KInNeSS: A Modular Framework for Computational Neuroscience

Making use of very detailed neurophysiological, anatomical, and behavioral data to build biological-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalabiltiy, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multu-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions of ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further developement of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effecitively collaborate using a modern neural simulation platform.Center for Excellence for Learning Education, Science, and Technology (SBE-0354378); Air Force Office of Scientific Research (F49620-01-1-0397); Office of Naval Research (N00014-01-1-0624

Coherent response of the Hodgkin-Huxley neuron in the high-input regime

We analyze the response of the Hodgkin-Huxley neuron to a large number of uncorrelated stochastic inhibitory and excitatory post-synaptic spike trains. In order to clarify the various mechanisms responsible for noise-induced spike triggering we examine the model in its silent regime. We report the coexistence of two distinct coherence resonances: the first one at low noise is due to the stimulation of "correlated" subthreshold oscillations; the second one at intermediate noise variances is instead related to the regularization of the emitted spike trains.Comment: 5 pages - 5 eps figures, contribution presented to the conference CNS 2006 held in Edinburgh (UK), to appear on Neurocomputin

Channel noise induced stochastic facilitation in an auditory brainstem neuron model

Neuronal membrane potentials fluctuate stochastically due to conductance changes caused by random transitions between the open and close states of ion channels. Although it has previously been shown that channel noise can nontrivially affect neuronal dynamics, it is unknown whether ion-channel noise is strong enough to act as a noise source for hypothesised noise-enhanced information processing in real neuronal systems, i.e. 'stochastic facilitation.' Here, we demonstrate that biophysical models of channel noise can give rise to two kinds of recently discovered stochastic facilitation effects in a Hodgkin-Huxley-like model of auditory brainstem neurons. The first, known as slope-based stochastic resonance (SBSR), enables phasic neurons to emit action potentials that can encode the slope of inputs that vary slowly relative to key time-constants in the model. The second, known as inverse stochastic resonance (ISR), occurs in tonically firing neurons when small levels of noise inhibit tonic firing and replace it with burst-like dynamics. Consistent with previous work, we conclude that channel noise can provide significant variability in firing dynamics, even for large numbers of channels. Moreover, our results show that possible associated computational benefits may occur due to channel noise in neurons of the auditory brainstem. This holds whether the firing dynamics in the model are phasic (SBSR can occur due to channel noise) or tonic (ISR can occur due to channel noise).Comment: Published by Physical Review E, November 2013 (this version 17 pages total - 10 text, 1 refs, 6 figures/tables); Associated matlab code is available online in the ModelDB repository at http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=15148

The space-clamped Hodgkin-Huxley system with random synaptic input: inhibition of spiking by weak noise and analysis with moment equations

We consider a classical space-clamped Hodgkin-Huxley model neuron stimulated by synaptic excitation and inhibition with conductances represented by Ornstein-Uhlenbeck processes. Using numerical solutions of the stochastic model system obtained by an Euler method, it is found that with excitation only there is a critical value of the steady state excitatory conductance for repetitive spiking without noise and for values of the conductance near the critical value small noise has a powerfully inhibitory effect. For a given level of inhibition there is also a critical value of the steady state excitatory conductance for repetitive firing and it is demonstrated that noise either in the excitatory or inhibitory processes or both can powerfully inhibit spiking. Furthermore, near the critical value, inverse stochastic resonance was observed when noise was present only in the inhibitory input process. The system of 27 coupled deterministic differential equations for the approximate first and second order moments of the 6-dimensional model is derived. The moment differential equations are solved using Runge-Kutta methods and the solutions are compared with the results obtained by simulation for various sets of parameters including some with conductances obtained by experiment on pyramidal cells of rat prefrontal cortex. The mean and variance obtained from simulation are in good agreement when there is spiking induced by strong stimulation and relatively small noise or when the voltage is fluctuating at subthreshold levels. In the occasional spike mode sometimes exhibited by spinal motoneurons and cortical pyramidal cells the assunptions underlying the moment equation approach are not satisfied

Predicting spike times of a detailed conductance- based neuron model driven by stochastic spike arrival

Reduced models of neuronal activity such as Integrate-and-Fire models allow a description of neuronal dynamics in simple, intuitive terms and are easy to simulate numerically. We present a method to fit an Integrate-and-Fire-type model of neuronal activity, namely a modified version of the Spike Response Model, to a detailed Hodgkin-Huxley-type neuron model driven by stochastic spike arrival. In the Hogkin-Huxley model, spike arrival at the synapse is modeled by a change of synaptic conductance. For such conductance spike input, more than 70% of the postsynaptic action potentials can be predicted with the correct timing by the Integrate-and-Fire-type model. The modified Spike Response Model is based upon a linearized theory of conductance-driven Integrate-and-Fire neuron

Simulation of networks of spiking neurons: A review of tools and strategies

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 next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. 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 synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.Comment: 49 pages, 24 figures, 1 table; review article, Journal of Computational Neuroscience, in press (2007