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: : THE GENESIS USER'S GROUP
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: :. NEWSLETTER #1
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[][][][][][][][] : APRIL 1, 1991
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This newsletter officially establishes the GENESIS Users Group, BABEL. This users group consists of individuals and laboratories interested in serious use of GENESIS for either research and/ or for educational purposes. At present BABEL includes 74 users out of the total of more than 500 sites worldwide who have obtained the software.
The purpose of BABEL is to provide serious users with the information and facilities necessary to exchange GENESIS expertise as well to provide these users with more direct access to the results of ongoing GENESIS developments both remotely and at Caltech.
BABEL itself will operate from an Internet accessable SUN SPARCstation 2 at Caltech. Users will be able to browse BABEL directories as well as transfer files to and from their host machines. In addition, we have established a BABEL newsgroup for the exchange of information, posting of questions, bug reports and hints for setting up GENESIS simulations.
The following sections describe those BABEL features that are now available
and outline our plans for the near future.
New Distribution of GENESIS
On July 10, 1990 the first full GENESIS source code was made available for
distribtion from Caltech. This version of the system will continue to be
the standard distribution for those casually interested in the system.
However, as part of the initiation of the GENESIS users group, we are now
making a new March 1991 release of GENESIS available to BABEL members only.
This version has numerous bug fixes as well as new features, and also
executes about 40% faster than the previous version. These improvements are
described in 'newdocs/genesis.changes' within the BABEL directory. This new
version is completely compatable with the previous release so all your
scripts will run as before. The GENESIS development team has a strong
commitment to maintaining compatibility with previous versions.
Documentation
A compressed postscript file containing a new and revised manual for GENESIS
(not available as part of the "free" distribution) can be found in the
directory '/usr/genesis/Doc/tex', along with the TeX source files. The
'README' file in this directory gives information on printing the
documentation. In addition, further new documentation is included in the
BABEL directory 'newdocs'. As additional documentation is written, it will
be added to this directory. Periodically, the new documentation will be
incorporated into the full GENESIS manual. While documentation will
inevitably lag behind the development of new GENESIS features, we have made
a strong commitment and have generated the financial support necessary to
continue to improve the documentation. We are also in the process of
negotiating with a publisher to produce a professional printed version of
the documentation along with other projects. As described below, we also
hope to encourage and support the involvment of members of BABEL in this
effort.
BABEL Bulletin Board
In order to facilitate the exchange of ideas, problems, and solutions related
to GENESIS, we are establishing a bulletin board for use by BABEL members.
The bulletin board, which will be operational by the end of April, can be
accessed by logging into your babel account and typing "rn". The bulletin
board will include all past BABEL newsletters and will be set up as an open
forum for the exchange of GENESIS related information in particular, and
information about neural simulations in general. The bulletin board will
also be used to post information on relevent graduate and postdoc training
opportunities, summer courses, and faculty positions. 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
NEWSSERVER babel.cns.caltech.edu" prior to executing remote readnews on your
local machine. Consult your local system manager for details.
"The Neuron Exchange"
One of the advantages of using a highly modular standard simulation
environment such as GENESIS is that modelers may structure their own
simulations from libraries of previously defined neural components such as
channels, compartments, or entire cells. Thus, by sharing simulation
components, it becomes possible to construct simulations by simply
organizing previously constructed elements into new arrangements. We offer
two mechanisms for the exchange of such simulation components. One of these
is an enhanced version of the 'neurokit' simulation, available in the
'genesis/Scripts/neurokit' directory. Neurokit provides a standard method
for constructing single neurons from a library of component prototypes. The
results may be saved in neuron descriptor files, which concisely specify the
geometry and electrical properties of the neurons.
The other, less integrated, approach is maintained in a library of GENESIS functions for creating cells and cell components. These functions are designed to be easily incorporated into your own simulations. They may be found in various subdirectories of the 'libraries' directory and are now accompanied by supporting documentation and simple demonstration scripts which illustrate their use.
It is also possible to extend the functionality of GENESIS by linking user-written libraries containing additional functions and objects into the simulator base code. This allows one to write efficient code in C which may then be easily incorporated into GENESIS when needed. The BABEL directory 'objects/testlib' contains examples showing how this may be done. The 'objects' directory also contains code for a number of user-contributed objects which are not part of the general GENESIS distribution.
The directory 'contrib' has the write protection set so that all members of
BABEL are allowed to copy or ftp files to the directory. It is intended as
a temporary storage place for user-contributed files. We encourage you to
place documentation notes, GENESIS scripts, source code for new GENESIS
objects or functions, or anything else which you would like to contribute in
this directory. Files placed here will be periodically reviewed by members
of the GENESIS support staff and placed in appropriate permanent locations.
All contributions will be fully atributed to their authors.
GENESIS tool exchange
In addition to simulation components, we would also like to encourage the
exchange of graphical and analysis components to the GENESIS system. The
tool exchange will be used for this purpose.
Simulation depository
We would also like to encourage BABELers to deposit interesting simulations
for common access. We would especially encourage authors to post GENESIS
based simulations that have served as a basis for published modeling work.
We are in the process of discussing with several publishers the possibility
of directly linking these deposits with publication of results.
Tutorial depository
In addition to its use as a tool for ongoing research, GENESIS was also
explicitly designed to support the teaching of computational techniques in
neurobiology. There are currently efforts underway in several institutions
to develop undergraduate and graduate curricula based on GENESIS tutorials.
Again, we would like to encourage these efforts by providing a means to
exchange tutorial programs. The tutorial depository will be used for this
purpose. There are now several updated and new tutorials in the 'tutorials'
directory.
Future developments
To some extent the future development of BABEL as well as GENESIS is in the
hands of its users. However, there are several developments at Caltech that
may be of interest. In particular, Dr. Bower is one of the principle PIs on
the project to establish a new Intel Delta Touchstone concurrent computer at
Caltech. This machine will be installed in late April and represents a peak
computing performance of around 30 gigaflops. Dr. Bower has also aquired
funds and personel to port the GENESIS system to this machine. Accordingly,
the possibility exists that BABELers may be able to apply for access to the
substantial comuping resources represented by this machine. We anticipate
working out the logistical details between now and the begining of fall of
1991. More information will be available in subsequent newsletters. Funds
have also been acquired to support further development of the GENESIS base
code. A major effort over the next several months will be the incorporation
of implicit integration routines and other improvements to increase the
speed and efficiency of GENESIS.
Accessing the BABEL Directories and confirming your BABEL membership
You may request a BABEL account and password by sending email to our system
administrator, uhley@babel.cns.caltech.edu. Please keep us informed of any
changes in your email address, so that you may continue to receive these
newsletters. If you wish to be removed from the mailing list, please let us
know.
Once a BABEL account has been created you can access it at any time over the internet. For those of you with internet access, just use "rlogin" or "telnet" to connect to the host babel.cns.caltech.edu. At the login prompt enter your assigned user name and password. You will automatically be deposited in your own private home directory from which you can browse or copy the BABEL files. The directory '/usr/genesis/babel' contains the subdirectories which we call the "BABEL directories". The remaining files and subdirectories in '/usr/genesis' constitute the new distribution of GENESIS. The BABEL directory 'archives' ('/usr/genesis/babel/archives') is of particular note as it contains compressed "tar format" archive files of most of the other directories, so that they may be efficiently transfered to your machine. For example, 'genesis.tar.Z' contains the complete directory tree of the March 1991 distribution of GENESIS. The 'README' file in the 'archives' directory gives further instructions for the transfer and extraction of these archived files.
The local babel newsgroups can be accessed from your account by typing 'rn'. 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.
Once you have changed to the 'babel' directory, you should look at the
'README' file there. This will give you a reasonably current description of
what you will find in the various subdirectories. Recent announcements and
news of new additions (also posted on the bulletin board) may be found in
the 'news' subdirectory. A list of other BABEL members may be found in
'news/babel.members'. Files which are intended for the various depositories
may sent by ftp to the 'contrib' subdirectory.
Limitations to BABEL support
In the original disclaimer associated with the intial distribution of GENESIS
we were careful to state that distribution should imply no commitment on the
part of Caltech or the GENESIS development team to support the use of this
system. Time and funding limitations require that we take the same position
with respect to BABEL. However, providing a software platform for the
cooperative development and sharing of neural simulation software was one of
our primary design objectives. We view the BABEL users group as the
organization to make this a reality. Accordingly, it should be obvious that
the more individual BABELers contribute to the enterprise, the more
cooperation they can expect from the Caltech development group.
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
Dave Beeman
Chief editor
BABEL newsletter
GENESIS and BABEL are supported by funds provided by the National Science Foundation.