Models that contain the Implementer : Lytton, William [bill.lytton at downstate.edu]

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    Models   Description
1.  Artificial neuron model (Izhikevich 2003, 2004, 2007)
A set of models is presented based on 2 related parameterizations to reproduce spiking and bursting behavior of multiple types of cortical neurons and thalamic neurons. These models combine the biologically plausibility of Hodgkin Huxley-type dynamics and the computational efficiency of integrate-and-fire neurons. Using these model, one can simulate tens of thousands of spiking cortical neurons in real time (1 ms resolution) using a desktop PC.
2.  Broadening of activity with flow across neural structures (Lytton et al. 2008)
"Synfire chains have long been suggested as a substrate for perception and information processing in the nervous system. However, embedding activation chains in a densely connected nervous matrix risks spread of signal that will obscure or obliterate the message. We used computer modeling and physiological measurements in rat hippocampus to assess this problem of activity broadening. We simulated a series of neural modules with feedforward propagation and random connectivity within each module and from one module to the next. ..."
3.  CA3 pyramidal cell: rhythmogenesis in a reduced Traub model (Pinsky, Rinzel 1994)
Fig. 2A and 3 are reproduced in this simulation of Pinsky PF, Rinzel J (1994).
4.  Computational Surgery (Lytton et al. 2011)
Figure 2 in Neocortical simulation for epilepsy surgery guidance: Localization and intervention, by William W. Lytton, Samuel A. Neymotin, Jason C. Wester, and Diego Contreras in Computational Surgery and Dual Training, Springer, 2011
5.  Computer model of clonazepam`s effect in thalamic slice (Lytton 1997)
Demonstration of the effect of a minor pharmacological synaptic change at the network level. Clonazepam, a benzodiazepine, enhances inhibition but is paradoxically useful for certain types of seizures. This simulation shows how inhibition of inhibitory cells (the RE cells) produces this counter-intuitive effect.
6.  Cortical network model of posttraumatic epileptogenesis (Bush et al 1999)
This simulation from Bush, Prince, and Miller 1999 shows the epileptiform response (Fig. 6C) to a brief single stimulation in a 500 cell network of multicompartment models, some of which have active dendrites. The results which I obtained under Redhat Linux is shown in result.gif. Original 1997 code from Paul Bush modified slightly by Bill Lytton to make it work with current version of NEURON (5.7.139). Thanks to Paul Bush and Ken Miller for making the code available.
7.  Electrostimulation to reduce synaptic scaling driven progression of Alzheimers (Rowan et al. 2014)
"... As cells die and synapses lose their drive, remaining cells suffer an initial decrease in activity. Neuronal homeostatic synaptic scaling then provides a feedback mechanism to restore activity. ... The scaling mechanism increases the firing rates of remaining cells in the network to compensate for decreases in network activity. However, this effect can itself become a pathology, ... Here, we present a mechanistic explanation of how directed brain stimulation might be expected to slow AD progression based on computational simulations in a 470-neuron biomimetic model of a neocortical column. ... "
8.  Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011)
"Coordination of neocortical oscillations has been hypothesized to underlie the "binding" essential to cognitive function. However, the mechanisms that generate neocortical oscillations in physiological frequency bands remain unknown. We hypothesized that interlaminar relations in neocortex would provide multiple intermediate loops that would play particular roles in generating oscillations, adding different dynamics to the network. We simulated networks from sensory neocortex using 9 columns of event-driven rule-based neurons wired according to anatomical data and driven with random white-noise synaptic inputs. ..."
9.  Excitatory and inhibitory interactions in populations of model neurons (Wilson and Cowan 1972)
Coupled nonlinear differential equations are derived for the dynamics of spatially localized populations containing both excitatory and inhibitory model neurons. Phase plane methods and numerical solutions are then used to investigate population responses to various types of stimuli. The results obtained show simple and multiple hysteresis phenomena and limit cycle activity. The latter is particularly interesting since the frequency of the limit cycle oscillation is found to be a monotonic function of stimulus intensity. Finally, it is proved that the existence of limit cycle dynamics in response to one class of stimuli implies the existence of multiple stable states and hysteresis in response to a different class of stimuli. The relation between these findings and a number of experiments is discussed.
10.  Feedforward heteroassociative network with HH dynamics (Lytton 1998)
Using the original McCulloch-Pitts notion of simple on and off spike coding in lieu of rate coding, an Anderson-Kohonen artificial neural network (ANN) associative memory model was ported to a neuronal network with Hodgkin-Huxley dynamics.
11.  Gamma oscillations in hippocampal interneuron networks (Wang, Buzsaki 1996)
The authors investigated the hypothesis that 20-80Hz neuronal (gamma) oscillations can emerge in sparsely connected network models of GABAergic fast-spiking interneurons. They explore model NN synchronization and compare their results to anatomical and electrophysiological data from hippocampal fast spiking interneurons.
12.  Hippocampus temporo-septal engram shift model (Lytton 1999)
Temporo-septal engram shift model of hippocampal memory. The model posits that memories gradually move along the hippocampus from a temporal encoding site to ever more septal sites from which they are recalled. We propose that the sense of time is encoded by the location of the engram along the temporo-septal axis.
13.  Hopfield and Brody model (Hopfield, Brody 2000) (NEURON+python)
Demonstration of Hopfield-Brody snychronization using artificial cells in NEURON+python.
14.  JitCon: Just in time connectivity for large spiking networks (Lytton et al. 2008)
This simulation is primarily an illustration and is not well optimized for actually running large networks. jitcon.mod contains a large amount of C level code, understanding of which requires some knowledge of Neuron internals
15.  Motor cortex microcircuit simulation based on brain activity mapping (Chadderdon et al. 2014)
"... We developed a computational model based primarily on a unified set of brain activity mapping studies of mouse M1. The simulation consisted of 775 spiking neurons of 10 cell types with detailed population-to-population connectivity. Static analysis of connectivity with graph-theoretic tools revealed that the corticostriatal population showed strong centrality, suggesting that would provide a network hub. ... By demonstrating the effectiveness of combined static and dynamic analysis, our results show how static brain maps can be related to the results of brain activity mapping."
16.  Neural Query System NQS Data-Mining From Within the NEURON Simulator (Lytton 2006)
NQS is a databasing program with a query command modeled loosely on the SQL select command. Please see the manual NQS.pdf for details of use. An NQS database must be populated with data to be used. This package includes MFP (model fingerprint) which provides an example of NQS use with the model provided in the modeldb folder (see readme for usage).
17.  NEURON interfaces to MySQL and the SPUD feature extraction algorithm (Neymotin et al. 2008)
See the readme.txt for information on setting up this interface to a MySQL server from the NEURON simulator. Note the SPUD feature extraction algorithm includes its own readme in the spud directory.
18.  Parallelizing large networks in NEURON (Lytton et al. 2016)
"Large multiscale neuronal network simulations and innovative neurotechnologies are required for development of these models requires development of new simulation technologies. We describe here the current use of the NEURON simulator with MPI (message passing interface) for simulation in the domain of moderately large networks on commonly available High Performance Computers (HPCs). We discuss the basic layout of such simulations, including the methods of simulation setup, the run-time spike passing paradigm and post-simulation data storage and data management approaches. We also compare three types of networks, ..."
19.  Prosthetic electrostimulation for information flow repair in a neocortical simulation (Kerr 2012)
This model is an extension of a model (<a href="http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=138379">138379</a>) recently published in Frontiers in Computational Neuroscience. This model consists of 4700 event-driven, rule-based neurons, wired according to anatomical data, and driven by both white-noise synaptic inputs and a sensory signal recorded from a rat thalamus. Its purpose is to explore the effects of cortical damage, along with the repair of this damage via a neuroprosthesis.
20.  Signal integration in LGN cells (Briska et al 2003)
Computer models were used to investigate passive properties of lateral geniculate nucleus thalamocortical cells and thalamic interneurons based on in vitro whole-cell study. Two neurons of each type were characterized physiologically and morphologically. Differences in the attenuation of propagated signals depend on both cell morphology and signal frequency. See the paper for details.
21.  Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010)
"... We sought to measure how the activity of the network alters information flow from inputs to output patterns. Information handling by the network reflected the degree of internal connectivity. ... With greater connectivity strength, the recurrent network translated activity and information due to contribution of activity from intrinsic network dynamics. ... At still higher internal synaptic strength, the network corrupted the external information, producing a state where little external information came through. The association of increased information retrieved from the network with increased gamma power supports the notion of gamma oscillations playing a role in information processing."
22.  Synaptic scaling balances learning in a spiking model of neocortex (Rowan & Neymotin 2013)
Learning in the brain requires complementary mechanisms: potentiation and activity-dependent homeostatic scaling. We introduce synaptic scaling to a biologically-realistic spiking model of neocortex which can learn changes in oscillatory rhythms using STDP, and show that scaling is necessary to balance both positive and negative changes in input from potentiation and atrophy. We discuss some of the issues that arise when considering synaptic scaling in such a model, and show that scaling regulates activity whilst allowing learning to remain unaltered.
23.  Thalamic quiescence of spike and wave seizures (Lytton et al 1997)
A phase plane analysis of a two cell interaction between a thalamocortical neuron (TC) and a thalamic reticularis neuron (RE).
24.  Thalamocortical augmenting response (Bazhenov et al 1998)
In the cortical model, augmenting responses were more powerful in the "input" layer compared with those in the "output" layer. Cortical stimulation of the network model produced augmenting responses in cortical neurons in distant cortical areas through corticothalamocortical loops and low-threshold intrathalamic augmentation. ... The predictions of the model were compared with in vivo recordings from neurons in cortical area 4 and thalamic ventrolateral nucleus of anesthetized cats. The known intrinsic properties of thalamic cells and thalamocortical interconnections can account for the basic properties of cortical augmenting responses. See reference for details. NEURON implementation note: cortical SU cells are getting slightly too little stimulation - reason unknown.
25.  The virtual slice setup (Lytton et al. 2008)
"In an effort to design a simulation environment that is more similar to that of neurophysiology, we introduce a virtual slice setup in the NEURON simulator. The virtual slice setup runs continuously and permits parameter changes, including changes to synaptic weights and time course and to intrinsic cell properties. The virtual slice setup permits shocks to be applied at chosen locations and activity to be sampled intra- or extracellularly from chosen locations. ..."
26.  Tonic-clonic transitions in a seizure simulation (Lytton and Omurtag 2007)
"... The authors have ... computationally manageable networks of moderate size consisting of 1,000 to 3,000 neurons with multiple intrinsic and synaptic properties. Experiments on these simulations demonstrated the presence of epileptiform behavior in the form of repetitive high-intensity population events (clonic behavior) or latch-up with near maximal activity (tonic behavior). ... Several simulations revealed the importance of random coincident inputs to shift a network from a low-activation to a high-activation epileptiform state. Finally, a simulated anticonvulsant acting on excitability tended to preferentially decrease tonic activity."

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