Xnbc V8

XNBC stands for Xwindow Neuro_Bio_Clusters. Xwindows is the UNIX windowing system, Neuro_Bio is for biological neurons, and Clusters is for the way the neurons are grouped. (A cluster is a group of model neurons sharing the same membrane properties.) This powerful and flexible program was first developed in France about 12 years ago by computational neurobiologists and software engineers to run on Unix workstations. Its current version is 8.25 (July, 1999). The user manual, written by Jean-Fran├žois Vibert, the XNBC project leader, is available on line at http://www.b3e.jussieu.fn8G/logiciels/xnbc8_manual/index.html.

XNBC v8 has a user-friendly, interactive interface from which the following tools can be accessed:

Two neuron (SGL) editors (a phenomenological model editor and a conductance-based (HH) model editor) Two network editors (simple and full-featured) A drug editor tool (drugs affect ion channels) A simulator tool A visualization tool

A time series analysis tool (to perform point-process statistics on the spike trains of the model). A cluster activity analysis tool. An expert system (under development).

The user can visualize in time neuron spikes, transmembrane potentials, epsps, ipsps, and ionic conductances and currents.

To quote from the History and Implementation portion of the online user manual.

XNBC is written in portable ANSI C, and was compiled on [computers running under] Ultrix, Digital Unix, IBM AIX, Sun Solaris, HP Ux, Linux and DEC VMS and open VMS [operating systems]. XNBC runs on Xwindow workstations and needs the Motif library. When possible, the GNU C compiler (gcc) should be preferred. XNBC produces generally simple ASCII data files that can easily be converted to any format required by common graphic programs or spreadsheets. It produces native color PostScript files (that can be directly used to prepare figures). XNBC is a public domain software package available freely for academic research purpose on Internet (ftp://ftp.b3e.jus-sieu.fr/pub/XNBC) and informations [sic] about new versions at URL http://www.b3e.jussieu.fr/logiciels/xnbc.html.

The XNBC v8 simulation program is user-friendly and interactive. For example, the user interface for the conductance-based model graphic editor (G_neuron) allows setting 12 different transmembrane currents and two synaptic currents. Simplified HH kinetics are used. The user can select one of three integration routines for the simulation (Euler, fourth order Runge-Kutta, and exponential). Simulation parameters are adjusted with a mouse by moving dial cursors, or typing in numerical values, while a real-time display shows the neuron membrane potential (including spikes) and the ionic currents as the parameters are adjusted. A graphic utility also allows one to plot any variable vs. any other variable. Voltage clamp and current clamp experiments can be simulated to adjust better the conductance parameters. (Note that the current clamp is in effect an ideal current source or sink to the neural element, while the voltage clamp requires a negative feedback system that adjusts the current to maintain a preset membrane potential.) The program also allows the user to simulate the effects of the drugs TEA (tetraethylammonium) and TTX (tetrodotoxin) on conductances, as well as introduce the effects of long-term NMDA neuromodulation from glutamate-releasing synapses. Whether conductance-based neurons are modeled or the more succinct leaky integrator (RPFM) spike generator is used, the user can add broadband Gaussian noise to the membrane potential (generator potential) specified by standard deviation and mean to emulate synaptic noise (see Section 1.3.4). (Noise bandwidth is evidently not an adjustable parameter.)

In summary, it appears that XNBC v8 is a very versatile, user-friendly, and flexible neural modeling program, whether single neurons or small assemblies are being considered. The program graphic user interfaces (GUIs) make it easy to use.

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