JT, White JA. (2002). Comparison of algorithms for the simulation of action potentials with stochastic sodium channels. Annals of biomedical engineering. 30 [PubMed]

Mélykúti B, Burrage K, Zygalakis KC. (2010). Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation. The Journal of chemical physics. 132 [PubMed]

Neher E, Stevens CF. (1977). Conductance fluctuations and ionic pores in membranes. Annual review of biophysics and bioengineering. 6 [PubMed]

Orio P, Soudry D. (2012). Simple, fast and accurate implementation of the diffusion approximation algorithm for stochastic ion channels with multiple states. PloS one. 7 [PubMed]

• Simple and accurate Diffusion Approximation algor. for stochastic ion channels (Orio & Soudry 2012) [Model]

Schmandt NT, Galán RF. (2012). Stochastic-shielding approximation of Markov chains and its application to efficiently simulate random ion-channel gating. Physical review letters. 109 [PubMed]

• Markov Chain-based Stochastic Shielding Hodgkin Huxley Model (Schmandt, Galan 2012) [Model]

Schmidt-Hieber C, Bischofberger J. (2010). Fast sodium channel gating supports localized and efficient axonal action potential initiation. The Journal of neuroscience : the official journal of the Society for Neuroscience. 30 [PubMed]

• Fast sodium channel gating in mossy fiber axons (Schmidt-Hieber et al. 2010) [Model]

Schoppa NE, Sigworth FJ. (1998). Activation of Shaker potassium channels. III. An activation gating model for wild-type and V2 mutant channels. The Journal of general physiology. 111 [PubMed]

Vandenberg CA, Bezanilla F. (1991). A sodium channel gating model based on single channel, macroscopic ionic, and gating currents in the squid giant axon. Biophysical journal. 60 [PubMed]

Kilinc D, Demir A. (2015). Simulation of noise in neurons and neuronal circuits Proceedings of the IEEE/ACM international conference on computer-aided design (ICCAD).

• A neuronal circuit simulator for non Monte Carlo analysis of neuronal noise (Kilinc & Demir 2018) [Model]