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Nodus

Nodus is a user-friendly package designed to simulate the electrical behaviour of neurons and small networks on Macintosh computers. It supports any format using Hodgkin-Huxley type algorithms for user-specified conductances in excitable membrane models. 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. For Simulations two integration methods are available: an accurate Fehlberg method (5th 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. Colour 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. 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. Neurons can have up to 4,000 compartments. With a maximum of 6 connections per compartment (soma compartment: 24 connections), there is automatic control over connection consistency. Compartments can be split or fused manually or automatically to keep their electrotonic length within user-defined bounds. 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.

Year of production: 1999 for current version (v3.2)
Medium: Downloadable from: http://www.bbf.uia.ac.be/SOFT/NODUS_load.html
System requirements: Macintosh OS 7-9. Nodus 3.2 is available in three versions. Most users will want to use the PowerMac version Nodus 3.2P. The older versions (the Standard version Nodus 3.2 which runs on any Mac with 68020/30/40 CPU and a FPU and the Quadra version Nodus 3.2Q which runs only on Macs with a 68040 CPU) are provided for backward compatibility. An extensive user manual is available
Price: Freeware
Note: The author does not intend to further upgrade or debug this program; but as many users still find it a useful resource, it is still distributed. Please cite “De Schutter E.: Computer software for development and simulation of compartmental models of neurons. Computers in Biology and Medicine 19: 71-81 (1989)” in any publications or work using this free copy of Nodus