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Software

Nodus 3.2 Information

Copyright (c) 1983-1999 by Erik De Schutter.
Compiled with MacFortran(TM) II, Copyright (c) Absoft Corp. 1988.

Compartmental Modeling on Macintosh (TM) Computers

Nodus is a software package designed for simulation of the electrical behavior of neurons and small networks. Nodus 3.2 runs on Apple Macintosh(TM) computers and makes full use of the user friendly interface. Nodus is slower than some other simulation packages, but it is much easier to use. Neurons can have passive or excitable membrane, or both. Several commands support the easy maintenance of large, morphologically detailed, compartmental models. Nodus supports any format using the Hodgkin-Huxley formalism for user specified conductances in excitable membrane models. Concentration pools with buffers, diffusion and pumps are implemented. For network models graded transmitter release and several types of postsynaptic conductances are supported.

Nodus combines a powerful simulator with sophisticated model database management. Models are defined in separate files: conductance definition files, neuron definition files and network definition files. All files specifying one model are linked together in a hierarchical structure and automatically loaded when the top file is opened. Several conductance and neuron files can be open at the same time. A simulation database is build from user specified definition files and can be saved in a separate file, together with specific settings for graphic or text output, experiments, etc.

Open file

All file types have their own menu, which is enabled when the window at the front belongs to the corresponding file type. General file commands are available from the File menu. Neuron definitions can be imported from text files, different formats are supported (Eutectics(TM), Genesis, NINDS,...).

Standard Macintosh printing of graphics and text is available. Nodus can compute in the background, but one can also interrupt and afterwards restart lengthy simulations with the Automatic Saving command.

Edit menu

Picture data can be copied and pasted to other applications with the Edit menu. Default settings that can be controlled by the Preferences menu include sign of current, default settings for initial values and different methods to select subranges of campartments in large neuron models.

Simulation menu

For Simulations two integration methods are available: an accurate Fehlberg method (fifth order Runge-Kutta) and a fast forward Euler method, both with variable time steps. The value of any simulation database parameter can be manipulated by the user during simulations.

Simulation example

In all output and experiment commands the model structures (compartments, conductances, synapses, pools, etc.) are selected with popup menus (see Figure). Color graphic output and/or text output to disk of all membrane potentials, ionic and synaptic conductances and currents, conductance (in)activation factors and time constants, transmitter release, concentrations, injected and voltage clamp currents is supported. Up to 24 variables can be plotted on 4 axes. On screen measurement of plotted results is possible.

Currents (constant, repetitive pulses, ramps, sinus, noise, from text file) can be injected in any compartment of the model. One can voltage clamp two neurons simultaneously, with superposition of traces. Synapses can be preset to fire at specified times or to fire stochastically. Ionic currents can be blocked selectively during simulations.

Network menu

Networks are `hard-wired', with up to 200 neurons and a maximum of 60 synaptic connections with a delay and/or 20 electric connections for each neuron. Synaptic plasticity will become available in future releases.

Neuron menu

Neurons can have up to 4000 compartments. Neuron models are defined by global equivalent cable parameters and by entering size and connections for each compartment (or by importing morphology from a file). Maximum of 6 connections per compartment (soma compartment: 24 connections), there is automatic control over connection consistency. Membrane resistance and conductance can vary between compartments. Compartments can be split or fused manually or automatically to keep their electrotonic length within user defined bounds. Sets of ionic currents, transmitter release, synaptic current and concentration pool parameters are constructed in separate, named subdefinitions. For each compartment the user can select some of these subdefinitions with popup menus or none for a passive membrane compartment.

Subdefinitions for each compartment

Current subdefinitions contain up to 13 different conductances with their maximum conductance (specified either as mS/cm2 or as nS) and reversal potential (Nernst potentials can be computed). Transmitter release can be constant, voltage dependent or concentration pool dependent. Synaptic conductances include standard alpha and dual exponential functions, but can also be conductance dependent (for example for a NMDA receptor channel). Pool subdefinitions can be either simple pools or shells; with diffusion, pumps and buffers or with simple exponential decay.

Conductance menu

Conductances can be specified by a standard Hodgkin-Huxley equation, or any type of equation can be used to generate an external conductance parameter file (either activation factor and tau, or alpha and beta). Conductances can be calcium-dependent.

Examples of Simulation Outputs:

A simple model of spiking in an invertebrate neuron:

A simple model of spiking in an invertebrate neuron

Demonstration of summation of postsynaptic potentials:

Demonstration of summation of postsynaptic potentials

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