Demo Neural Simulation Software (fwd)
parzberg at nsf.gov
Tue Jul 20 20:14:26 EST 1993
Neural simulation demonstrations at
The Society for Neuroscience Annual Meeting 1993
Sponsored by the National Science Foundation
This announcement contains information on an
opportunity to demonstrate state of the art computer
simulation techniques in computational neuroscience at the
annual Society For neuroscience meeting to be held in
Washington DC during the second week of November.
Please distribute this announcement to other
groups which might be interested in demonstrating their
The primary purpose of these demonstrations will be
to expose large numbers of neuroscientists to the use of
computer simulation techniques in neurobiology. In
addition, we want to provide technical information on
simulation methods, the range of simulation software
currently available, and demonstrations of several aspects
of new computer technology that are relevant to efforts to
simulate and understand the brain.
The Neural Simulation Technology Demonstration will
consist of three separate components. First, a series of
simulation software demonstrations while be organized to
provide a balanced and as complete as possible view of
available non commercial software. Second, machines
will be made available to participants in the meeting
whose regular poster or oral presentations involve
simulations so that they can demonstrate the simulations
on which their paper presentations are based. Finally, a
separate demonstration will focus on state of the art
simulation technology including inter-computer
communication, concurrent computing, and graphical
Simulation software demonstrations
This announcement seeks applicants for the simulation
software demonstrations. This demonstration will be
organized very much like a regular poster session, except
that computers will be available for actual demonstrations
of the modeling software and each demonstration will
remain in place throughout the meeting. The session itself
will be set up within the exhibit space of the meeting.
Each presenter will be required to construct a poster
as well as demonstrate their software on a computer. The
poster presentations are intended to provide those
interested in the simulators an understanding of what they
will see when they actually look at the software on the
adjacent computer. As such, the poster should include
descriptions of the simulator itself, what it is best used
for, and how it is used.
We will provide an overview of the demonstrated
software packages as a handout.
We would also like to provide some basis of comparison
between the simulators. For this reason we are asking that
groups demonstrating unix software for compartmental modeling
present the quantitative results obtained from the first three
standard simulations in the Rallpack standards (Bhalla et
al., Trends in Neurosci. 15: 453-458, 1992), which
can be obtained by anonymous ftp from
What to do
If you are interested in being considered as a
simulations software demonstrator, you should fill out the
application attached to the end of this document and return
it to erik at cns.caltech.edu.
You should note that the National Science Foundation has
stipulated that applications cannot be accepted from vendors
of commercial software, but only from "not for profit" concerns.
Applications will be reviewed as they are received, deadline
is October 1, 1993. Invitations will then be send out immediately
based on this review. Criteria for acceptance of demonstrations
will include the apparent maturity of the effort as well as
evidence that the simulation software is being or could be
used outside of the laboratory in which it was developed.
Some packages are well known and established (De Schutter,
Trends in Neurosci. 15: 462-464, 1992) and will be
accepted with minimal review (i.e. submit application by
e-mail). Applications for newer packages should send
additional documentation (like manuals, information sheets,
papers,...) by mail to help in the evaluation.
In order to increase the likely success of the
demonstrations, each accepted participant will be asked to
ship their own computer to the meeting. This will avoid
difficulties with hardware incompatibilities, or novel
system configurations. Our technical staff will aid with
setting up the machines at each meeting.
Accepted participants will be provided support on a
reimbursement basis in the following forms:
1) computer shipping expenses
2) reimbursement of meeting registration costs for
one person designated as responsible for the software
For further information contact:
Jim Bower or Erik De Schutter
Div. of Biology 216-76
Pasadena, CA 91125
jbower at cns.caltech.edu, erik at cns.caltech.edu
This form can be e-mailed to erik at cns.caltech.edu,
or mailed to Erik De Schutter, Div. of Biology 216-76,
Caltech, Pasadena, CA 91125
PERSON DEMONSTRATING THE SOFTWARE
(if different from applicant)
COMPUTER USED FOR THE DEMONSTRATION:
Purpose (80 characters or less):
Hardware platforms on which code has been tested:
Parallel implementation (if yes, which platform)?
Programming language source code:
Source code available?
Current version number:
When was this version released?
Continued development/upgrades of the package?
How many programmers involved in continued development?
User expandable (yes only if explicitly supported by the code):
Interface type (answer yes or no):
all features in a single program?
interactive model creation/editing?
compartments/channels described by arbitrary codes/indexes?
compartments/channels described by user selected names?
Mac type interface (dialogs, buttons, popup menus)?
graphic interface (point to dendrite to select etc.)?
supports grouping of objects for easy selection?
File I/O for model description:
reads morphology files?
saves interactively created models?
reads file formats other software packages (list names):
outputs file formats other software packages (list names):
I/O of results (answer yes or no):
graph versus time during simulation?
color representation of cell ('schematic')?
color representation of cell ('3-dim')?
output multiple variables during same run?
output any computed variable?
incorporates analysis routines for results?
are Rallpack data available?
variable time step?
automatic detection of model setup errors?
storage of initial values for variables?
model size limited only by available memory?
Neuron modeling features (answer yes or no):
detailed morphology of dendritic/axonal trees?
standard Hodgkin-Huxley channels?
other channel types using Hodgkin-Huxley type equations?
other channel types using any equation?
Ca2+-dependent (in)activation of channels?
synaptic channels (alpha equation)?
simple concentration pools (Ca2+, exponential decay)?
complex concentration pools (buffers, diffusion)?
second messengers, enzymatic kinetics?
Network modeling features (answer yes or no):
small network (<= 100 cells)?
big networks (> 100 cells)
mixed cell model types possible?
automatic/random generation of connections?
network learning (e.g. backprop)?
synaptic/axonal delays implemented?
network growth during simulations?
is the manual complete (i.e. describes all program features, commands)?
number of pages in manual:
does the manual contain screen dumps?
reference manual only or also tutorials?
On line help?
Compiled program on disk/tape?
Compiled program by ftp?
As source code by ftp?
Fee (how much)?
Upgrades by ftp?
Available to foreign users?
How long has this package been available?
How many upgrades have been released?
How many scientists use this package in your group?
How many other groups in the USA use this package?
How many foreign groups use this package?
Optional and confidential:
list 3 users (including e-mail address or FAX) who currently use
the software package and who have never worked in your laboratory.
List max 2 publications describing this software package.
List max 5 publications describing simulation results obtained
with this software package.
CONTACT ADDRESS FOR PROSPECTIVE USERS:
Preferred method of contact:
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