Installation of XNBC is based on Imake generated Makefiles. Consequently, you must have installed the xmkmf and imake programs, as well as the Imake template files. This is generaly distributed with the X11 distribution, and often installed by default (but not on AIX were you have to build it by following the /usr/lpp/X11/Xamples/README). HPux installation is also done using a special handwritten file, since the template files for imake are not distributed with HPux.
We succeded to install XNBC V8 on
If you build XNBC on a Unix system, you should run the install_xnbc8 script
host> sh install_xnbc8
On a linux system you must have installed Moo-Tif (Lesstiff, the freeware version of Motif is not yet completed, all programs compile correctly, but the menu button don't work, thus...). Since the XFree86 Imake templates do not define the Motif libraries they must be indicated namely. To be able to compile the XNBC package, you must have installed the C development package (Gnu gcc) and the Linux sources (system include files are necessary). Then you have to build XNBC by running the xnbc.install.linux_version script (or download a prebuild image -see below-).
Questions about your system specificities are asked. Default answers are provided.
On Linux, you must know were your XFree86 distribution is installed. Since some systems have Xlib in /usr/X11R6 (redhat) and other on /usr/X11 (a link) two separate files are provided. Nevertheless, Linux users can download a precompiled version of XNBC8 statically linked with the Moo-Tif libraries in order keep XNBC free from any commercial associated product.
The process takes from 3 mn on a Pentium II/333, 6 min on an AlphaStation 600/266, 15 mn on a Pentium 90 Mhz, up to 45 mn on a DecStation 5000/240.
At the end you have two files xnbc_env_system_wide and xnbc_env_private containing the environnement variable necessary for XNBC, according to your installation in order to define the environment variables.
The xnbc_env_system_wide must be used if XNBC is installed in the /usr/local filesystem. The xnbc_env_private must be used if XNBC is left in the installation directory.
You must verify in both file that the XNBC_BIN_REF_XTERM points on the correct Xterminal emulator, that the XNBC_BROWSER points on the correct web browser, and that XNBC_BIN_REF_PSVIEWER points in the correct PostScript viewer.
Nevertheless, for your convenience, the system wide file is copied locally as xnbc and defines the needed environment variables. This provides the simplest way to adapt XNBC8 it to your local installation. Call xbnc (the script) that will call xnbc8 (the actual xnbc program).
If you need to use the programs individually (uncomment the lines flagged for this in the installation script), you can remove the call to xnbc8 at the end of the xnbc_env_system_wide (or the xnbc_env_private) script and the source it in order to define the envorironment variables. For example, xtms can be used to analyse actual experimental data and be useful without the simulator.
This mode is automatically selected if you are not supersuser when you build xnbc. In this mode the system is installed in the XNBC8 tree :
binaries
uid files for Motif
object libraries
For this version the man directory stays empty after the installation, but all the documentation can be found in "TOP"/XNBC/doc.
You MUST be in superuser mode. In this mode the system is installed in the XNBC8 tree and in the system tree.
binaries
uid files for Motif
object libraries
binaries
html manual
uid files for Motif Installation
Normally,
If the binaries are stored in another directory, the environment variable XNBC_BIN_DIR_TOOLS must be set to this directory. uid files must be stored /usr/local/lib/uid or in the current directory, or in another directory named in the environment variable XNBC_UID_DIR.
If the binaries are stored in another directory, the environment variable XNBC_BIN_DIR_TOOLS must be set to this directory.
uid files must be stored /usr/local/lib/uid or in the current directory, or in another directory named in the environment variable XNBC_UID_DIR.
The following environment variables can be set by sourcing the xnbc_env_private or xnbc_env_system_wide, that you should adapt to your environment (for example, xnbc_xterm.dec and xnbc_xterm.sun give a different definition of the XNBC_BIN_REF_XTERM variable).
For example, on a Ultrix or Digital Unix machine:
setenv XNBC\_BROWSER "/usr/local/netscape/netscape"
setenv XNBC\_BIN\_DIR\_TOOLS "/usr/local/bin/nbc.bin/V8/"
setenv XNBC\_BIN\_REF\_XTERM "/usr/bin/X11/dxterm"
setenv XNBC\_BIN\_REF\_PSVIEWER "/usr/bin/X11/dxvdoc" etc...
For both modes, run the xnbc.install script in "TOP"/XNBC8. All compilation results are put in xnbc_install.log.
Expect to wait about 20 min if you use a 40 MIPS machine (DECstaion 5000/240, or RS 6000) 6 mn on an Alpha machine (AlphaStation 600/233), 3 mn on a Pentium II/333 under Linux. Expect to wait about 20 min if you use a 40 MIPS machine (DECstaion 5000/240, or RS 6000) and 6 mn on an Alpha machine (AlphaStation 600/233)
If you have any problem during installation, please mail us the part of the xnbc_install.log file where the problem has been detected.
XNBC was build on the following Unix systems, and should run, provided you have an ANSI C compiler and the Motif development kit:
A 140+ page user manual in html format is readable using any web browser. Each chapter can be printed separately (one for each XNBC tool). A color printer will allow to beneficiate from the screens snapshots in color.
The chapter of the manual describing the Conductance based model editor decribes G_neuron version 7.14 while the version distributed here is V8.0. It has exactly the same functionality than 7.14 and many more, and few bugs less (this why it is distributed here). The new functionalities (the recepteur and transmittors menus allowing to have several types of epsps on one neuron, according to the transmitor) is fully implemented -while not extensively tested...- for one neuron in G_neuron V8, but not yet included in the simulator itself. This will be added in XNBC V9. The full manual (in html, readable with any Web browser) is in the directory XNBC8/man/ and in the directory set by XNBC_ROOT_HTML
It is automatically installed. To re-install it, run the manual_install script. You can edit it to choose the directory where to put the file.
A full user paper manual is available on the same ftp site (ftp://ftp.jussieu.fr/pub/XNBC/xnbc_manual_8_21.ps.gz).
It is too large to be included in the same tar file because of the many screen captures.
The manual is also available on the Web at:
http://www.b3e.jussieu.fr/logiciels/xnbc8_manual/
This version is 8th.
In this version, the following tools have a full graphic interface:
The following tools have an caracter interface:
They are left because they allow to produce more versatile figures than the print menus of the programs with a graphic interface.
If the /usr/local/bin directory is in your path, to run xnbc, it should be enough to
> setenv DISPLAY my_machine:0.0
> xnbc &
If you have a specific environment:
> setenv DISPLAY my_machine:0.0
> source xnbc_env_private
> xnbc8
Then, follow the graphs and on line help...
A kind of tutorial will be found in doc directory as well as several user manuals of the individual tools. Nevertheless, the html manual is noe the only maintained manual.
For your conveniance, an example of the simulation of 2 networks is given in XNBC8/example_nbc. To run it, cd .. from the building directory (XNBC8) (i.e. go to its parent directory) an run xnbc. You will have a predefined small 50 neuron network (20 + 30), that you can simulate, visualize and analyze. Since presimulated files are provided, you could visualize and analyse it before any thing else in order to familiarize with these tools. Examples of other neuron files are in the directory XNBC8/neurons/
Don't miss to have also a look to the XNBC Web server, in order to be informed of new versions and related papers.
http://www.b3e.jussieu.fr/xnbc8/
XNBC is provided as an Open Source shareware.