From bnews@smaug.cns.caltech.edu Mon Apr 26 10:57:50 1993 Babelers, It has been a while since we have sent you anything concerning GENESIS. We would now like to update you on a few developments. One concerns the availability of Hebb Synapse objects and the other involves a new GENESIS port. We hope you find these useful. Shortly you will receive information in GENESIS version 2.0. The GENESIS developers have been working very hard on this new version which is intended to make GENESIS easier to use. Version 2.0 will also include the parallel port allowing GENESIS to be run across multiple networked workstations or on massively parallel computers. More on this later. Several of you have written letters refering to papers in preparation that have made use of GENESIS. In general, we would very much appreciate receiving citations for such papers. We would like to post them to the babel users group as well. Finally, Dave Beeman is working very hard on "The book of GENESIS" which we anticipate will be published sometime this fall. It will include chapters on both the use of GENESIS tutorials for educational purposes and also to learn to program in GENESIS. Again, more on that later. Jim Bower =========================================================================== Date: Tue, 16 Feb 93 13:20:33 PST From: dbeeman@dogstar.colorado.edu (Dave Beeman) Subject: New GENESIS Hebb objects available on babel for testing ============================================================================== The BABEL directory babel/objects/hebb now contains source code and demonstration scripts for some new objects which may used to implement Hebbian learning in GENESIS. These were written by Mike Vanier and are somewhat more sophisticated than a simpler implementation which was tested during the 1991 Methods in CNS Course at Woods Hole. Nevertheless, they should be considered as "experimental", as they have not been extensively tested. You may browse through the babel/objects/hebb to read the documentation, or pick up the whole package by ftp'ing babel/archives/hebb.tar.Z. Things have been set up so that you should be able to compile a new version of GENESIS with these libraries by just typing "make" in your version of the "hebb" directory. The "hebbdemo" subdirectory contains scripts for a simple demonstration of the Hebb synapses. To try the demo, compile the library, run the new version of "genesis", change to the "hebbdemo" directory and type "HebbDemo". A short description of the objects is given in "README.1st", and further documentation is given in the file "hebbdoc.README". Be sure to read this (and Mike's DISCLAIMER) before attempting to use these objects. Mike and I would both appreciate receiving feedback on these new objects. If they are found useful (and free of bugs), they will be incorporated into future versions of GENESIS. Dave Beeman dbeeman@dogstar.colorado.edu Mike Vanier mvanier@cns.caltech.edu ============================================================================== Date: Thu, 22 Apr 93 12:49:36 PDT From: dbeeman@dogstar.colorado.edu (Dave Beeman) Subject: GENESIS for X11R5 and 386bsd ANNOUNCEMENT - GENESIS patches for X11R5 and port to 386/486 PC unix Rich Murphey at the Univ. of Texas Medical Branch and Diana Smetters at MIT have submitted patches which allow GENESIS/XODUS to compile under X11R5. These patches, which have been tested using Nerurokit on the sun4, may be found in the babel/contrib/X11R5patches directory. Rich has also just finished an initial port of geneis to 386bsd, a freely redistributable 4.3 BSD Unix for the PC. On the 386bsd OS the scripts using Neurokit do not work yet but all other tutorials and demos have been tested successfully. There is more information and a guide to installation in the babel archive in /usr/genesis/babel/contrib/genesis-386bsd: genesis-1.4-386bsd-0.2-README (A short guide to installation) genesis-1.4-386bsd-0.2.tar.Z (386bsd binary distribution) genesis-1.4-386bsd-0.2.diff1.Z (C source patches) genesis-1.4-386bsd-0.2.diff2.Z (Makefile patches) genesis-1.4-X11R5-0.2.diff.Z (X11R5 patches) The major changes between X11R4 and X11R5 were the switch from asciiDiskWidgetClass to asciiTextWidgetClass for the help window and changes to the handling of Quarks in X11R5. Other changes to X resources and types are annotated in the file containing the X11R5 patches. As with other user-contributed code, we cannot offer any support or help for those who wish to use it. However, we are planning on incorporating these additions into a future release of GENESIS. For now, please contact the author to report any problems. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From bnews@smaug.cns.caltech.edu Fri Apr 30 12:14:54 1993 ========================================================================= From: anderson@cshl.org (John Anderson) Subject: printing graphs produced by GENESIS How do you print out graphs produced by GENESIS in a form suitable for a figure in a paper? Thanks John E. Anderson 1 Bungtown Road W. M. Keck Structural Biology Laboratory Cold Spring Harbor, NY 11724 Cold Spring Harbor Laboratory FAX 516-367-8873 ========================================================================= Reply from Dave Beeman - GENESIS Users Group Although the GENESIS xgraph and xdraw widgets may be printed using Ctrl-P, one can obtain a much better rendition of portions of a GENESIS/XODUS screen by using one of the various general purpose screen capture programs. My favorite is "xgrabsc". This copyrighted but freely distributable program can be compiled on most systems with Xwindows and will allow you to use the mouse to select a rectangular area of the screen to be captured into a postscript or X bitmap format file. A copy may be found in the babel/archives directory in the file "xgrabsc.tar.Z". Another good program is "xv", which allows viewing and conversion between a number of graphics formats as well as screen capture. The latest versions of "xv" and "xgrabsc" may be obtained by anonymous ftp from the usual archive sites for Xwindows, such as export.lcs.mit.edu in the "/contrib" directory. --------------------------------------------------------------------------- From bnews@smaug.cns.caltech.edu Wed May 5 09:43:11 1993 Subject: printing GENESIS graphs > >From: anderson@cshl.org (John Anderson) > Subject: printing graphs produced by GENESIS > > How do you print out graphs produced by GENESIS in a form suitable for > a figure in a paper? Thanks to Dave Beeman for the suggestion to use "xgrabsc" or "xv". Another way to print out GENESIS data is to send whatever you want to plot to an asc_file object. For example, to plot soma Vm create asc_file /output/ascfile sendmsg /cell/soma /output/ascfile SAVE Vm Then you can use whatever plotting program you want (I use gnuplot) to plot out the results. This gives you a good deal of flexibility in plotting styles and figure formats, and you can combine different kinds of data in a single figure easily. John --- John E. Anderson 1 Bungtown Road W. M. Keck Structural Biology Laboratory Cold Spring Harbor, NY 11724 Cold Spring Harbor Laboratory FAX 516-367-8873 ---------------------------------------------------------------------------