| | Models | Description |
| 1. |
3D model of the olfactory bulb (Migliore et al. 2014)
|
|
|
This entry contains a link to a full HD version of movie 1 and the NEURON code of the paper:
"Distributed organization of a brain microcircuit analysed by three-dimensional modeling: the olfactory bulb" by M Migliore, F Cavarretta, ML Hines, and GM Shepherd. |
| 2. |
Cell splitting in neural networks extends strong scaling (Hines et al. 2008)
|
|
|
Neuron tree topology equations can be split into two subtrees and solved
on different processors with no change in accuracy, stability, or
computational effort; communication costs involve only sending and
receiving two double precision values by each subtree at each time step.
Application of the cell splitting method to two published
network models exhibits good runtime scaling on twice as many
processors as could be effectively used with whole-cell balancing.
|
| 3. |
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. |
| 4. |
Large scale model of the olfactory bulb (Yu et al., 2013)
|
|
|
The readme file currently contains links to the results for all the 72 odors investigated in the paper, and the movie showing the network activity during learning of odor k3-3 (an aliphatic ketone).
|
| 5. |
Model of arrhythmias in a cardiac cells network (Casaleggio et al. 2014)
|
|
|
" ... Here we explore the possible processes leading to the occasional onset and termination of the (usually) non-fatal arrhythmias widely observed in the heart.
Using a computational model of a two-dimensional network of cardiac cells, we tested the hypothesis that an ischemia alters the properties of the gap junctions inside the ischemic area.
...
In conclusion, our model strongly supports the hypothesis that non-fatal arrhythmias can develop from post-ischemic alteration of the electrical connectivity in a relatively small area of the cardiac cell network, and suggests experimentally testable predictions on their possible treatments." |
| 6. |
Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007)
|
|
|
This package provides a series of codes that simulate networks of spiking neurons (excitatory and inhibitory, integrate-and-fire or Hodgkin-Huxley type, current-based or conductance-based synapses; some of them are event-based). The same networks are implemented in different simulators (NEURON, GENESIS, NEST, NCS, CSIM, XPP, SPLIT, MVAspike; there is also a couple of implementations in SciLab and C++).
The codes included in this package are benchmark simulations; see
the associated review paper (Brette et al. 2007). The
main goal is to provide a series of benchmark simulations of
networks of spiking neurons, and demonstrate how these are implemented in the
different simulators overviewed in the paper. See also details in the
enclosed file Appendix2.pdf, which describes these different
benchmarks. Some of these benchmarks were based on the
Vogels-Abbott model (Vogels TP and Abbott LF 2005).
|
| 7. |
Olfactory bulb cluster formation (Migliore et al. 2010)
|
|
|
Functional roles of distributed synaptic clusters in the mitral-granule cell network of the olfactory bulb. |
| 8. |
Parallel network simulations with NEURON (Migliore et al 2006)
|
|
|
The NEURON simulation environment has been extended to support parallel network simulations.
The performance of three published network models with very different spike patterns exhibits superlinear speedup on Beowulf clusters.
|
| 9. |
Parallel odor processing by mitral and middle tufted cells in the OB (Cavarretta et al 2016, 2018)
|
|
|
"[...] experimental findings suggest that
MC and mTC may encode parallel and complementary odor representations. We
have analyzed the functional roles of these pathways by using a morphologically
and physiologically realistic three-dimensional model to explore the MC and
mTC microcircuits in the glomerular layer and deeper plexiform layers. [...]"
|
| 10. |
Spike exchange methods for a Blue Gene/P supercomputer (Hines et al., 2011)
|
|
|
Tests several spike exchange methods on a Blue Gene/P supercomputer on up to 64K cores. |
| 11. |
Translating network models to parallel hardware in NEURON (Hines and Carnevale 2008)
|
|
|
Shows how to move a working network model written in NEURON from a serial processor to a parallel machine in such a way that the final result will produce numerically identical results on either serial or parallel hardware. |
