Neural Simulation Demonstration
Bartlett Mel
mel at cns.caltech.edu
Mon Jul 19 13:08:41 EDT 1993
ANNOUNCEMENT FOR
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 software.
Purpose
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.
Format
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 visualization.
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 mordor.cns.caltech.edu
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.
Arrangements
In order to increase the likely success of the demonstrations,
each accepted participant will be asked toship 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.
Support
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
demonstration.
For further information contact:
Jim Bower or Erik De Schutter
Div. of Biology 216-76
Caltech
Pasadena, CA 91125
jbower at cns.caltech.edu, erik at cns.caltech.edu
FAX 1-818-7952088
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APPLICATION FORM
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
APPLICANT
Name:
Title:
Address:
E-mail:
PERSON DEMONSTRATING THE SOFTWARE
(if different from applicant)
Name:
Title:
Address:
E-mail:
COMPUTER USED FOR THE DEMONSTRATION:
Type:
Operating system:
SOFTWARE PACKAGE
Purpose (80 characters or less):
Author:
Operating system(s):
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?
script language?
Mac type interface (dialogs, buttons, popup menus)?
graphic interface (point to dendrite to select etc.)?
object-oriented approach?
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):
file output?
graph versus time during simulation?
phase plots?
Sholl plots?
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?
Simulator features:
integration method(s):
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):
integrate-and-fire model?
compartmental model?
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)?
synaptic plasticity?
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?
Manual:
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?
Other documentation:
On line help?
Tutorials?
Classes?
Papers?
Distribution:
Compiled program on disk/tape?
Compiled program by ftp?
As source code by ftp?
Fee (how much)?
Free upgrades?
Upgrades by ftp?
Available to foreign users?
User support:
E-mail support?
Telephone support?
Newsletter?
Users group?
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.
REFERENCES:
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:
Address:
E-mail:
FAX:
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