Date: Thu, 1 Jul 93 12:06:58 PDT From: bnews@smaug.cns.caltech.edu (Babel News Account) Subject: New simulations and cell models This is to announce a new babel subdirectory of cell models, the availability of three new simulations and a publication of interest to GENESIS users. The new directory "babel/cells" contains simulations and figures from the publication: 'Exploring parameter space in detailed single neuron models: simulations of the mitral and granule cells of the olfactory bulb' Upinder S. Bhalla and James M. Bower, Journal of Neurophysiology Vol 69 No. 6, June 1993 pp 1948-1965 We welcome contributions for this new directory! The babel/newsims directory contains two additional simulations: burster (used with Neurokit) This is a tutorial on bursting molluscan neurons and the effects of the various types of ionic channels which are commonly found. The cell which is modeled is a "generic burster", loosely modeled after the Aplysia R15 cell, although it contains channel models taken from measurements on bursting neurons in Tritonia as well as Aplysia. Further details of the tutorial and the channel models will be given in Chapter 5 of "The Book of GENESIS", to be published in Fall 1993. piriform This is a tutorial version of Matt Wilson's piriform cortex simulation. (Wilson, M. and Bower, J.M. 1992 Simulating cerebral cortical networks: oscillations and temporal interactions in a computer simulation of piriform (olfactory) cortex. J. Neurophysiol. 67: 981-995; Wilson, M. and Bower, J.M. 1989 The Simulation of Large-Scale Neural Networks, in Methods in Neuronal Modeling, edited by C. Koch and I. Segev, MIT Press.) Although most of the underlying code is the same as in the original simulation, it has been scaled down in size and given a graphical interface by Alex Protopapas. In it's current state, the simulation can be used to study the basis of EEG patterns found experimentally. These scripts are based on a fairly old (1988) simulation, so we expect to modernize them to use the cell reader and other new GENESIS features sometime soon. Further details of the contents of these directories are given in the associated README files. =========================================================================== Dear GENESIS users, We would like to maintain a summary of various GENESIS modeling projects on BABEL, so that those with similar interests can contact each other. This summary would also be useful to us when making reports and proposals to agencies which support GENESIS development. We have recently compiled the following partial list of GENESIS-related modeling projects and publications of which we are aware. Any mention of ongoing research has been made with permission of the researchers. We would very much appreciate hearing about each of your efforts with GENESIS, so that we may add to the summary. If you could contribute a few sentences summarizing what you (or others in your group) are currently doing or have done, it would be a big help. If you have written anything (published, accepted, or submitted), some references to this work would be very useful. Of course, we want to be sure that we have your permission before mentioning any work in progress. As we add information to this summary, the current version will be archived in the file "genesis.uses" in BABEL directory /usr/genesis/babel/news". Thanks for your help, Dave Beeman ======================================================================== GENESIS-related publications and modeling projects --------------------------------------------------------------------------- Caltech, Department of Biology A list of recent publications may be found in the file "caltech.pubs" in the "/usr/genesis/babel/news" directory on BABEL. The main categories of current modeling efforts are explorations of the effects of synaptic inputs to the large Purkinje cell model and study of cortical networks. The latter involves more detailed pyramidal cell modeling, ranging from very detailed models of a single cell (Protopapas) to simpler cells which incorporate plasticity (Vanier) and can be used in large networks. Dieter Jaeger and Erik De Schutter model Purkinje cell responses to synaptic input, focussing on replicating experimental findings showing that Purkinje cells respond to a granule cell input with a prolonged depolarization. Mike Vanier is working to extend the functionality of the piriform cortex model in GENESIS, in order to both make it more realistic and to investigate functional properties of the network as an associative memory. A pyramidal cell model is being constructed which incorporates hebbian synapses, facilitating synapses and synapses whose properties are gated by neuromodulators. This will be used as a component of the new piriform cortex model which will be used to investigate properties of learning and memory in a realistic biological network. Alex Protopapas is working on a detailed model of a superficial pyramidal cell from the piriform cortex, using a realistic morphology traced from an actual cell. The current version has 510 compartments with 13 different types of channels. In the future this will be extended to a 2100 compartment model. --------------------------------------------------------------------------- Yale University, Department of Psychology Diana Blazis (blazis@compuslug.psych.yale.edu) Edward Kairiss (kairiss@venus.ycc.yale.edu) GENESIS is used 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) --------------------------------------------------------------------------- Dept. of Psychology, Harvard University Prof. Michael Hasselmo hasselmo@katla.harvard.edu GENESIS simulations have been used in the papers listed below. In addition, GENESIS has been used considerably in in teaching, including demonstrations for classes on Psychobiology and on Psychopharmacology, supervision of a senior thesis project by Greg Horwitz, and supervision of two Program in Neuroscience graduate students from the medical school. Edi Barkai, Ross E. Bergman, Gregory Horwitz and Michael E. Hasselmo, "Modulation of neuronal adaptation and cortical associative memory function" (CNS*93) The experimentally observed properties of adaptation in pyramidal cells were simulated with voltage and calcium dependent potassium currents in a biophysical simulation of piriform cortex developed using the GENESIS simulation package. Bergman, R.E., Vanier, M., Horwitz, G., Bower, J.M. and Hasselmo, M.E. 1993 Cholinergic modulation of associative memory function in a realistic computational model of piriform cortex. Computation and Neural Systems 1992, Kluwer Press. (in press). (Harvard University in collaboration with Caltech) Barkai, E. and Hasselmo, M.E. Modulation of the repetitive firing properties of rat piriform cortex pyramidal cells: Brain slice physiology and biophysical simulation. J. Neurophysiol. (submitted) Barkai, E., Horwitz, G., Bergman, R.E. and Hasselmo, M.E. Modulation of associative memory function in a biophysical simulation of the rat piriform cortex. J. Neurophysiol. (submitted) Hasselmo, M.E Neuronal adaptation and cortical associative memory function (to be presented at World Conference on Neural Networks, July 1993) ------------------------------------------------------------------- C.N.R.S. - University of Rennes I, France, and University of Texas Medical Branch, Galveston, Texas: Prof. Lee E. Moore (moore@univ-rennes1.fr) and C. Richard Murphey (rich@rice.edu) have used GENESIS as well as Mathematica and their own simulator for the simulations described in the following: Buchanan, J., Moore, L. E., Wallen, P., Hill, R. and Grillner, S. Synaptic transfer function of Mueller axon to spinal neuron in lamprey. Biol. Cybern. 67:123-131, 1992. Moore, L. E., Hill, R. H. and Grillner, S. Voltage clamp frequency domain analysis of NMDA activated neurons. J. exp. Biol. 175:59-87, 1993. Moore, L. E. and Buchanan, J. The effects of neurotransmitters on the integrative properties of spinal neurons of the lamprey. J. exp. Biol. 175:89-113, 1993. Moore, L. E.; Davis, J.T.; Buchanan, J.; Murphy, R. 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, 1992. Davis, J. and Moore, L. E. Neural Network Simulation of Locomotion in Lamprey. Neurosci. Soc. Abstr. 140.2, 1992. Murphey, R., Buchanan, J. and Moore, L. E. Parameter Estimation Methods of Lamprey Impedance Data. Neurosci. Soc. Abstr. 539.3, 1992. Murphey, C.R. and Moore, L.E. Parameter estimation in a model of a lamprey neuron. Tenth Annual Conference on Biomedical Engineering Research in Houston, 1992. Moore, L. E., Buchanan, J.and Murphey, C.R. Interaction of NMDA and non-NMDA receptors on peripheral dendrites. Abstract at Second Annual Computation and Neural System Meeting CNS*93, July 31 - August 7, 1993, Washington D.C. Murphey, C.R., Moore, L. E., and Buchanan, J.T. A model of a lamprey neuron based on admittance spectroscopy. Neurosci. Soc. Abstr., 1993. ---------------------------------------------------------------------------- University of Chicago, Dept. 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" (CNS*93) 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 Illinois Mark Nelson (nelson@vernal.npa.uiuc.edu) A Network Model of Automatic Gain Control in the Electrosensory System. (Payne JR, Xu Z, Nelson ME, Beckman Institute, Univ. of Illinois) We are using GENESIS to construct a biologically-detailed model of the neural circuitry in the electrosensory lateral line lobe (ELL) of weakly electric fish. (CNS*93) Modeling of Primary Electrosensory Afferent Response Dynamics. (Xu Z, Payne JR, Nelson ME, Beckman Institute, Univ. of Illinois) We are using GENESIS to model the response characteristics of primary afferent nerve fibers in weakly electric fish. (CNS*93) ---------------------------------------------------------------------------- Purdue University Prof. Samir Sayegh (sayegh@CVAX.IPFW.INDIANA.EDU) Pulin Sampat (sampat@CVAX.IPFW.INDIANA.EDU) Two models are being developed with GENESIS. The first one, described in the paper listed below and another one to be published, deals with facilitation and unblocking in a neuromuscular junction. The second modeling project is developing the visual pathway, making it as realistic as possible. This is a massive simulation and incorporates modelling several cortices connecting the retina to the hippocampus. We are now in the process of adding learning mechanisms to this pathway so as to demonstrate the place-cell phenomena. We would appreciate hearing from others who are doing similar work. S. Sayegh, R. Manalis and P. Sampat "Facilitation and Unblocking: A Quantitative Model" (CNS*93) GENESIS was used to develop a realistic computational model of facilitation, presynaptic and postsynaptic unblocking at the neuromuscular junction. ---------------------------------------------------------------------------- ERIM, Ann Arbor Dale Fay and Susan Werness "Porting GENESIS from SUN to Silicon Graphics" (CNS*93) ---------------------------------------------------------------------------- Universitaet des Saarlandes, Germany Achim Schneider, "Connectionist Simulation of Adaptive Processes in the Flight Control System of Migratory Locusts" (CNS*93) 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. ---------------------------------------------------------------------------- Rockefeller University Pratik Mukherjee has used both NEURON and GENESIS to model the temporal response properties of LGN cells. His GENESIS results were presented in Soc. Neurosci. Abstr. 18: 141 (1992) ---------------------------------------------------------------------------- Australian National University Steve Redman group(genesis@eccles.anu.edu.au) Bruce P. Graham (bruce@cns.edinburgh.ac.uk) Bruce P. Graham and Stephen J. Redman, "Dynamic behaviour of a model of the muscle stretch reflex", Neural Networks (in press). All the work described in this paper is based on a model of muscle stretch reflex implemented using GENESIS. Allan Coop has used GENESIS as part of his work in modeling the peristaltic reflex: Allan Coop and S. J. Redman, "A model of the peristaltic reflex" in "Computation and Neural Systems 1992", Kluwer Academic Publishers (1993) (in press) ---------------------------------------------------------------------------- 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. ---------------------------------------------------------------------------- Mt. Sinai Medical Center, Department of pharmacology Upinder S. Bhalla is continuing modeling of the olfactory bulb which was begun at Caltech. The current model contains several hundred reasonably detailed neurons (up to 50 compartments). It runs in parallel on 3 nodes of the Intel Delta and corresponds to 12 glomeruli. He has also started simulations for modeling second messenger dynamics. ---------------------------------------------------------------------------- Brown University, Department of Psychology J. Michael Walker (jmw@poppy.psych.brown.edu) is using GENESIS to model basal ganglia circuitry, starting with substantia nigra dopamine (DA) neurons. ---------------------------------------------------------------------------- Max-Planck-Institut fuer Biologische Kybernetik Dirk Kautz (kautz@tyto.mpib-tuebingen.mpg.de) is using GENESIS for simulating processes in the auditory system of barn owls. ========================================================================== NOTE: "CNS*93" indicates papers which have been accepted for presentation and publication in the proceedings of "Computation and Neural Systems `93", Washington, DC, August 1-4, 1993. =========================================================================== From bnews@smaug.cns.caltech.edu Tue Jul 20 10:33:02 1993 Here are some more reports which we have received summarizing some of the things which BABEL members are doing with GENESIS. The full updated summary of these reports may be found in the file "genesis.uses" in the BABEL directory "/usr/genesis/babel/news". If you or others in your research group are currently using GENESIS, we would very much appreciate hearing from you with a few sentences describing what you are doing. We will ask for your approval of the wording of our summary before distributing it. Dave Beeman - dbeeman@dogstar.colorado.edu - babelnews@babel.cns.caltech.edu ----------------------------------------------------------------------------- Sean Murphy (murphy-sean@PSYCH.YALE.EDU) has been working with Ed Kairiss studying spatio-temporal autoassociative information processing in cortical association networks (specifically, the prefrontal cortex). His GENESIS simulations use 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. A preliminary account of this work was described in: Murphy, S.D. and Kairiss, E.W. Simulations of adaptive interactions between limbic and neocortical structures. Society for Neuroscience Abstracts, 1992,18:1211. ----------------------------------------------------------------------------- Brown University, Department of Cognitive and Linguistic Sciences Gary Strangman (strang@cog.brown.edu) reports: Barry Connors and I are using GENESIS (version 1.4) to develop a biologically based model of layer 5 of the neocortex. The ion channel kinetics are based on the equations found in the papers by McCormick and Hugenard (1992), which were ported to the Genesis platform by myself for the construction of this model. The model itself consists of 3 types of cells: bursting cells, regular spiking cells, and inhibitory (fast spiking) cells. Each cell is currently a single compartment, with different types and densities of ion channels being incorporated to give the cells their respective properties. Currently, arrays of 196 cells (50% regular, 25% bursting, 25% inhibitory) are being run on a DECStation 5000, with 1 sec of data requiring some 12 hours of computer time. Some questions to be addressed include: 1) Are the "intrinsic" properties of each type of cell necessary for the replication of network behaviors? That is, do (e.g.) bursting cells have to "burst" in order for the network to function properly? 2) What is the importance of inhibition in this type of model? 3) How sensitive is the model to the various parameters included? 4) How does different types of inter-neural connectivity affect the behavior of the model? -----------------------------------------------------------------------------