From rob@bip.anatomy.upenn.edu Tue May 31 21:05:45 EDT 1994 Article: 16787 of comp.ai.neural-nets Xref: glinda.oz.cs.cmu.edu comp.ai.neural-nets:16787 Path: honeydew.srv.cs.cmu.edu!nntp.club.cc.cmu.edu!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!bip.anatomy.upenn.edu!rob From: rob@bip.anatomy.upenn.edu (Robert G. Smith) Newsgroups: comp.ai.neural-nets Subject: Announcement: NeuronC available Date: 24 May 1994 21:42:12 GMT Organization: University of Pennsylvania Lines: 52 Message-ID: <2rtsbk$gt0@netnews.upenn.edu> NNTP-Posting-Host: bip.anatomy.upenn.edu Summary: NeuronC, a biophysically-based compartmental simulator is available. Keywords: compartmental simulator computer model neural circuitry network X-Newsreader: TIN [version 1.2 PL2] It has recently come to my attention that several people were looking for my simulator, NeuronC, but could not locate the source. It is available by anonymous ftp from: retina.anatomy.upenn.edu:pub/nc.tgz Neuronc ("nc") is a general-purpose computer language somewhat like C that has special features for simulating large neural circuits using compartments. It allows creating large arrays and uses an iterative difference equation solver so that virtually any network geometry may be specified (e.g. geometry is not limited to "tree" structure, and may include loops). Since "nc" is primarily a language it does not contain a complete interactive pull-down menu system for describing and running a simulation. However, there is a complete graphics facility for displaying on standard devices such as X11, PostScript, and VGA. If you have access to a mainframe computer but your mainframe terminal lacks graphics capability, you can run "nc" in a non-graphics mode and download ASCII (text) files that contain all the "nc" output graphics and data. These files may then be displayed locally on a PC. Nc is currently being developed in the C++ language with "gcc", although a procedure is provided to convert the source into standard ANSI C. The capabilities of the "nc" language are described in: Smith, R.G. (1992) NeuronC: a computational language for investigating functional architecture of neural circuits. J. Neurosci. Meth. 43: 83-108. Several additions have been made since the publication of this paper. They include voltage-sensitive calcium channels, calcium diffusion and calcium-sensitive potassium channels. The simulator runs under most Unix systems, including SGI, Sun, IBM AIX, and Linux. Nc is available free to the scientific community. It was developed with funds from NIMH and I hope to benefit from any feedback (error reports, suggestions about additions, etc.) that users can provide. Let me know if you would like more information or need help compiling "nc". Robert G. Smith rob@retina.anatomy.upenn.edu Article 17477 of comp.ai.neural-nets: Xref: glinda.oz.cs.cmu.edu comp.ai.neural-nets:17477 Path: honeydew.srv.cs.cmu.edu!nntp.club.cc.cmu.edu!godot.cc.duq.edu!newsfeed.pitt.edu!gatech!newsxfer.itd.umich.edu!gumby!wupost!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!bip.anatomy.upenn.edu!rob From: rob@bip.anatomy.upenn.edu (Robert G. Smith) Newsgroups: comp.ai.neural-nets Subject: Announcement: NeuronC available with POVRAY output Date: 25 Jun 1994 04:38:07 GMT Organization: University of Pennsylvania Lines: 38 Message-ID: <2ugcbf$djg@netnews.upenn.edu> NNTP-Posting-Host: bip.anatomy.upenn.edu Summary: NeuronC, a compartmental neural simulator displays Ray-Traced output. Keywords: neural circuit, ray-trace, 3D, compartmental simulator X-Newsreader: TIN [version 1.2 PL2] My neural circuit simulator "NeuronC" now produces ray-traced scenes for rendering with the "POVRAY" simulator (as well as standard X11, VGA, and PS outputs). The simulator is a general-purpose compartmental simulator that can construct a morphological- and biophysically-based neural circuit and run a physiology experiment on it. The "NeuronC" simulator was originally designed for vision experiments on large neural circuits. It includes a 2D light stimulus (with optical blur and photon noise) and photoreceptor models complete with spectral sensitivities and time-responses. A flexible set of synapse and membrane channel models is also included, including HH, sequential-state, and calcium-dependent versions. Any network geometry can be simulated (including electrical loops) and a virtually unlimited number of voltage- clamp/current clamp and recording sites may be specified and plotted. NeuronC is described in J. Neurosci. Meth (1992) 43:83-108. You can obtain the distribution along with compilation information and a complete 100-page manual by anonymous ftp to: retina.anatomy.upen.edu The distribution is in "pub/nc.tgz" and the documentation is in the "nc/doc" subdirectory. The distribution has been compressed with "gzip"; if you don't have this program, a gzip source distribution is available in the same directory. NeuronC is free to the scientific community and was developed under a grant from NIMH. Hope this is useful, Rob Smith