This is a summary describing significant research projects using GENESIS,
drawn from information provided by BABEL members. We have not included all
responses, but only those from groups that appear to have actively used
GENESIS and published results, or are close to the publication stage.
Please note:
- Some of this information is not current, and some email addresses may not be
valid - Please be considerate in your use of the email addresses, and do not
bother people unnecesarily - Let us know if you want to be removed or added to this list, or have updated
information to provide
Arizona State University
Daryl Kipke (kipke@asu.edu) - Bioengineering program
GENESIS is used to develop biologically plausible cell models of auditory
neurons in the brainstem. These are used to test hypotheses concerning
auditory neural networks before performing physiological experiments. These
neural simulations are then used to improve the animal experiments and propose
new experiments.
Levy, K.L and Kipke, D.R. (1998) Mechanisms of the cochlear nucleus octopus
cell's onset response: synaptic effectiveness and threshold. J. Acoust. Soc.
Am. 103: 1940-1950.
Levy, K.L., and Kipke, D.R. (1995a). "The importance of membrane properties
and synaptic location in octopus cells of the mammalian cochlear nucleus",
in The Neurobiology of Computation, (J. M. Bower, Ed.), Kluwer Academic
Press, Boston, MA, pp. 93-99.
Levy, K.L. and Kipke, D.R. (1995b). "Indications that octopus cells of the
cochlear nucleus precisely respond to the envelope of tones and speech in
background noise: A modeling study". Assoc. Res. in Otolaryngol. Abstr.
18:128.
Levy, K.L. and Kipke, D.R. (1995c). "Modeling the effects of cochlear
electrical stimulation on responses of the cochlear nucleus octopus cell".
Conference on Implantable Auditory Prostheses. August, 1995, Asilomar, CA.
Levy, K.L. and Kipke, D.R. (1996) A biologically plausible model of
neurons in the cochlear nucleus that computes accurate spike times
for complex stimuli in real time.
In J. M. Bower (Ed.), Computational Neuroscience: Trends in Research
1995 Academic Press, NY, 101-106.
Peyton, S. F. and D. R. Kipke, D. R. (1995) A compartmental model of
ventral cochlear nucleus stellate cells: Responses to constant and
amplitude-modulated tones. In J. M. Bower (Ed.) The Neurobiology of
Computation. Kluwer Academic Publishers, Boston, 117-122.
Australian National University
Steve Redman group (Steve.Redman@anu.edu.au)
Bruce P. Graham (bruce@cns.edinburgh.ac.uk)
All the work described in this paper is based on a model of muscle stretch
reflex implemented using GENESIS:
Bruce P. Graham and Stephen J. Redman (1993) "Dynamic behaviour of a model
of the muscle stretch reflex", Neural Networks 6: 947-962.
Allan Coop has used GENESIS as part of his work in modeling the peristaltic
reflex:
Allan Coop and S. J. Redman (1993) "A model of the peristaltic reflex" in
Computation and Neural Systems, 313-320, F. H. Eeckman and J. M. Bower (eds.),
Kluwer Academic Publishers
Boston University
Michael Hasselmo (hasselmo@berg.bu.edu
Ross Bergman (hyjinx@berg.bu.edu)
Gene Wallenstein (gw@berg.bu.edu)
Ajay Kapur (ajay@berg.bu.edu)
Recently, we've been using GENESIS to develop detailed network
biophysical simulations of hippocampal subregions, starting with a
simulation of region CA3 which is a simplified version of the Traub
network model. Usually, we use about 500-1000 pyramidal cells in this
network. We've explored effects of cholinergic modulation on
oscillatory dynamics in this network, and the role of cyclical GABAB
modulation of synaptic transmission in theta phase precession of place
cell responses. More recently, we've been exploring the role of
modulatory influences on interneurons in storage of sequences, and the
role of cholinergic modulation in oscillatory dynamics in the
entorhinal cortex. The long term goal is development of a GENESIS
based simulation of the entire hippocampal formation for analysis of
the cellular basis of episodic memory function.
Hasselmo, M.E., Wyble, B.P. and Wallenstein, G.V. (1997)
Encoding and retrieval of episodic memories: Role of cholinergic
and GABAergic modulation in the hippocampus. Hippocampus 6: 693-708.
Wallenstein, G.V. and Hasselmo, M.E. (1997a) Functional transitions
between epileptiform-like activity and associative memory in hippocampal
region CA3. Brain Res. Bull. 43: 485-493.
Wallenstein, G.V. and Hasselmo, M.E. (1997b) GABAergic modulation of
hippocampal activity: Sequence learning, place field development, and the
phase precession effect. J. Neurophysiol. 78: 393-408.
Wallenstein, G.V. and Hasselmo, M.E. (1997c) Bursting and oscillations in a
biophysical model of hippocampal region CA3: Implications for associative
memory and epileptiform activity. In J.M. Bower (Ed.) Computational
Neuroscience, Trends in Research, 1997. Plenum Press: New York, pp. 547-552.
Wallenstein, G.V. and Hasselmo, M.E. (1997d) Are there common
neural mechanisms for learning, epilepsy, and Alzheimer's disease? In
Neural Networks and Psychopathology, D.J. Stein (Ed.), Cambridge University
Press, Cambridge, U.K., In press.
Wallenstein, G.V. and Hasselmo, M.E. (1998) Neuromodulation of hippocampal
population coding: Place field development and phase precession, in
Computational Neuroscience: Trends in Research 1998 (J. M. Bower, Ed.),
Plenum Publishing Co., NY pp. 119-124.
Wallenstein, G.V., Eichenbaum, H.B. and Hasselmo, M.E. (1998) The hippocampus
as an associator of discontiguous events. Trends Neurosci. 21: 317-323.
Hasselmo, M.E. and Barkai, E. (1995) Cholinergic modulation of
activity-dependent synaptic plasticity in the piriform cortex
and associative memory function in a network biophysical simulation.
J. Neurosci. 15: 6592-6604.
Hasselmo, M.E. (1995) Neuromodulation and cortical function:
modeling the physiological basis of behavior. Behav. Brain Res.
67: 1-27.
Hasselmo, M.E. and Linster, C. (1996) Modeling the piriform cortex.
In: E.G. Jones and P.S.Ulinski (eds.) Cortical Models. Cerebral
Cortex Vol. 12 Plenum Press: New York.
Hasselmo, M.E. (1995) Physiological constraints on models of behavior.
In L. Niklasson, M.B. Boden (eds.) Current Trends in Connectionism.
Lawrence Erlbaum Assoc.; Hillsdale, NJ, p. 15-32.
Hasselmo, M.E., Barkai, E., Horwitz G. and Bergman, R. E.D. (1993) "Modulation
of neuronal adaptation and cortical associative memory function" in Neurons
and Neural Systems, F. Eeckman, Ed., Kluwer Academic Publishers, pp. 287-292.
Barkai E., Bergman, R.E., Horwitz, G. and Hasselmo M.E. (1994) Modulation
of associative memory function in a biophysical simulation of rat piriform
cortex. J. Neurophysiol. 72:659-677.
Barkai E. and Hasselmo M.E. (1994) Modulation of the input/output function
of rat piriform cortex pyramidal cells. J. Neurophysiol. 72:644-658.
Boston University, Biomedical Engineering Department
Hearing Research Center
Socrates Deligeorges <sgd@engc.bu.edu>
I am trying to create models of several types of cells from the periphery
to the IC in the auditory system and interconnect them. My models to date
have been siganl processing and written from the ground up in C. I would
like to use GENESIS as a means of speeding up model development and
incorporating more precise anatomical and physiolgical characteristics. In
the short term, I would like to start by creating models like those of Levy
and Kipke (1997) {Octopus cells in the CN}.
East Carolina University
Focused Research Program in Computational Neuroscience (FRPCN)
Director: John Bickle
http://www.ecu.edu/frpcn/
Marica Bernstein (mcb1204@mail.ecu.edu)
The first application of GENESIS to one of FRPCN's (Focused Research
Program in Computational Neuroscience) research projects is simulating
the effects of spacial distibution of excitatory and inhibitory synapses
onto thalamic lateral geniculate (LGN) relay cells. GABAergic
projections from thalamic reticular nucleus (TRN) synapse more
proximally to the axon hillock than do excitatory feedback projections
from V1 cortical columns.
FRPCN uses GENESIS to develop biologically plausible computational models of
certain components of the visual system. We have developed a 19-compartment
model of an LGN relay neuron which reflects the spatial distibution of
excitatory and inhibitory synapses. We are currently developing a 72-neuron
(1152-compartments) network of these neurons (60 LGN and 12 V1 units) to test
a functional hypothesis that we initially suggested in:
J. Bickle, M. Bernstein, M. Heatley, C. Worley, and S. Stiehl. (1999) A
functional hypothesis for LGN-V1-TRN connectivities suggested by computer
simulation, J. Computat. Neurosci. 6: 251-261.
Upcoming projects include use of GENESIS to model intra-cingulate circuitries
to address questions concerning the effects of feedback projections from
anterior cingulate cortex to dorsolateral prefrontal cortex. This work bears
not only on FRPCN's work on sequential saccade generation, but will generalize
and speak to the mechanisms that might underlie particular deficits seen in
schizophrenics and persons with drug abuse problems.
Other publications which report results with GENESIS models are:
Mendez, K. and J. Bickle, J. (1999) Modeling corticothalamic excitatory and
intrathalamic inhibitory synapses on simulated thalamic relay neurons.
Soc. Neurosci. Abstr. 25: 153.
Bickle, J., Worley, C. and Bernstein, M. (2000). Vector subtraction
implemented neurally: A neurocomputational model of sequential cognitive and
conscious processing, Consciousness and Cognition 9: 117-144.
Bernstein, M., Bickle, J. and Stiehl, S. (2000) The effect of motivation on
the stream of consciousness: Generalizing from a neurocomputational model of
cingulo-frontal circuits controlling saccadic eye movements. In R. Ellis and
N. Newton (eds.) The Caldron of Consciousness: Motivation, Affect, and
Self-Organization An Anthology. New York: John Benjamins.
Emory University, Department of Biology
Ronald L. Calabrese, PI (rcalabre@biology.emory.edu)
Jin Lu, Postdoctoral Fellow (jlu@biology.emory.edu)
Andrew Hill, Postdoctoral Fellow (andy@calabreselx.biology.emory.edu)
Dieter Jaeger, Assistant Professor (djaeger@emory.edu)
http://calabreselx.biology.emory.edu/
http://www.biomed.emory.edu/Faculty/Jaeger.html
Our lab studies the neural circuit that controls the heart of the medicinal
leech. We record the behavior of neurons in this circuit with
microelectrodes. Using voltage clamp techniques, we isolate and characterize
the individual ionic currents which contribute to this behavior. We study how
the structure of these neurons affects their behavior using dynamic imaging
and selective dendritic laser ablation. To understand how these currents and
structures interact to produce the behavior of the circuit, we simulate the
ionic currents and cell connectivity with realistic biophysical models.
Existing models of leech heart neurons using the Nodus simulation
software are now being converted to GENESIS. These simulations will be
used in close conjunction with experimental data to improve our
understanding of neural processing in the leech heart system.
For a GENESIS tutorial and model of the leech heartbeat timing network,
see http://calabreselx.biology.emory.edu/software.html.
Hill, A. (1999) Phase lag between oscillators of a realistic neuronal network
model of the leech heartbeat motor pattern generation system. In J.M. Bower
(ed.) Neurocomputing 1999, Plenum Press: New York.
Hill, A., Masino, M.A., Lu, J. and Calabrese, R.L. (1998) A realistic model of
segmentatal oscillators of the heartbeat neuronal network of the leech. Soc.
Neurosci. Abstr. 24: 1672.
Dieter Jaeger is using GENESIS to model synaptic input processing in
cerebellar Purkinje cells (J. Neurosci. 17: 91-106, 1997). Current projects
include the development of models for cerebellar interneurons and globus
pallidus neurons. The future goal is to create small canonical microcircuit
models of cerebellum and the basal ganglia. GENESIS is also used for teaching
computational neuroscience to a split-level undergraduate-graduate level
course at Emory University.
Environmental Research Institute of Michigan (ERIM) and NIH
Tom Vogl (tvogl@wo.erim.org)
(Also see listing under George Mason University)
GENESIS is being used to model the photoarray in a single Hermissenda eye.
This model demonstrates many of the information processing capabilities that
have been studied in electrophysiological and behavioral studies of
Hermissenda's visual sensors, and the importance of heterogeneity in the
efficient and robust operation of biological networks.
Blackwell, K. T., Vogl, T. P., Alkon, D. L. (1996) Channel model of
second messenger mediated transformation of GABA induced currents.
In J. M. Bower (Ed.), Computational Neuroscience: Trends in Research
1995, Academic Press, NY, 3-8.
Blackwell, K., Dettmar, H., Vogl, T. and Alkon, D. (1993) Ionic Current
Modeling of Light Responses from Hermissenda B Photoreceptor, Soc. Neurosci.
Abstr. 19:1335.
Werness, S.A, Fay,D., Blackwell, K.T., . Vogl, T.P., and Alkon, D.L.
(1994) "Computational Hermissenda Photoarray Model" in Computation in Neurons
and Neural Systems, F. Eeckman, Ed., Kluwer Academic Publishers, pp. 79-84.
Werness, S. A., Fay, S. D., Blackwell, K. T., Vogl, T. P. and Alkon,
D. L. (1992) "Associative learning in a network model of Hermissenda
crassicornis I.", Biol. Cybernetics 68: 125-133.
Werness, S. A., Fay, S. D., Blackwell, K. T., Vogl, T. P. and Alkon,
D. L. (1993) "Associative learning in a network model of Hermissenda
crassicornis II.", Biol. Cybernetics 69: 19-28.
George Mason University
Avrama Blackwell (kblackw1@osf1.gmu.edu)
GENESIS is being used to model calcium dynamics in the Hermissenda B
photoreceptor cell. The purpose of the research is to investigate the role
of calcium in learning in Hermissenda, in particular, the sensitivity to
interstimulus interval and intertrial interval. The model includes IP3
induced calcium release, as well as buffers, pumps, diffusion and voltage
dependent calcium currents.
Blackwell K.T. (2000) Evidence for a distinct light-induced calcium-dependent
potassium current in Hermissenda crassicornis. J. Comput. Neurosci. In Press
Blackwell K.T. (2000) Does calcium mediate the interaction between paired
stimuli in classical conditioning? Presented at the ninth annual
computational neuroscience meeting CNS*2000.
Blackwell K.T. (2000) Characterization of the light-induced currents in
Hermissenda. Neurocomputing, In Press.
Blackwell K.T., (1999) Dynamics of light-induced current in Hermissenda.
Neurocomputing 26-27: 61-67
Blackwell, K.T., Vogl, T.P., and Alkon, D.L. (1998) "Cellular mechanisms of
calcium elevation involved in long term memory" in Computational Neuroscience:
Trends in Research 1998 (J. M. Bower, Ed.), Plenum Publishing Co., NY pp.
137-142.
(Also see previous work under ERIM.)
Harvard University Medical School
Steven Matthysse, Professor, Department of Psychiatry
steven_matthysse@harvard.edu
I am an applied mathematician working in the field of neuro-psychiatric
research. Primarily, we would like to consider applying GENESIS to the
study of large realistic neural systems involved in the control of certain
physiological processes that are known to be abnormal in schizophrenic
patients. An example is smooth-pursuit eye tracking, which is abnormal in
many of the patients and also a high proportion of their first-degree
relatives. What we would like to do with the simulations might be described
as "virtual neuropathology" -- we change parameters of the network such as
dendritic spine densities, neurotransmitter reuptake, etc. and see what the
effects on the smooth-pursuit eye tracking behavior are. Then we compare
the simulated behavioral changes with the actual deficits in patients, and
reason backwards to conclude that certain neuropathological abnormalities,
rather than others, are the cause. No one thinks that schizophrenia is
actually caused by defective smooth pursuit eye tracking, etc., but it is
plausible that the neuropathology in this physiological system might
generalize to the much less readily studied systems involving thought and
emotion that underlie the patients' symptoms.
Hebrew University, Israel
Department of Physiology, Hadassah Medical School
Yehuda Albeck (albeck@music.md.huji.ac.il)
Simulations of the effect of inhibition on Nucleus Laminaris neurons in
barn owls.
Neurons in the nucleus laminaris (NL) of barn owls are sensitive
to interaural time difference (ITD). Since the relevant band for
the owl is centered at 6-7 kHz, these cells need to detect ITDs
of order of magnitude of 10 usec. We have no biophysical data about
these cells, though, we can try to extrapolate from NL cells of the
chick that are sensitive to much lower frequencies.
The model tries to suggest a combination of channels and synapsestrengths
that might force the cell to respond to a coincidence of
spikes when they are separated by less that ~50 usec, and ignore
them if the difference is longer.
In a related model, the question of dynamic range is raised. A cell
that responds to a coincidence of spikes cannot tell the difference
between a coincidence of two spikes from the two ears, and a coincidence
of two spikes from the same ear. At high sound intensity the input
rate from each side may becomes so high that monaural coincidence becomes
likely and the ITD sensitivity is lost. Right now, I try to solve this
problem by introducing a combination of excitatory and inhibitory
inputs that control the threshold dynamically, and keep its sensitivity
throughout the input dynamic range.
Pena, J.L., Viete, S., Albeck, Y. and Konishi, M. (1996) Tolerance
to sound intensity of binaural coincidence detection in the nucleus
laminaris of the owl. J. Neurosci. 16: 7046-7054.
Albeck, Y. (1994) A model for the role of inhibition in interaural time
difference in the brainstem of barn owls. Soc. Neurosci. Abstr. 20:136.
Heinrich Heine University, Dusseldorf
C. & O. Vogt Institute for Brain Research
Rolf Koetter (rk@hirn.uni-duesseldorf.de)
http://www.hirn.uni-duesseldorf.de/rk/
GENESIS is being used for:
- Large-scale simulations of striatal network with an interest in basal
ganglia disorders such as Parkinson's disease and Huntington's disease.
(These use a 20 x 20 network of striatal spiny neurons.) - Simulations involving learning rules and modifiable synapses for dendritic
spines in the striatum. - We are starting to look at the simulation of dopaminergic nigrostriatal
neurons.
Kotter, R. and Feizelmeier, M. (1998) Species-dependence and relationship of
morphological and electrophysiological properties in nigral compacta neurons.
Prog. Neurobiol. 54: 619-632.
Kotter, R. and Wickens, J.R. (1998) Striatal mechanisms in Parkinson's
disease: New insights from computer modeling. Artif. Intell. Med. 13:
37-55.
Kotter, R. (1999) Motor fluctuations in Parkinson's disease: A
postsynaptic mechanism derived from a striatal model. Prog. Brain Res.
121: 283-294.
Kotter, R. and Schirok, D. (1999) Towards an integration of biochemical
and biophysical models of neuronal information processing: a case study
in the nigro-striatal system. Rev. Neurosci. 247-266.
Koetter, R., Alexander, M. E. and Wickens, J. R. (1995) Effects of asymmetric
neuronal connectivity and dopamine on striatal function: Simulation and
analysis of a model for Huntington's disease. In J. M. Bower (Ed.) The
Neurobiology of Computation. Kluwer Academic Publishers, Boston, 239-244.
Koetter, R. and Feizelmeier, M. (1996) Computer simulation study of ionic
mechanisms underlying voltage traces recorded from dopaminergic neurons. Soc.
Neurosci. Abs. 22: 2028.
Koetter, R. and Feizelmeier, M. (1996) Relationship between morphological and
electrophysiological properties of dopaminergic neurons. In J. M. Bower
(Ed.), Computational Neuroscience: Trends in Research 1995 Academic Press, NY,
89-94.
Koetter, R. and Wickens, J. (1995a) Interactions of glutamate and dopamine in
a computational model of the striatum. J. Comput. Neurosci. 2: 195-214.
Koetter, R. and Wickens, J. (1995b) Effects of an excitatory synaptic
conductance and a slow membrane potassium conductance in an inhibitory
striatal network model. In: Herrmann HJ, Wolf DE, Poppel E (eds.)
Supercomputing in Brain Research: From Tomography to Neural Networks. World
Scientific, Singapore, pp. 257-263.
Hospital Ramon y Cajal, Madrid
Dr. Oscar Herreras (oscar.herreras@hrc.es)
We are making a GENESIS model of CA1 pyramidal cells based on the 1994 Traub
model and the Warman et al model of the CA1 pyramidal cell, since that
is the region we are using in our experiments.
Hungarian Academy of Sciences
KFKI Research Institute for Particle and Nuclear Physics, Budapest, Hungary
http://www.rmki.kfki.hu/biofiz/cneuro/cneuro.html
http://www.rmki.kfki.hu/biofiz/cneuro/projects.html
Inhibitory synapses are thought to be distributed throughout the dendrites and
the soma of pyramidal cells in several cortical regions. Recent experimental
evidence suggests that inhibitory synapses of different locations are
associated with specific actions based on their position. It has been observed
that IPSP responses to GABA have different time-courses corresponding to the
different locations of receptors. This can be explained by either the
electrotonic filtering by the dendritic tree or different subspecies of
GABA(A) receptors giving rise to distinct responses.
Our simulations showed that it is possible to reproduce the differences seen
between somatic and dendritic IPSP as measured at the soma by Miles and
coworkers, thus raising the possibility that although there are a number of
known GABA(A) receptors, interneuron to pyramidal cell synapses use the same
one regardless of location. This is supported by that we simulated the
electrotonic attenuation with morphological distances comparable to that seen
in reconstructed cells. Future simulations can describe the functional effects
of this electrontonic attenuation of IPSPs on the bursting behavior of
pyramidal cells.
Lengyel, M., Kepecs, A. and Erdi, P. (1999) Location-dependent differences
between somatic and dendritic IPSPs. Neurocomputing 26-27: 193-197.
Adorjan, P. Barna, G., Erdi, P., Grobler, T., Kepecs. A., Lengyel, M. and
Ventriglia, F. (1996) Multicompartmental modeling of hippocampal pyramidal
cells and interneurons with the GENESIS software tool. Neurobiology, 4:
247-249.
Bazso, F., Kepecs, A., Lengyel, M., Payrits, S., Szalisznyo, K., Zalanyi, L.
and Erdi, P. (1999) Single cell and population activities in cortical-like
systems. Rev. Neurosci.10(3-4):201-212.
Institute of Neuroinformatics, Zurik
Daniel Blank <dan@neuroinf.ethz.ch>
With Rodney Douglas, is simulating a network of spiny stellate cells from
layer 4 of cat primary visual cortex.
Konrad Kording <koerding@ini.phys.ethz.ch>
http://www.ini.unizh.ch/~koerding
Used Genesis in simulations of learning in oscillatory systems
(submitted) of cooperative computation between top-down and bottom-up
streams (submitted) and maybe later in simulations of learning with
calcium spikes.
Markus Siegel, Konrad Kording and Peter Konig. Integrating top-down and
bottom-up influeces in active dendrites (Opening Symposium of the Center for
Neuroscience 1999, Zuerich)
Manuel Sanchez-Montanes, Konrad Koding, Paul Verschure and Peter Konig. Local
and global gating of plasticity (Opening Symposium of the Center for
Neuroscience 1999, Zuerich)
King's College London
Institue of Psychiatry
Gavin S. Dawe (G.Dawe@iop.kcl.ac.uk)
Modelling interneuronal interactions between pairs of, and small populations
of, granule cells and interneurones to elucidate paired-pulse depression
phenomena in the dentate gyrus of the hippocampal formation following
stimulation of the lateral and medial perforant paths.
Montana State University
Center for Computational Biology
Sharon Crook <crook@nervana.montana.edu>
I am currently using GENESIS for modeling and simulations of cricket cercal
system interneurons. The cell models are biophysically-based with several
thousand compartments. I am also working on incorporating realistic
synaptic inputs and then plan to use the GENESIS simulations to do
parameter searches.
I am also writing a grant that will fund a much larger effort that will use
GENESIS to model this system. If I receive the grant, I anticipate funding a
grad student to develop a more sophisticated simulation environment. We will
design the environment to interact with Matlab routines for calculating
information theoretic measures based on stimulus/response data obtained from
the models. It's particularly important to us that the scripts use the cell
reader so that they'll be useful for modeling other systems in the future. We
are also interested in the fact that GENESIS is portable...Java will make that
even easier. Another factor in our choice of GENESIS is that we'll be able to
utilize the database of channel types, cell types, objects, etc. We are
interested in making our scripts and objects available to others later in the
project and hope to do that through your database.
We have several publications submitted but none in press yet.
National Centre for Biological Sciences, Bangalore, India
Upinder S. Bhalla (bhalla@ncbs.res.in)
http://www.ncbs.res.in/~faculty/upi.html
The computational work addresses many levels of neuronal computation, from the
molecular to the systems level. Each of these levels contributes to
information processing, and furthermore, they interact extensively. This has
major implications for understanding neuronal information processing, since
one cannot focus exclusively on one level of neuronal organization. For
example, cellular signaling pathways such as G-proteins and kinases are
intimately involved with synaptic changes, which in turn profoundly affect
neuronal and network behaviour. We study neuronal computation at all of these
levels utilizing the neuronal simulator GENESIS . We have been developing and
using a graphical user interface Kinetikit within GENESIS for designing,
editing, and keeping track of parameters for complex signaling pathways.
Single neuron modeling work has been done using the Neurokit interface.
Properties of interacting signaling pathways, and the behaviour of networks of
neurons in the olfactory system will be specific areas of research in the lab.
Selected publications:
Bhalla, U.S. and Iyengar, R. (1999) Emergent properties of networks of
biological signaling pathways, Science 283: 381-387.
Bhalla, U.S. (2000) Simulations of biochemical signaling. in: Computational
Neuroscience, Realistic modeling for experimentalists, Ed. E. De Schutter. CRC
Press.
Bhalla, U.S. (2000) The many faces of a biological switch. Computation in
Cells workshop, University of Hertfordshire, UK, April 2000
Bhalla, U.S. (2000) Temporal pattern decoding by synatpic signaling pathways.
CNS2000, Brugge, Belgium, July 2000
Bhalla, U.S., and Bower, J.M. (1993) Exploring parameter space in
detailed single neuron models: Simulations of the mitral and granule cells
of the olfactory bulb. J. Neurophysiol.69: 1948-1965
The Neurosciences Institute, San Diego, CA
Jeff Krichmar krichmar@nsi.edu
Neuroscientists are convinced that dendritic morphology plays an important
role in neural computation, but there are very few attempts to investigate
this role quantitatively. We are systematically studying the effect of the
geometry and topology of neurons on their electrical behavior by means of
computational simulations using the GENESIS simulator.
Washington, S. D., Ascoli, G.A. and Krichmar, J.L. (2000) "Statistical
Analysis of Dendritic Morphology's Effect on CA3 Pyramidal Cell
Electrophysiology.", Neurocomputing, In Press.
S. Nasuto, J. Krichmar, R. Scorcioni, G. Ascoli: Algorithmic analysis of
electrophysiological data for the investigation of structure-activity
relationship in single neurons. InterJournal Complex Syst. Submitted (2000).
Krichmar, J.L., Nasuto, S.J., Washington, S.D., Ascoli, G.A. "Effects of
Dendritic Morphology on CA3 Pyramidal Cell Physiology", In preparation.
Ohio University, Dept. of Biological Sciences
William R. Holmes (holmes@cneuro.zool.ohiou.edu)
Adam Weaver (aw288589@oak.cats.ohiou.edu)
The Holmes lab uses GENESIS to model dentate granule cells with detailed single
cell models. At some point we will go to network models but much of the
anatomy may still be included.
Aradi, I. and Holmes, W. R. (1999) Role of Multiple Calcium and
Calcium-Dependent Conductances in Regulation of Hippocampal Dentate Granule
Cell Excitability J. Comput. Neurosci. 6: 215-235.
Aradi, I. and Holmes, W. R. (1999) Active dendrites regulate spatio-temporal
synaptic integration in hippocampal dentate granule cells. Neurocomputing
26-27: 45-51.
Aradi, I. and Holmes, W.R. (1998) Classification of model interneurons of the
hippocampal dentate gyrus dur to their dendritic structure and spike frequency
adaptation. Soc. Neurosci. Abstr. 24: 1161
Adam Weaver has made single-compartment models of two neurons in the
crustacean Stomatogastric system (i.e., STG LP and STG PY). He has also
converted many STG Eutectic files into GENESIS format in order to make more
complex multi-compartment models.
Weaver, A.L., DiCaprio, R.A. and Hooper, S.L. (1996) Existing
stomatogastric neuron models predict some, but not all, responses to
rhythmic input, Soc. Neurosci. Abst. 22: 131.
Oregon State University
George J. Mpitsos (gmpitsos@Slugo.hmsc.orst.edu)
Neurocircuits are being constructed with GENESIS to resemble those in our
experimental animal, the carnivorous sea slug Pleurobranchaea californica,
to examine how networks change during the learning process, and how memory
is distributed in multifunctional networks, i.e., networks that are capable
of generating many different responses using the same network parameters.
Otago University Medical School, New Zealand
Jeff Wickens (anatjrw@otago.ac.nz)
Used GENESIS to study the character of burst firing in a simulated network
of striatal medium-sized spiny neurons. This is critically influenced by
the symmetry of radial inhibitory interactions and by the amount of
after-hyperpolarization accumulating in a dopamine-dependent way with
prolonged spiking activity.
Koetter, R., Alexander, M. E. and Wickens, J. R. (1995) Effects of asymmetric
neuronal connectivity and dopamine on striatal function: Simulation and
analysis of a model for Huntington's disease. In J. M. Bower (Ed.) The
Neurobiology of Computation. Kluwer Academic Publishers, Boston, 239-244.
Wickens J.R., Koetter R. and Alexander, M.E. (1995) Effects of local
connectivity on striatal function: Simulation and analysis of a model. Synapse
20: 281-298.
(Also see entry for Heinrich Heine University)
Otto-von-Guericke University
Faculty of Medicine
Dr. Robert Driesang <Robert.Driesang@Medizin.Uni-Magdeburg.DE>
Projection neurons in the basolateral amygdaloid complex are characterized by
their propensity to generate low-threshold oscillations of the membrane
potential. A 39-compartment model of projection neurons with 4 different
types of ionic conductances was used to understand this behavior. The model
indicates that low-threshold oscillations critically depend on the window
component of the fast Na and the M-type K current. The slow persistand Na
keeps the membrane depolarized and enables the cells to produce an alternating
sequence of action potentials and low-threshold oscillations.
Driesang , R.B., White, J.A. and Pape, H.-C. (1998)
A mathematical multicompartmental model of low-threshold oscillations in
amygdaloid projection neurons. Soc. Neurosci. Abstr. 24: 679
Oxford Brookes University
School of Computing & Mathematical Sciences
Nigel Crook (ntcrook@brookes.ac.uk)
Chris Dobbyn (C.Dobbyn@brookes.ac.uk)
The primary aim of our research is to develop accurate models of
biological neurons and neural circuits which support current
investigations in neuroscience. We are working closely with two
neuroscientists from Oxford Brookes: Dr Steve Ray and Dr Isabel
Bermudez. They are looking at learning and memory at both the network
and neuron level in invertebrates. Dr Ray has identified an
elementary form of learning (habituation) in the land snail Helix
aspersa. This seemed at frist to be an ideal subject for a computer
simulation because the neural circuits involved are relatively simple
and easy to identify, and the learning behavior is directly observable
(eye stalk withdrawal reflex). Dr Ray has collected all of the
necessary learning data and is currently in the process of identifying
the neural circuits involved. The sensory pathways have already been
identified, but it is taking longer to identify the effector pathways
because they are more complex than at first anticipated.
Research at the cellular level will involve modelling the behavior of
specialised receptors in the cell membrane. The Molecular Neuropharmacology
Group (BMS) lead by Dr Bermudez, are currently investigating insecticide
receptors in invertebrates and are interested in supporting this research with
computer modelling. We have already begun discussions with Dr Bermudez on the
possibility of future collaborative research.
Pennsylvania State University
Department of Neuroscience & Anatomy
Dr. Linda Larson-Prior (ljlp@brain.neuro.hmc.psu.edu)
GENESIS has been used to construct a 15 compartment model of a
cerebellar granule cell and will be used in the future study of a
network model based on multiple granule cells.
Seratonin has been shown to reduce potassium conductances found in
cerebellar granule cells. When these conductances are reduced in the
granule cell model, the response of the soma to hyperpolarizing and
depolarizing currents mirrors the serotenergic effects seen in whole cell
recordings under current clamp.
Lu, H. and Larsen-Prior, L.J. (1996) Effects of serotonin on cerebellar
granule cell electrical properties. Soc. Neurosci. Abst. 22:1627.
Lu, H., Prior, F.W. and Larson-Prior, L.J. (1995) Signal Transduction in a
cerebellar granule cell: a modeling approach. Soc. Neurosci. Abst. 21:916.
Lu, H., Prior, F. W. and Larson-Prior, L.J. (1997) Information processing in a
cerebellar granule cell. In J. M. Bower (Ed.), Computational Neuroscience,
Trends in Research, 1997. Plenum Press: New York, pp. 115-121.
Lu, H., Prior, F. W. and Larson-Prior, L.J. (1998) The role of feedforward and
feedbackinhibition on frequency-dependent information processing in a
cerebellar granule cell. In Computational Neuroscience: Trends in
Research 1998 (J. M. Bower, Ed.), Plenum Publishing Co., NY pp. 453-458.
Larsen-Prior, L.J. and Lu, H. (1999) Serotonergic modulation of the cerebellar
granule cell network. Neurocomputing 26-27: 419-426.
Purdue University
Samir Sayegh
Two models are being developed with GENESIS. The first one (Sayegh, et al.
1993), deals with facilitation and unblocking in a neuromuscular junction.
The second modeling project (Jaboori, et al. 1995) is developing the visual
pathway, making it as realistic as possible. GENESIS was used to construct a
16 layer network model, using cells derived from the GENESIS implementation of
the Traub et al. (1991) model cell, in order to model the mammalian central
visual pathway and its effects on hippocampal place cell activity. Hebbian
learning mechanisms have been added to this pathway, so as to demonstrate the
place-cell phenomenon.
Sayegh, S,, Manalis R., and Sampat P. (1993) "Facilitation and Unblocking: A
Quantitative Model" in Computation in Neurons and Neural Systems, F.
Eeckman, Ed., Kluwer Academic Publishers, pp. 235-240.
Jaboori, S. A., Sampat, P. and Sayegh, S. I. (1995), Analyzing the
hippocampal place-cell phenomenon by modeling the central visual
pathway. In J. M. Bower (Ed.) The Neurobiology of Computation.
Kluwer Academic Publishers, Boston, 233-237.
Rockefeller University
Pratik Mukherjee (mukherj@rockvax.rockefeller.edu)
Pratik Mukherjee has used both NEURON and GENESIS to model the temporal
response properties of LGN cells. His GENESIS results were presented in:
Mukherjee P., and Kaplan. R. (1992) State dependent modulation of the
temporal transfer properties of cat lateral geniculate nuerons. Soc.
Neurosci. Abstr. 18: 141.
Royal Institute of Technology
Department of Numerical Analysis and Computing Science
Erik Fransen <erikf@nada.kth.se>
I am using GENESIS in my research since about 2 years. I am working
on a model of entorhinal cortex. See also my web page:
http://www.nada.kth.se/~erikf
A post doc in our lab, Alexander Kozlov, has also started to use GENESIS.
Recently he started to test pGENESIS on an IBM SP system in our institute.
Fransen, E., Dickson, C., Magistretti, J., Alonso, A. and Hasselmo, M.
(1998) Modeling the Generation of Subthreshold Membrane Potential
Oscillations of Entorhinal Cortex Layer II. Soc. Neurosci. Abstr. 24: 2036.
Fransen, E., Alonso, A. and Hasselmo, M. (1999) Intrinsic Properties of Rat
Entorhinal Cells Relevant to Working Memory. Soc. Neurosci. (submitted
abstract)
Fransen, E., Wallenstein, G.V., Alonso, A.A., and Dickson, C.T. and Hasselmo,
M.E. (1999) A biophysical simulation of intrinsic and network properties of
entorhinal cortex. Neurocomputing 26-27: 375-380.
Swinburne University of Technology, Australia
David Liley (dliley@swin.edu.au)
GENESIS is being used on an 18 processor SGI Power Challenge for large scale
simulations of mammalian neocortex in an effort to identify stochastic
relationships between single neuron behaviour and LFP/ECoG/EEG. Conical
pyramidal and stellate neurons were simulated using the GENESIS simulation
package. Model neurons were leaky integrate-and-fire and consisted of from
four to nine passive compartments. Neurophysiological measurements, based on
single-cell recordings and patch-clamp experiments, provided estimations for
the simulation of cortical neurons: transmitter-activated conductances,
passive membrane time constants and axonal delays. Simulations of up to 6400
cortical neurons, approaching the scale of an individual cortical column,
confirmed previous findings with smaller networks. Limit-cycle behaviour
emerged in the network, in the frequency in the range of the mammalian alpha
and beta rhythms (8-20 Hz).
Liley, D.T., Alexander, D.M., Wright J.J. and Aldous M.D. (1999)
Alpha rhythm emerges from large-scale networks of realistically coupled
multicompartmental model cortical neurons. Network 10: 79-92.
Technical University of Darmstadt, Zoological Institute
Ward Tomlinson (tomlinson@bio1.bio.th-darmstadt.de)
I am using GENESIS to simulate the central auditory nervous system in
mammals and am interested in the processing of acoustic signals with
periodic structure (tonal sounds, vowel sounds) by neural circuits.
Tomlinson, R.W.W. and Langner, G. (1998) "Temporal processing in the auditory
system: The functional significance of neural noise" in "Proceedings of the
NATO Advanced Study Institute on Computational Hearing" pp.123-128
Preprint at: http://neuro.bio.tu-darmstadt.de/langner/ward/Asi98/tomlin2.htm
Technical University of Graz, Austria
Institute for Theoretical Computer Science
Wolfgang Maas
Berthold Ruf (bruf@igi.tu-graz.ac.at)
Thomas Natschlager (tnatschl@igi.tu-graz.ac.at)
http://www.cis.tu-graz.ac.at/igi/tnatschl/research.html
Our interest is to investigate the computational power of more
realistic models of neural networks (e. g., with spiking neurons) and
to compare them with traditional artificial neural networks and other
models of computation.
Here we demonstrate with the help of computer simulations using
GENESIS that biologically more realistic neurons can compute linear
functions in a natural and straightforward way based on the basic
principles of the construction given by Maass.
Maass, W. and Natschlager, T. (1997) Networks of spiking neurons can emulate
arbitrary Hopfield nets in temporal coding, Network: Computation in Neural
Systems, 8:355-372.
Maass, W. and Natschlager, T. (1998) Emulation of Hopfield networks with
spiking neurons in temporal encoding, in Computational Neuroscience: Trends in
Research 1998 (J. M. Bower, Ed.), Plenum Publishing Co., NY pp. 221-226.
Maass, W. and Natschlager, T. (1999) A model for fast analog computation based
on unreliable synapses. Neural Computation.
Ruf, B. (1996) Pattern recognition with networks of spiking neurons.
Workshop on Neural Networks Dynamics and Pattern Recognition, Toulouse.
Ruf, B. (1997) Computing functions with spiking neurons in temporal coding. In
J. Mira, R. Moreno-Diaz, and J. Cabestany, editors, Biological and artificial
computation: From neuroscience to technology. In Lecture Notes in Computer
Science, 240: 265-272. Springer, Berlin
Ruf, B. (1998) Networks of spiking neurons can compute linear functions using
action potential timing. In T. Lindblad, editor, Proc. of the VI-Dynn 98
conference.
United States Naval Academy
Ellen C Wooten
GENESIS was used to model the neural control of flight in a locust.
Wooten, E. C. (1992) "Modeling the Control of Flight Locomotion in a
Locust", Proceedings of the 23 Annual Pittsburg Conference on Modeling
and Simulation. May, 1992.
Universidade de Sao Paulo, Campus de Ribeirao Preto
Departamento de Fisica e Matematica
Dr. Antonio Carlos Roque da Silva <antonior@neuron.ffclrp.usp.br>
Marilene de Pinho <marilene@neuron.ffclrp.usp.br>
Marcelo B. Mazza <marcelo@neuron.ffclrp.usp.br>
Dr. Antonio Carlos Roque da Silva reports (6/99):
GENESIS is used by myself and four graduate and one undergraduate students
developing research under my supervision. At present I am using GENESIS to
construct large-scale models of some sensory systems, namely somatosensory,
auditory and visual systems. I am also starting a project in which GENESIS
will be used in the construction of a model of the dorsolateral
telencephalon of a weakly electric fish.
I teach a graduate course on Neural Networks at my department and the first
part of it is dedicated to Computational Neuroscience. During this part I
use GENESIS to make some demonstrations of the Hodgkin-Huxley model and the
compartmental modeling approach. I have been teaching this course regularly
every first semester of the year since 1995. At the moment, I am preparing
a new graduate course exclusively on Computational Neuroscience to be
offered from the year 2000 on in the Psychobiology Graduate Program of my
university and GENESIS will be more extensively used in it.
Mazza, M. B. and Roque da Silva, A. C. A computational model of topographic
reorganization in somatosensory cortex in response to digit lesions.
Neurocomputing 26-27: 435-441.
de Pinho, M. and Roque da Silva, A. C. (1999) A realistic computational model
of formation and variability of tonotopic maps in the auditory cortex.
Neurocomputing 26-27: 355-359.
Mazza, M. B., de Pinho, M. and Roque da Silva, A. C. (1999)
Biologically plausible models of topographic map formation in the somatosensory
and auditory cortices. Int. J. Neural Syst. 9:265-271.
Mazza, M. B. and Roque da Silva, A. C. A realistic computer simulation
of primary somatosensory cortex replicating static properties of
topographic organization. In: Braga, A. P. and Ludermir,
T. B. (Eds.). Proceedings of the V Brazilian Simposium on Neural
Networks, Belo Horizonte, MG. IEEE Computer Society, Los Alamitos, CA,
pp. 169-173, 1998.
de Pinho, M. and Roque da Silva, A. C. A computer simulation of the
formation of tonotopic maps in the primary auditory cortex. In: Braga,
A. P. (Ed.). Anais do V Simposio Brasileiro de Redes Neurais, Belo
Horizonte-MG. Sociedade Brasileira de Computacao/UFMG, pp. 213-216,
1998.
Mazza, M. B. and Roque da Silva, A. C. Realistic Computer Simulation
of Cortical Lesion Induced Imbalances in Properties of Somatotopic
Maps. Presented at the Eighth Computational Neuroscience Meeting
- CNS*99, Pittsburgh, PA, July 18-22, 1999.
de Pinho, M. and Roque da Silva, A. C. A Biologically Plausible
Computer Simulation of Classical Conditioning Induced Reorganization
of Tonotopic Maps in the Auditory Cortex. Presented at the
Eighth Computational Neuroscience Meeting - CNS*99, Pittsburgh, PA,
July 18-22, 1999.
University of Aachen
Dirk Kautz (kautz@tyto.bio2.rwth-aachen.de)
GENESIS is being used for simulating processes in the auditory system of barn
owls.
University of Alicante, Spain
Department of Physiology
Etelvina Andreu Sanchez (eandreu@juanvi.fisi.ua.es)
Three people are using GENESIS for Simulation of K-ATP channels and
the study of gap junction coupling.
University of Antwerp, Theoretical Neurobiology Unit
http://bbf-www.uia.ac.be/TNB_index.html
Erik De Schutter - PI (erik@bbf.uia.ac.be)
Reinoud Maex, MD - postdoc (reinoud@bbf.uia.ac.be)
Rogene M. Eichler West - postdoc (rogene@bbf.uia.ac.be)
Guy Bormann - PhD student - (guy@bbf.uia.ac.be)
Our present work is focused on modeling the mammalian cerebellum. We have
constructed active membrane compartmental models of the Purkinje cell (De
Schutter and Bower 1994a, De Schutter and Smolen 1997) and a network model
of the granular layer of cerebellar cortex (Maex et al. 1996).
The Purkinje cell model is used to investigate synaptic integration (De
Schutter and Bower 1994b). These simulations have suggested new theories on
the function of the Purkinje cell in the cerebellum. For example, we have
proposed that dendritic calcium channels amplify distal synaptic inputs more
than proximal ones, resulting in a somatic response independent of the
location of parallel fiber synaptic input (De Schutter and Bower 1994c).
Another model prediction is that the normal in vivo firing behavior of the
Purkinje cell requires a net inhibition of the dendrite (Jaeger et al.
1997), instead of a net excitation! We have also proposed that cerebellar
synaptic plasticity (long-term depression) is not involved in motor learning
at all (De Schutter 1995, De Schutter and Maex 1996).
Currently we are studying new versions of the Purkinje cell model that
include detailed representations of the regulation of the calcium
concentration, including buffered diffusion, electrogenic pumps, uptake and
release by calcium stores and IP3-evoked release (De Schutter 1996, De
Schutter and Smolen 1997). R. Eichler West uses evolutionary algorithms (R.
Eichler West et al. 1997) to explore the full parameter space of such
models, as good experimental data on a lot of the parameters needed is
lacking. We use these models to explore the effect of electrogenic channels
on Purkinje cell firing and the role of calcium release from stores
(calcium-evoked or by metabotropic receptor activation) during synaptic
integration (De Schutter and Smolen 1997).
R. Maex is building a large-scale realistic neural network model of the
cerebellar cortex. This anatomically detailed network model will be based on
active membrane models of the five main neuronal types of the cerebellar
cortex. This project is part of an international collaboration to further our
understanding of how the cerebellum works. In first instance, R. Maex has
created a large network model of the granular layer of the cerebellum, based
on simple single cell models. This work has led to the important prediction
that the feedback excitation of Golgi cells by the parallel fibers may lead to
synchronized firing of Golgi and granule cells (Maex et al. 1996, 1998). The
complete network model will be used in the future to explore how Purkinje
cells integrate realistic patterns of parallel fiber synaptic inputs and how
these responses are influenced by the inhibitory interneurons. Recently,
large cerebellar network models have been studied using PGENESIS on
128-processor Cray T3E (Howell et al., 2000).
Our main software development effort is towards GENESIS. E. De Schutter and
R. Eichler West contribute to the development of efficient numerical methods
in GENESIS ('hsolve' development). We have also developed a new library for
the simulation of buffered calcium diffusion and of calcium release from
stores (De Schutter and Smolen 1997). G. Bormann is developing new methods to
model 3D diffusion in GENESIS using a Monte Carlo method. Finally, we study
methods to parallelize large, morphologically realistic single cell models and
network models containing such cells.
Some representative publications involving GENESIS:
Howell F.W., Dyrhfjeld-Johnsen J., Maex R., Goddard N., and De Schutter E.
(2000) A large scale model of the cerebellar cortex using PGENESIS
Neurocomuting (in press).
De Schutter E., Vos B.P., Maex R. (2000) The function of cerebellar Golgi cells
revisited. Progress in Brain Research, De Zeeuw C.I., Ruigrok T.J.H. and N.M.
Gerrits N.M. editors, 124: 81-93.
Maex R., Vos B.P. and De Schutter E. (2000) Weak common parallel fibre
synapses explain the loose synchrony observed between rat cerebellar Golgi
cells. J. Physiol. (London) 523: 175-192.
Maex, R. and De Schutter, E. (1998) Synchronization of Golgi and granule cell
firing in a detailed network model of the cerebellar granule cell layer.
J. Neurophysiol. 80: 2521-2537.
De Schutter, E. (1999) Using realistic models to study synaptic integration
in cerebellar Purkinje cells. Reviews in the Neurosciences 10: 233-245.
De Schutter, E. (1998) Dendritic voltage and calcium-gated channels amplify
the variability of postsynaptic responses in a Purkinje cell model. J.
Neurophysiol. 80: 504-519
E. De Schutter: Cerebellar long-term depression might normalize
excitation of Purkinje cells: a hypothesis. Trends in Neurosciences
18: 291-295 (1995).
E. De Schutter and J.M. Bower: An active membrane model of the
cerebellar Purkinje cell. I. Simulation of current clamps in slice.
Journal of Neurophysiology 71: 375-400 (1994a).
E. De Schutter and J.M. Bower: An active membrane model of the
cerebellar Purkinje cell: II. Simulation of synaptic responses.
Journal of Neurophysiology 71: 401-419 (1994b).
E. De Schutter and J.M. Bower: Simulated responses of cerebellar
Purkinje cells are independent of the dendritic location of granule
cell synaptic inputs. Proceedings of the National Academy of Sciences
USA 91: 4736-4740 (1994).
D. Jaeger, E. De Schutter and J.M. Bower: The role of synaptic and
voltage-gated currents in the control of Purkinje cell spiking: a
modeling study. The Journal of Neuroscience 17:91-106 (1997)
C. Staub, E. De Schutter and T. Knopfel: Voltage-imaging and
simulation of effects of voltage and agonist activated conductances on
soma-dendritic voltage coupling in cerebellar Purkinje cells. Journal
of Computational Neuroscience 1: 301-311 (1994) .
E. De Schutter: A New Functional Role for Cerebellar Long Term
Depression. Progress in Brain Research, C.I. De Zeeuw, J. Voogd, P.
Strata editors, 114: 531-544 (1997).
De Schutter, E. and Smolen, P. (1998) Calcium dynamics in large neuronal
models. in Methods in neuronal modeling: from ions to networks, C. Koch
and I. Segev editors, MIT Press, Boston. 211-250.
E. De Schutter: Modelling the cerebellar Purkinje cell: experiments in
computo. Progress in Brain Research, J. van Pelt, M.A. Corner, H.B.M.
Uylings and F.H. Lopes da Silva editors, 102: 427-441 (1994).
University of Auckland, New Zealand
and Universitaet des Saarlandes, Germany
Achim Schneider (A_Schneider@cs.aukuni.ac.nz)
Achim Schneider, "Connectionist Simulation of Adaptive Processes in the
Flight Control System of Migratory Locusts" (CNS*93poster presentation)
Achim Schneider "Connectionist Simulation of Adaptive Processes in the
Flight Control System of Migratory Locusts" (full paper), Proceedings of
ANNIE'93, ASME Press, St. Louis, MO
GENESIS was used to build a connectionist simulation which aims at modeling
the flight control system and reproducing the adaptive processes with an
approach based upon Kohonen's self-organizing feature maps.
Abstract
The flight control system of migratory locusts is able to adapt its
steering behaviour to varying conditions in its motor system or in the
animals' immediate environment. A connectionist simulation model based
on a Kohonen network extended by multi-dimensional output signals was
employed to reproduce the adaptive control performances. For the
output signals of the network a trial and error learning procedure was
used. Several simulation experiments were carried out to show the
suitability of the method used.
University of California,Berkeley
Department of Molecular & Cell Biology
James Ingram <james_ucb@hotmail.com>
Yang Dan <yang@impulse.berkeley.edu>
Yang Dan's lab here at UCB is interested in computational, physiological
and developmental neurobiology of the mammalian visual system. We are
currently developing a large(-ish) scale model of cat primary visual
cortex. The inititial stage of the project, which is nearing completion, is
to duplicate an existing model of orientation tuning, developed by David
Somers (Somers et al., J.Neuroscience, 1995, 15(8): 5448-5465.). The
Somers' model, which was not GENESIS, focused on layer 4 of cortex only,
and we want to extend it to include other cortical layers. Ideally this
will lead to a better understanding of the circuitry of V1 and the
contribution of each layer to receptive field properties of simple and
complex cells in this cortical area.
Still very much a work in progress, but an abstract has been submitted for
1999 Society of Neuroscience Conference and a paper is in preparation.
University of California, Los Angeles
Valiriy Nenov (nenov@neurosurg.medsch.ucla.edu)
John Klopp (jklopp@ucla.edu)
Parallel GENESIS is being used to develop a model of the hippocampal
formation in order to define parameters necessary for memory encoding
that may also contribute to epileptogenesis. This five layer model
combines memory and epilepsy related data in an attempt to integrate
disparate levels of research, from neuro-anatomical connections and
synaptic physiology to the clinical EEG characteristics of human
complex partial epilepsy.
Klopp, J. and Nenov, V. (1997) Does epilitogenesis involve memory
mechanisms? In J. M. Bower (Ed.), Computational Neuroscience '96,
Plenum Publishing Co., NY (in press)
University of California, San Diego, Dept. of Cognitive Science
Randy Gobbel (gobbel@cogsci.ucsd.edu)
Present address: gobbel+@andrew.cmu.edu
GENESIS is being used to simulate dopaminergic and cholinergic
modulatory effects in the neostriatum. The model is now being
expanded beyond the neostriatum, in order to simulate loops through
the neostriatum, thalamus, and cortex, showing how these circuits
could mediate sequential actions, and showing how dopamine depletion
can produce parkinsionian symptoms.
Gobbel, J. R. (1996). Dopaminergic and cholinergic modulation in a
biophysical model of the neostriatum. In J. M. Bower (Ed.),
Computational Neuroscience: Trends in Research 1995 Academic Press,
NY, 185-190
Gobbel, J. R. (1995). Dopamine-acetylcholine interactions in a biophysical
model of the neostriatum. Neuroscience Abstracts, 21: 912.
Gobbel, J. R. (1995). A biophysically-based model of active short-term memory
in single neurons of the neostriatum. Poster presented at the second annual
meeting of the Cognitive Neuroscience Society, San Francisco, CA.
Gobbel, J. R. (1995). A biophysically-based model of the neostriatum as a
reconfigurable network. In M. Boden & L.-E. Niklasson (Eds.), Current Trends
in Connectionism: Proceedings of the Second Swedish Conference on
Connectionism, Skoevde, Sweden, March 1995. Hillsdale, NJ: Erlbaum.
Gobbel, J. R. (1996). A biophysical model of cortico-striato-thalamic loops
and action/motor control in the normal and Parkinsonian neostriatum.
Neurosci. Abstr. 22: 2208.
University of Chicago, Dept. of Organismal Biology and Anatomy
Jill M. Nicolaus (jmni@quads.uchicago.edu)
Jill M. Nicolaus and Philip S. Ulinski, "Hyperpolarizing Sag Currents in
Inhibitory Neurons in Turtle Visual Cortex" in: Computation in Neurons and
Neural Systems, F. Eeckman, Ed., Kluwer Academic Publishers, pp. 91-96.
Used GENESIS to model the inward "sag" current which is observed in
inhibitory neurons of turtle visual cortex. Data from intracellular current
clamp experiments gave estimated kinetic parameters which were sufficient to
completely specify the conductances needed to model the sag currents.
University of Colorado at Boulder
Robert Eaton <mauthner@spot.colorado.edu> (Professor)
Janet Casagrande <casagran@spot.colorado.edu> (postdoctoral student)
Graham I Cummins <graham.cummins@colorado.edu> (doctoral student)
We are working on the escape response in fish, which has led us to
computation in the Mauthner cell of the fish reticulo-spinal system. This
large cell appears to solve underwater sound localization problems using an
XNOR logic gate. I have modeled this gate using GENESIS (results in a
poster at Neuro-ethology in San Diego this Aug 23). The Muathner cell has a
unique K+ rectifier, many "stock" interesting channels including NMDA. In
addition to it's auditory processing it seems likely to do sensory
integration, memory on a limited scale, and complex self-inhibition. All
present interesting GENESIS problems. In the course of the work I've written
several new channels and objects for GENESIS.
J.L. Casagrand, G.I. Cummins, R.C. Eaton (1998) A computational analysis of
the Mauthner cell. 5th International Congress Satellite Symposium
International Congress of Neuroethology Electroreception and
Electrocommunication. San Diego August 28 - 30, 1998.
University of Connecticut Health Center
The Kim Auditory Neuroscience Laboratory
http://www3.uchc.edu/~kimdolab/
GENESIS is used to develop models of different neurons in the auditory system.
The GENESIS Neurokit environment is being used in a simulation of a bushy cell
of the cochlear nucleus.
Kim D.O. and D'Angelo, W.R. (2000). Computational model for the bushy
cell of the cochlear nucleus. Neurocomputing, in press.
University of Edinburgh
Centre for Cognitive Science
Bruce Graham (bruce@cns.ed.ac.uk)
GENESIS is being used to study action potential propagation along
inhomogeneous branching axons and synaptic integration in detailed
compartmental models of cortical pyramidal cells.
(See previous work at Australian National University)
University of Illinois
Mark Nelson (nelson@vernal.npa.uiuc.edu)
We are using GENESIS to model the response characteristics of primary afferent
nerve fibers in weakly electric fish.
Payne, J. R., Xu, Z. and Nelson M. E. (1993) "A Network Model of Automatic
Gain Control in the Electrosensory System" in Computation in Neurons and
Neural Systems, F. Eeckman, Ed., Kluwer Academic Publishers, pp. 203-208.
Xu, Z., Payne, J. R. and Nelson M. E. (1994) "System Identification and
Modeling of Primary Electrosensory Afferent Response Dynamics" in
Computation in Neurons and Neural Systems, F. Eeckman, Ed., Kluwer Academic
Publishers, pp. 197-202.
University of London
Thelma Williams (thelma@sghms.ac.uk)
I have been using genesis to model systems of coupled oscillators, with
reference to the pattern generator for locomotion in the spinal cord of the
lamprey.
University of Manitoba, Dept. of Physiology
Larry Jordan (larry@scrc.umanitoba.ca)
Gilles Detillieux (Gilles@scrc.UManitoba.CA)
Yue Dai (ydai@scrc.umanitoba.ca)
We use GENESIS to build three types of cat lumbar motoneurone model (S, FR,
FF) to study the changes of membrane properties observed during fictive
locomotion. The models are also expected to use in teaching in the future. The
following is a list of our papers (published or to be published) using
GENESIS.
Dai, Y., Jones, K.E., Fedirchuk, B., Krawitz, S., and Jordan, L.M. (1998a).
Modeling the lowering of motoneurone Voltage threshold during fictive
locomotion. In Neuronal Mechanisms for Generating Locomotor Activity.
Kiehn O., Harris-Warrick R.M., Jordan L.M., Hultborn H. and Kudo N (Eds),
pp 492-495. Annals of the New York Academy of Sciences, New York.
Dai, Y., Jones, K., Fedirchuk, B. and Jordan, L.M. (1998b) Computer
simulation: a study of excitability of the cat lumbar motoneurons during
fictive locomotion. Soc. Neurosci. Abstr. 24: 1077
Dai, Y., Jones, K.E., Fedirchuk, B., and Jordan, L.M. (2000a). Effects of
voltage trajectory on action potential voltage threshold in simulations of
cat spinal motoneurones. Neurocomputing, Vol. 23-33: pp. 105-111.
Dai, Y., Jones, K.E., Fedirchuk, B., McCrea, D.A., and Jordan, L.M. (2000b).
A modeling study of locomotion induced hyperpolarization of voltage threshold
in cat lumbar motoneurones. J Physiology (Lond), To be submitted in July,
2000.
University of Massachusetts at Amherst
Andrew Hill
Andrew Hill performed a developmental study using compartmental models of
an identified cricket neuron. The compartment models make it possible to
see how changes in the morphology of the neuron influence synaptic
integration.
Hill, A. (1993) The electrotonic structure of a cricket neuron is
preserved during neuronal growth. Soc. Neurosci. Abstr. Vol 19.
Hill, A. A. V., Edwards, D. H. and Murphey, R. K. (1994) "The effect of
neuronal growth on synaptic integration", J. Comp. Neurosci. 1:239-254.
University of Miami School of Medicine
Raymond L. Ownby, MD, PhD (rownby@ibm.net)
I use it for illustrations of single neuron computational modelling to
residents in Neurology and Psychiatry.
I'm using GENESIS for single neuron studies of the effects of chronic
ethanol on CA3 neurons and the possible relations of these effects to
neuropsychiatric disorders. I would like to pursue small network
studies in this same area. I'm also interested in applications of
single-neuron models in Alzheimer's disease, but have done nothing in
this area to date. GENESIS was used in studies described in the
following published abstracts:
Ownby RL, Mason BJ: Autorhythmicity in hippocampal CA3 neurons: effects
of chronic ethanol. Alcoholism: Clinical and Experimental Research
1996;20(Suppl):51A.
Ownby RL, Mason BJ: Effects of chronic ethanol treatment on hippocampal
CA3 neurons. Biological Psychiatry 1996;39:506.
University of Newcastle upon Tyne, Medical School
J. Mark Blanchard (J.M.Blanchard@newcastle.ac.uk}
I am using GENESIS to model the lobula giant movement detector (LGMD) of the
locust (O'Shea and Williams 1974). The LGMD responds selectively to objects
approaching the animal (Rind and Simmons 1992).
The model will be a large network rather than a single neurone. My aim is to
use computer-generated visual stimuli which will allow comparison between the
model and the biological system. To this end I will model the eye of the
locust and the neural circuitry behind the eye that synapses onto the LGMD
(Rowell et al. 1977).
University of Oregon
Institute of Neuroscience
Thomas Marston Morse <morse@chinook.uoregon.edu> reports (6/99):
There are three people at the University of Oregon that I know of
that are using GENESIS. For now we are looking at STG cells and
implementing models that have been implemented in other simulators. This
is just an academic (learning) project. I am working
with one graduate student and one student who has his BS and will be
applying to grad school next year. I am a research assoc (postdoc).
I hope to eventually use it in C. elegans modeling projects for
publication.
University of Pennsylvania
http://www.neuroengineering.upenn.edu
Leif Finkel
Howard Crystal (hcrystal@aecom.yu.edu) (Visiting from Albert Einstein College
of Medicine)
Shih-Cheng Yen (syen@ganymede.seas.upenn.edu)
Elliot Menschik (menschik@jupiter.seas.upenn.edu)
http://www.neuroengineering.upenn.edu/~menschik
Elliot Menschik reports:
One project (my thesis work in particular) relates to the construction of a
functional, realistic model of the hippocampus at the cellular level,
beginning with region CA3. The ultimate goal is to have a model detailed
enough to permit investigations into hippocampal disease such as Alzheimer's,
traumatic brain injury and epilepsy. While there is still much debate as to
the precise function of the hippocampus, most people agree that it is critical
for the processing of novel stimuli whether it be spatial, episodic or
declarative memory. To create a network with the most general memory
properties, I've started by implementing a Hopfield-type attractor network
using Traub's 66-compartment pyramidal cells and 51-compartment interneurons.
The second project (Shih-Cheng's thesis work) has been in development
for several years and deals with modeling aspects of visual perception
using the cortical properties of primary visual cortex. In particular
Shih-Cheng and Leif's most recent paper (submitted to Vision Research)
is a model for contour extraction based upon synchronous firing of
cortical neurons. The main goal now is to apply their model to detailed
cells. Again, we're using Traub's pyramidal cells and interneurons.
(GENESIS and parallel GENESIS were used on a four-processor SGI Origin. The
models used 66 compartment CA3 pyramidal cells and 51 compartment
interneurons, with up to 1032 cells.)
GENESIS is the core element of my research endeavors and I use it for
everything from small simulations of reduced neurons to large-scale network
simulations on multiple-processor servers. In addition, I direct several
smaller research projects for graduate and undergraduate students that also
involve modeling with GENESIS from the biochemistry of synaptic plasticity to
generating reduced model neurons from highly realistic models or physiological
recordings.
Finkel,L.H.,Yen,S-C. and Menschik ED (1998) Synchronization: The Computational
Currency of Cognition. ICANN 98, Proceedings of the 8th International
Conference on Artificial Neural Networks Skovde, Sweden, 2-4 September 1998.
Niklasson L, Boden M, Ziemke T (eds.). New York: Springer-Verlag, 1998.
Menschik, E. D. and Finkel, L. H. (1998) Neuromodulatory control of
hippocampal function: Towards a model of Alzheimer's disease. Artificial
Intelligence in Medicine 13:99-121.
Menschik, E. D. and Finkel, L. H. (1998) Neuromodulation of synaptic
plasticity in a reconstructed hippocampal CA3 pyramidal cell model. Soc.
Neurosci. Abstr. 24: 1911.
Menschik, E.D. and Finkel, L.H. (1999) Cholinergic neuromodulation and
Alzheimer's disease: from single cells to network simulations. Progress in
Brain Research, 121:19-45.
Menschik, E.D and Finkel, L.H. (in 2000) Cholinergic neuromodulation of an
anatomically reconstructed hippocampal CA3 pyramidal cell. Neurocomputing. in
press.
Menschik, E., Yen, S-C. and Finkel, L.H. (1998) Attractor Dynamics in
Realistic Hippocampal Networks. In Computational Neuroscience: Trends in
Research 1998 (J. M. Bower, Ed.), Plenum Publishing Co., NY pp. 465-470.
Menschik, E., Yen, S-C. and Finkel, L.H. (1999) Model- and scale-independent
performance of a hippocampal CA3 network architecture. Neurocomputing 26-27:
443-453.
Yen, S-C., Menschik, E., and Finkel, L.H. (1998) Cortical synchronization and
perceptual salience. In Computational Neuroscience: Trends in Research 1998
(J. M. Bower, Ed.), Plenum Publishing Co., NY pp. 125-130.
Yen, S-C., Menschik, E.D. and Finkel, L.H. (1999) Perceptual grouping in
striate cortical networks mediated by synchronization and desynchronization.
Neurocomputing, 26-27: 609-616.
University of Pittsburgh, Department of Neuroscience
Nathan Urban (urban@bns.pitt.edu)
(1) Development of a multicompartmental model of CA3 pyramidal cells
(hippocampus) that accounts for experimental data on synaptic
integration.
(2) Integration of a reduced version of the above model in order
to explain some oscillatory phenomena observed in area CA3.
University of Quebec at Chicoutimi
Jean Rouat (JRouat@UQAC.UQuebec.CA)
Ping Tang (ptang@uqac.uquebec.ca)
Modeling of the processing of time varying signals in the
auditory system: cochlear nucleus and colliculus.
Tang, P., Dutoit, P., Villa, A. and Rouat, J. (1997). "Effect of
the membrane time constant in a model of a chopper-S neuron of the
anteroventral cochlear nucleus : a neuroheuristic approach". Meeting
of the Association for Research in Otolaryngology, Feb. 97.
Tang, P., and Rouat, J. (1996) "Modeling neurons in the anteroventral cochlear
nucleus for amplitude modulation (AM) processing: Application to speech
sound" Proc. International Conference on Spoken Language Processing,
October 3-6, Philadelphia, USA.
Furthermore, the Master Thesis (in French) of Ping Tang has been based on
intensive simulations via GENESIS.
University of Rennes, France
and University of Texas Medical Branch, Galveston, Texas
Prof. Lee E. Moore (moore@univ-rennes1.fr)
C. Richard Murphey (rich@rice.edu)
GENESIS as well as Mathematica and their own simulator were used for the
simulations described in the following:
Buchanan, J., Moore, L. E., Wallen, P., Hill, R. and Grillner, S. (1992)
Synaptic transfer function of Mueller axon to spinal neuron in lamprey.
Biol. Cybern. 67:123-131.
Moore, L. E., Hill, R. H. and Grillner, S. (1993) Voltage clamp frequency
domain analysis of NMDA activated neurons. J. Exp. Biol. 175:59-87.
Moore, L. E. and Buchanan, J. (1993) The effects of neurotransmitters on the
integrative properties of spinal neurons of the lamprey. J. Exp. Biol.
175:89-113.
Moore, L. E., Buchanan, J. and Murphey, C.R. (1994) Anomalous increase in
membrane impedance of neurons during NMDA activation, in Computation in
Neurons and Neural Systems, F. Eeckman, Ed., Kluwer Academic Publishers, pp.
21-26.
Moore, L. E.; Davis, J.T.; Buchanan, J.; Murphy, R. (1992) Simulations of
neuronal behavior related to locomotion in the lamprey spinal cord. Jacques
Monod Conference: Locomotion from Neural Networks to Cognition, Aussois,
March 30-April 4.
Davis, J. and Moore, L. E. (1992) Neural Network Simulation of Locomotion in
Lamprey. Soc. Neurosci. Abstr. 18:316.
Murphey, C.R., Moore, L. E., and Buchanan, J.T. (1993) A model of a lamprey
neuron based on admittance spectroscopy. Neurosci. Soc. Abstr. 19.
Murphey, C.R. and Moore, L.E. (1992) Parameter estimation in a model of a
lamprey neuron. Tenth Annual Conference on Biomedical Engineering Research
in Houston.
Murphey, C.R., Buchanan, J. and Moore, L. E. (1992) Parameter Estimation
Methods of Lamprey Impedance Data. Neurosci. Soc. Abstr. 18:1278.
University of Southern California
Terrance Brannon (brannon@rana.usc.edu)
GENESIS is used for modelling of direction selectivity in the
somatosensory cortex by use of Hebbian synapses.
University of Texas at Dallas
http://www.utdallas.edu/~lcauller/labs/cauller.html
Larry Cauller - PI (lcauller@utdallas.edu)
Mark Jackson (mjackson@utdallas.edu)
James Patterson
Kush Paul
Three of my graduate students, Mark Jackson, James Patterson and Kush Paul are
using GENESIS as a central tool in their dissertations and have presented
their results at major meetings. In our neuroscience program at UTD, five of
us use Genesis at least weekly. I use Genesis to teach my Computational
Neuroscience course to about 10 graduate students. My grad students and I use
Genesis on our Sparc20 with quad 90mhz cpu which makes our most intensive
simulation of over 1000 interconnected simplified neuron models run about
1ms/sec realtime.
We are using the morphological and physiological results of the intracellular
studies to build realistic computational models of neocortical neurons for use
in large-scale simulations of cortico-cortical interactions (Jackson and
Cauller, 1993). The large-scale networks of model neurons simulating cortical
areas are interconnected with simulated projections based upon the patterns
determined in our Neuroanatomy Project. Simulations of local synaptic
interactions in small networks have demonstrated dynamical properties
characteristic of fractal complexity and chaos (Jackson, Patterson and
Cauller, 1995). These local circuit stimulations provide a novel method to
study neural chaos which is nearly impossible in living preparations that are
non-stationary (Paul and Cauller, 1995). Initial large-scale simulations of
cortico-cortical interactions using GENESIS have demonstrated that the
forward/backward patterns of reciprocal cortical connections serve to
distribute both bottom-up and top-down influences across the sensory
topography by reentrant synchronization of reverbatory activation. Current
studies in chronically implanted behaving rats are aimed at testing the
validity of the simulated model by cross-correlation and spike pattern
analysis of multiple neuron activities recorded simultaneously at several
sites in the auditory system (Mark Jackson, Doctoral project).
Jackson, M. and Cauller, L. (1993) Simplified Computational Models of
Neorcortical Neurons for use in Anatomically Realistic Network Simulations
of Interareal Cortical Oscillations , Soc. Neurosci. Abstr. Vol 19
Jackson, M.E. and Cauller, L.J., (1997) Evaluation of simplified
computational models of reconstructed neocortical neurons. Brain
Res, Bull. 44: 717.
Jackson, M. E. and Cauller, L.J. (1999) The function of reciprocal
corticocortical connections: Computational modeling and electrophysiological
studies. In: Oscillations in Neural Systems. D. S. Levine, V. R. Brown and T.
Shirey. New York, Lawrence Erlbaum.
Jackson, M.E., Patterson, J. and Cauller, L.J. (1996) Dynamical
analysis of spike trains in a simulation of reciprocally connected
"chaoscillators": Dependence of spike pattern fractal dimension on
strength of feedback connections. In J. M. Bower (Ed.), Computational
Neuroscience: Trends in Research 1995 Academic Press, NY, 209-214.
Paul, K., and Cauller, L.J. (1995) Using biologically realistic models
of neuronal networks to identify neural chaos. Soc. Neurosci. Abst. 21:146.
Patterson, J., Jackson, M.E., and Cauller, L.J. (1998) Analysis of coupled
chaoscillators embedded within thalmocortical and corticocortical reentrant
loops encompassing dyamics on multiple time scales. In Computational
Neuroscience: Trends in Research 1998 (J. M. Bower, Ed.), Plenum Publishing
Co., NY pp. 89-93.
Paul, K., Jackson, M., and Cauller, L.J (1998) Presence of a chaotic region
between subthreshold oscillations and rhythmic bursting in a simulation of
thalamocortical relay and reticular neurons. In Computational
Neuroscience: Trends in Research 1998 (J. M. Bower, Ed.), Plenum
Publishing Co., NY pp. 95-100.
University of Virginia, Health Sciences Center
William B Levy (wbl@galen.med.virginia.edu)
David A August (daa6s@virginia.edu)
Our laboratory uses biophysical modeling to complement
hippocampal physiology and anatomy studies in order to investigate
synaptic plasticity and neural information processing. Recently,
we have been using GENESIS (running on Silicon Graphics machines)
for several modeling projects, including:
(1) Injecting a randomly varying current waveform into a model soma, and then
reconstructing this signal from the resultant spike train. We previously used
another neural simulator (NEURON), but found GENESIS easier to use and better
documented. Further, the availability (through BABEL) of code for a variety
of spike generators enables us to extend this research area easily, once the
initial GENESIS program is complete.
(2) Attempting to match a neuron's electronic structure to its spike generator
to optimize information transmission. We found GENESIS well-suited for this
task -- several pre-compiled objects (e.g. "random" and "spike") saved us a
great deal of programming time. Note that since this study requires
coordinated activity patterns of all the synapses on a cell, it can currently
only be done through modeling.
August, D. A. and Levy, W. B. (1995) Information maintenance by retinal
ganglion cell spikes, in: Proceedings of the Third Annual Computation and
Neural Systems Meeting, J. M. Bower (Ed.), Kluwer Academic Publishers,
Boston, 41-46.
"A Neurally Plausible Method for Transmitting an Analog
Signal with Action Potentials", W B Levy and D August, in preparation.
University of Washington
Venkatesh Murthy (venk@salk.edu)
Murthy, V. N. and Fetz, E. E. (1993) "Effects of input synchrony
on the response of a model neuron", in Computation and Neural Systems,
475-479, F. H. Eeckman and J. M. Bower (eds.), Kluwer Academic Publishers
Murthy, V. N. and Fetz, E. E. (1994) "Effects of input synchrony
on the response of a three-conductance cortical neuron model", Neural
Computation 6:1111-1126.
Yale University, Department of Psychology
Tom Carew (Principal Investigator) (tcarew@yalevm.yale.edu)
Edward Kairiss (kairiss@yale.edu)
Diana Blazis (blazis@compuslug.psych.yale.edu)
Sean Murphy
GENESIS was used to explore interneuronal interactions in the siphon
withdrawal reflex of the marine mollusc Aplysia. In particular, the effects of
a recurrent inhibiotry circuit that has intrinsic plasticity -- namely,
use-dependent potentiation of inhibition that results in a diminished reflex
input to MNs responsible for the reflex. A number of features of the
recurrent inhibition are described in:
Blazis, Diana E.J., Fischer, Thomas M. and Carew, Thomas J., "A Neural
Network Model of Inhibitory Information Processing in Aplysia", Neural
Computation 5: 213 (1993).
D. E. J. Blazis, D. A. Berkowicz, E. W. Kairiss and T. J. Carew, "A network
model of inhibitory information processing in the siphon withdrawal reflex
of Aplysia", Soc. Neurosci. Abstr. 17: 1302 (1991)
Blazis, Diana E.J., Fischer, Thomas M. and Carew, Thomas J., Soc. Neurosci.
Abstr. 18 (1992). (Studies of the plasticity of this circuit)
Sean Murphy (now at U. Penn.) worked with Ed Kairiss studying spatio-temporal
autoassociative information processing in cortical association networks
(specifically, the prefrontal cortex). His parallel GENESIS simulations used
very large networks (on the order of 10,000 cells) spread out over a
heterogenous network of about 20 SGI's and SPARC/10's.
Murphy, S.D. and Kairiss, E.W. (1992) Simulations of adaptive interactions
between limbic and neocortical structures. Soc. Neurosci. Abst., 18:1211.
Murphy, S.D. and Kariss, E.W. (1997) Dynamical behavior of networks of active
neurons. In J. M. Bower (Ed.), Computational Neuroscience, Trends in
Research, 1997. Plenum Press: New York, pp. 423-428.
A biological neuron can be viewed as a match-filter that instantiates a
mapping, M, from spatiotemporal (synaptic) events to one- dimensional temporal
events (action potentials). An abstraction of a biological neuron called a
Spatio-Temporal Event Mapping (STEM) cell has been designed to perform this
mapping in a general way. We show that the STEM-cell is capable of learning M
for a biophysical model of a neuron, and that it offers advantages over a
biophysical model in terms of computational efficiency and analytical
tractability.
Murphy, S.D. and Kairiss, E.W.(1995) The stem cell: A computational model of
biological neurons useful for spatio-temporal pattern recognition, in
in The Neurobiology of Computation, (J. M. Bower, Ed.), Kluwer Academic
Press, Boston, MA, pp. 105-110.