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       [_][_]           :                  THE GENESIS USER'S GROUP
       [_][_][_][_]     :          
       [_][_][_][_][_][_]                        NEWSLETTER #2
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     [][][][][][][][][][][]                     OCTOBER 31, 1991
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In this second issue of the GENESIS Users Group Newsletter, we announce a new version of GENESIS, the installation of the long-awaited BABEL bulletin board, and some new material available in the "BABEL directory". These may be accessed over the Internet from your account on babel.cns.caltech.edu. To find information on the latest additions to BABEL, read the file "/usr/genesis/babel/LATEST.NEWS" after logging in. If you are a member of BABEL and have not yet requested an account, you may do so by sending email to dbeeman@boulder.colorado.edu. Please provide a user name of eight characters or less. If the email address to which this newsletter was addressed is not your preferred address for receiving communications fron BABEL, please let us know.

Recent Developments

Two new staff members have joined us to help in the development and distribution of GENESIS. Chris Ploegaert (cp@cns.caltech.edu) is the new administrator for GENESIS and BABEL. She will be handling the correspondence and record-keeping for BABEL registrations. Maneesh Sahani is our new X-windows programmer. He is working on an extensive re-write of the XODUS code for the next major revision of GENESIS. We are in the process of hiring a person to re-write the GENESIS/XODUS manual.

Michael Speight (mds3@cns.caltech.edu) has been working on porting GENESIS to parallel computers. GENESIS is now running on the Gamma (a 64 node i860 based parallel computer), being used to examine large parameter spaces with a large Purkinje cell model. At the moment, it is being used for 64 independent Genesis simulations. The long-range plan will be to spread a single simulation over the multiple processors. The Intel Touchstone Delta, a 512 node machine, has now arrived and the code developed for the Gamma is being installed. Mike is also putting together a Transputer based system for the next stage of the parallelisation effort.

Mike Vanier (mvanier@cns.caltech.edu) is developing a set of Hebbian synapses, to be incorporated into the next version of GENESIS.

As distributed, GENESIS runs on the SUN family of workstations and the DECstation 3100 and 5000. Several members of BABEL have been active in developing ports of GENESIS to HP720, IBM RS6000, and IRIS workstations. We welcome postings to the BABEL bulletin board on this subject.

GENESIS Version 1.3

The directory "/usr/genesis" now contains version 1.3 of GENESIS. You may obtain the complete distribution of the new GENESIS by using ftp to download the file "genesis.tar.Z" from the directory "/usr/genesis/babel/archives". The "README" file in this directory provides instructions. Instructions for compiling and installing GENESIS are found in "/usr/genesis/src/README". The new features which are available in version 1.3 are:

New integration methods

        There are now eleven methods for numerical integration in GENESIS,
        including two fast implicit methods which use Hines' method.
        These are described in Doc/integ.doc.  This also describes the
        "setmethod" command, which is used instead of the "method" field in
        elements which perform a numerical integration.  This change means
        that scripts which set this field to change the integration method
        will have to be modified in order to run under the new version.
        This is the only incompatibility with previous versions of GENESIS
        and has no effect upon any scripts which were released with the
        previous version.

2) New options available with the view and fileview widget

        It is now possible to have an icon change size in only the x, y, or
        z direction to represent the value of a field.  This makes it
        possible to display time-dependent bar graphs which could be used to
        represent propagation of Vm along a cable, for example.

3) A "dia" field has been added to compartment and symcompartment elements to

represent the compartment diameter.

4) New elements

        There is now a dendro-dendritic synapse element (ddsyn) and an hsolve
        element used for the Hines method of integration.  This last element
        is created from a new library, "hines", in genesis/src.  The new
        .simrc and Makefiles reflect the addition of this library.  If you
        are compiling your own elements and functions, you should include
        this library.  Be sure to replace your ".simrc" files with the new
        one.

5) New demonstration scripts

        The Scripts directory contains a new version of "neurokit" which
        takes advantage of some new GENESIS features and improvements in the
        cell reader.  Many new channel prototypes have been added, and there
        are three short tutorials based on neurokit (channels, vclamp and
        int_methods).  There is also a Scripts/examples directory containing
        short demonstrations of the use of the Hines integration methods,
        the elements in the concen library and the dendro-dendritic synapse.

6) Revised manual

        The manual (in Doc/tex) has new and revised sections to document the
        Hines library, the ddsyn element, and the new view and fileview
        options.  There are also a number of other corrections and revisions.

7) Additional help

        Three new files have been added to the Doc directory in order to
        provide on-line help.  These are "integ.doc", "read_cell.doc" and
        "nxgenesis.doc".

8) Using GENESIS without XODUS

        The file "Doc/nxgenesis.doc" describes how to compile a version of
        GENESIS which does not use the XODUS X windows routines.  This is
        useful for running long "batch mode" simulations which send their
        output to files instead of graphics displays.

9) Unified convention for current direction.

        In previous versions of GENESIS, the "hh_channel" and "tabchannel"
        elements used a different convention for the direction of positive
        current flow from that used by other elements.  Now, all elements
        use the convention that treats a flow of positive ions into the cell
        as a positive current.

10) Miscellaneous bug fixes and other changes

        There are a number of new options available with the cell reader,
        described in "read_cell.doc", and some bug fixes for elements in the
        concen library.  The random number generator has been replaced by a
        machine-independent one, which will result in consistent results for
        simulations running on different machines.  The Makefiles have been
        revised to facilitate the porting of GENESIS to other machines.
        Details of the changes are given in /usr/genesis/src/CHANGES.

BABEL Bulletin Board

The bulletin board is now operational. We encourage you to use it for the exchange of ideas, problems, and solutions related to GENESIS. This can be accessed by logging into your babel account and typing "rn", in order to access the local BABEL newsgroups. (If you have changed your ".login" and ".cshrc" files from the default ones which are provided, you will have to add "/cit/news/bin" to your path.) Messages can be posted to newsgroups using the "Pnews" command. You can type 'man rn' or 'man Pnews' to get help for using these commands. A remote readnews server will also be running on this machine, allowing those of you who use remote readnews software to read babel news without having to login to the babel machine. This can usually be accomplished by doing a "setenv NNTPSERVER babel.cns.caltech.edu" prior to executing remote readnews on your local machine. Consult your local system manager for details.

New Additions to BABEL

The directory "/usr/genesis/babel" contains a number of new additions. As before, there is a "README" file in this directory and each of its subdirectories to explain the directory contents. Some of the notable additions are:

The "newdocs" directory contains several new pieces of documentation.
A new directory, "newsims", contains some new simulations which are intended for use in teaching concepts in neuroscience. Although these simulations are still under development, we feel that they are at a stage where they will be useful to others. We invite your suggestions for features to be added and for exercises to be used by students.
The "tutorials" directory contains new and revised tutorials which guide the user through the process of constructing GENESIS simulations.

Additional questions / comments

If you have additional questions, comments, or suggestions with respect to BABEL please address them to:

        Prof. David Beeman
        Dept. of Electrical and Computer Engineering
        Campus Box 425
        University of Colorado
        Boulder, CO 80309

        dbeeman@boulder.colorado.edu   (303) 492-2852

Reports of bugs or other problems with GENESIS may be sent to:

genesis-bugs@cns.caltech.edu

Written correspondence concerning BABEL registration should be sent to:

        BABEL
        Computational Neural Systems Program
        Caltech, 216-76
        Pasadena, CA 91125

Dave Beeman
Chief editor
BABEL newsletter

GENESIS and BABEL are supported by funds provided by the National Science Foundation.