Next: The phenomenologic model graphic Up: XNBC8 User Manual V8.21 Previous: Presentation of XNBC

The XNBC control panel

The control panel is displayed by the xnbc command that allows to control all the modelling process.

Many printed outputs are produced automatically by XNBC. It is wyse, before to start XNBC, to define the convenient printer. This printer must be a PostScript printer. The printer name is controlled by the environment variable PRINT_PLOT_PS that should be positionned with the right print command and printer indicated.

For example in csh (or bsh or tcsh):

		csh> setenv PRINT\_PLOT_PS "lpr -Plaser "

of with ksh (or sh)

		ksh% PRINT_PLOT_PS="lpr -Plaser "
		ksh% export PRINT_PLOT_PS

The XNBC control panel is run by typing at the unix prompt:

		csh> xnbc &

XNBC is made of a collection of programs launched by a control program displaying a user friendly control panel (fig. 2.1). The control panel proposes several pushbuttons, each representing a task and launching this task when pressed. Pushbuttons are linked by arrows that symbolically represent the succession of tasks to run to perform a simulation.

**Figure:** **The XNBC V8 control panel**
$\begin{figure}\centerline{\psfig{file=xnbc_8_21.ps,width=15cm} } \end{figure}$

A Keep PostScript files pushbutton allows to keep output PostScript files after they are printed (this button controls if graphic PostScript files are printed and deleted or only kept for further reprinting or use as a figure to include in a publication).

A Browse the XNBC full manual pushbutton allows to spawn a navigator (defined by the environment variable XNBC_BROWSER) to browse the user manual. The Help Menu qllows to directly browse the Control Panel manual (help on control panel).

Simulations (here called Experiments) are assigned a name, chosen by the user. All files created during a given experiment are stored in a directory whose name starts when the experiment name and ends with _nbc. Keeping the same name as the basename of the directory, allows XNBC to open automatically the necessary files with asking questions. This name is kept in a file in the home directory in the file .xnbcrc in the home directory. This file records 4 important informations:

the current simulation directory
the current project name
the current network name
the current simulation name

This file is read by all components of xnbc to automatically propose the correct current worked file. Therefore it is not recommended to modify the experiment name during the experiment, since files will be no more automatically opened and will be asked to the user.

When moving the mouse, a dynamic one line short help text explains the pushbutton usage in the blue ribbon at the bottom of the screen.

Pulldown menus

The control panel proposes two pulldown menus (that can be teared off if the version of Motif is 1.2 or upper and if the tear off behavior is enabled in the Mwm personal control file). These menus allow to manage the simulation name (Experiment menu) and to call plotting programs (Graphic menu).

Experiment
Current: gives the name of the current experiment name and directory
New: Creates a new directory to store files for a new experiment. This button opens a file selection box with the *_nbc directories already existing.
Open: Open an existing directory to store files for an existing experiment. This button opens a file selection box with the *_nbc directories already existing.
Quit: exits xnbc.
Graphics
Global activity of clusters: calls a program run in an xterm window. This program allows to plot the global activity of clusters or nuclei. Several representation options are proposed (Y axis units, length of X axis, control of what part of the experiment is plotted, number of pages, etc.). This program produces PostScript files, and is intended to prepare figures. When actions are took during the simulation (stimulation, parameter change, etc.), this is indicated on the graph. The same kind of plot can be obtained using the visualization program, but without the control provided by this program (Fig. 2.2).


Figure: Global activity of 2 nuclei obtained with the graphic tool.
$\begin{figure}\centerline{\psfig{file=circuit_jfv_act_clust.ps,width=15cm,clip=}} \end{figure}$

Intracellular recording: calls a program run in an xterm window. This program allows to plot the membrane potential of selected units. Units are selected by giving their sequential number in the whole network (starting from 1): unit 1 is the unit 1 of nucleus (or cluster) 1. When all units are selected, type 0 to end the selection. Several representation options are proposed (Y axis size, length of X axis, number of pages, etc.). This program produces PostScript files, and is intended to prepare figures. The same kind of plot can be obtained using the visualization program, but without the control provided by this program (Fig. 2.3).


Figure: Membrane potential of 3 units obtained with the graphic tool.
$\begin{figure}\centerline{\psfig{file=circuit_jfv_intra_cell.ps,width=15cm,clip=}} \end{figure}$

Membrane potential (3D): Same as the previous, but membrane potential are represented side by side, and can be viewed in a 3D representation whose rotations in X, Y and Z directions can be adjusted. This program produces PostScript files, and is intended to prepare figures (Fig. 2.4).


Figure: 3D representqtion of the activity of all units obtained with the graphic tool.
$\begin{figure}\centerline{\psfig{file=circuit_jfv_pmb_3d.ps,height=20cm,clip=}} \end{figure}$

View PostScript Files: calls the PostScript previewer to preview the produced PostScript files by the simulation and analysis programs.

**Figure:** **Global activity of 2 nuclei obtained with the graphic tool.**
$\begin{figure}\centerline{\psfig{file=circuit_jfv_act_clust.ps,width=15cm,clip=}} \end{figure}$

**Figure:** **Membrane potential of 3 units obtained with the graphic tool.**
$\begin{figure}\centerline{\psfig{file=circuit_jfv_intra_cell.ps,width=15cm,clip=}} \end{figure}$

**Figure:** **3D representqtion of the activity of all units obtained with the graphic tool.**
$\begin{figure}\centerline{\psfig{file=circuit_jfv_pmb_3d.ps,height=20cm,clip=}} \end{figure}$

Programs launched by the control panel

The programs launched by the control panel are a) two graphic editors to adjust the neuron parameters (for the leaky integrator model (LIM) and for the conductance based model (CBM)), b) two network graphic editors (simple and fully featured), c) the simulator, d) the visualization tool and e) two analysis tools (time series and frequency analysis). The control panel displays pushbuttons arranged to guide the user to perform simulations and analyses. The user sequentially

i) chooses the parameters of the neuron models,
ii) builds a neural network
iii) runs the simulation
iv) visualizes the simulation results
v) analyzes the simulated network bwhavior.

Nevertheless, the simulator itself (whose name is nbc_x, described in the corresponding chapter 8) allows to control also, in the same way, all the simulation process, using pulldown menus instead of graphic pushbuttons.

The pushbuttons launch the following tools. A separate chapter is devoted to each tool.

First choose the parameters of the neuron models. There exist two graphic editors to adjust the neuron parameters.

Leaky integrator NEURON This pushbutton launches the phenomenologic neuron graphic editor to create PUM, LIM and BUM neuron types (or clusters). This tool is described in chapter 3.
Conductance NEURON This pushbutton launches the conductance based neuron model graphic editor to create CBM neuron types (or clusters). This tool is described in chapter 4.
Virtual NEURON The neuron model can also be a ``virtual model'', that is, an actually recorded neuron, whose spike time arrivals are used as input on the simulated neurons or networks. This allows to build hybrid networks. The pushbutton ``Virtual cluster'' gives a list of the available neuron files representing actual neurons (Fig. 2.5).

**Figure:** **The virtual cluster window**
$\begin{figure}\centerline{\psfig{file=virtual_neur.ps,width=7cm}} \end{figure}$

Once the neuron models are defined, neurons can be grouped toghether into networks, it is possible to build a neural network.

The connection matrix of the modeled network can be described using one of the two graphic network editors. According to the pushbutton selected above the network editor pushbutton (dark blue text), the simple or the full featured network editor is launched when the NETWORK pushbutton is pressed.

The simple network editor
It allows to build nuclei containing only one cluster each. It does not allow to see individually the neurons inside the clusters, nor to work in Horsley-Clarke coordinates. It does not allow to describe the NMDA connctions. This tool is described in chapter 5.
The full featured network editor
It allows to build nuclei containing several clusters each. It allows to finely edit the connection matrix and to choose the connection density around a given neuron. Connections with glutamate release acting on NMDA receptors can also be specified. This is a rather sohpisticated tool. This tool is described in chapter 6.

Once the network is built, the simulation can be run using the SIMULATORpushbutton. This tool is described in chapter 8.

After the simulation, the user can

visualize the simulation results by pressing the VISUALIZATION pushbutton. This tool is described in chapter 9.
analyze the simulated network behavior. Two analysis tools are available:
the TIME SERIES ANALYSIS pushbutton launches XTMS for time series analysis, and is mainly devoted to analyze the individual unit discharges (point process analysis). This tool is described in chapter 10.
the CLUSTER ACTIVITY ANALYSIS pushbutton launches XCAA to analyze the nuclei activity. This tool is described in chapter 11.

Behavior of the control panel

When a task is launched and as long as it is active, the control panel pushbuttons become inactive (unsensitive, indicated by the grey color of their text).

When a task is launched, a waiting message appears, and then automatically disappears after 10 s. If a task don't succeed, it is possible that this message stays displayed for few seconds before to be able to start again.

Sometimes, a window disappears from the screen, but the control panel stays unsensitive. The window is probably hidden by the control panel. Move it, or lower it using the window manager top left menu.

Files

Input and output: /.xnbcrc

Diagnostics and problems

Self explaining diagnostics are provided on errors.

If a launched task stops abnormally, it is possible that the control pannel stays insensitive, since it did not received the signal that the task has terminated normally. In this case, exit and rerun the control panel. Normally no data is lost, except those produced by the dead task. Only this one should be rerun.

Next: The phenomenologic model graphic Up: XNBC8 User Manual V8.21 Previous: Presentation of XNBC

Jean-Francois Vibert
1998-08-26