Alternatives Database

NeuroSim - Neural Function Simulator (v3.0)

NeuroSim is a package for use in teaching neurophysiology at the undergraduate and beginning graduate-student level. It also provides useful insights for experienced neurophysiologists. Each of its 5 programs operates independently and simulates a particular aspect of neural function, but with a common style of interface. The screen display is similar to that of an oscilloscope in a genuine experiment. Parameters can be varied to explore the effects of various conditions and can be saved as disk files. Each simulation can be configured for use at different levels, so that students are only exposed to details appropriate to their learning objectives. Tutors can hide specified parameter values from users, so that students can be set the task of discovering them by experiment.

a. HH simulates the Hodgkin-Huxley model of a nerve impulse. Two stimulus pulses can be applied in either current clamp or voltage clamp mode, each with square or ramp waveform and user-defined amplitude and timing. A wide range of phenomena can be simulated, including refractory period, threshold accommodation, voltage clamp tail currents, single channel patch clamp conductances and many others. An animated cartoon shows the action of molecular gates in the cell membrane. Various drugs can be applied and the temperature and ionic concentrations can be varied.

b. NEURON models voltage-dependent and synaptic conductances. It is for investigating more complex cellular systems than that of the standard HH model, but it provides similar current clamp and voltage clamp experimental facilities. Up to 9 voltage-dependent channel types can be included, each with user-defined maximum conductance and equilibrium potential, and with activation and inactivation kinetics defined using a built-in equation editor. Intracellular calcium concentration fluctuations can be simulated, and any channel can be made calcium dependent. NEURON replicates many classical simulations from the literature. In addition to the voltage-dependent channels, up to 5 ligand gated (synaptic) channel types can also be included.

c. PATCH simulates the kinetic properties of single ion channels. Three ready-made models are supplied: a simple 2-state (open/shut) channel, a 3-state agonist-activated channel (shut/unbound, shut/bound, open/bound), and a 3-state (shut/open/blocked) channel. The program can also model a channel with up to 5 states with user-defined transition rate constants. The simulation develops open-time and shut-time histograms in combination with animated cartoons showing the molecular states of the channels. Multi-exponential curves can be superimposed on the histograms, with a chi-squared goodness-of-fit measure. Raw data of open and shut times can be exported as ASCII files.

d. NETWORK allows the user to construct arbitrary circuits of neurons interconnected by non-spiking or spiking chemical synapses and rectifying or non-rectifying electrical synapses. Many of the membrane properties of each neuron can be set individually, including making it an endogenous burster. Although active membrane events are simplified for speed optimisation, spike characteristics such as threshold accommodation can be included. Experimental current pulses of defined amplitude and timing can be injected into any neuron. Many different types of synapses can be defined. The display shows the membrane potential of up to 5 neurons against time as in a standard oscilloscope recording. Membrane potentials of all neurons can be displayed as an animated bar graph, or the spike activity of all neurons can be displayed as an animated scatter graph against time.

e. CABLE simulates passive conduction in a long non-spiking length of axon. It demonstrates how signal attenuation is dependent on the properties of time constant and space constant, and shows how these relate to the fundamental axon characteristics of membrane resistance and capacitance, and axon diameter. Temporal summation can be demonstrated.

Year of production: 1998 Medium: 3.5" disk; CD-ROM System requirements: Windows (all versions) Price: US$300.00, £199.00, €399.00; free demo downloadable fromwebsite