| | Models | Description |
| 1. |
Ca+/HCN channel-dependent persistent activity in multiscale model of neocortex (Neymotin et al 2016)
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"Neuronal persistent activity has been primarily assessed in terms of electrical mechanisms, without attention to the complex array of molecular events that also control cell excitability. We developed a multiscale neocortical model proceeding from the molecular to the network level to assess the contributions of calcium regulation of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in providing additional and complementary support of continuing activation in the network. ..." |
| 2. |
Computing with neural synchrony (Brette 2012)
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"... In a heterogeneous neural population, it appears that synchrony patterns represent structure or sensory invariants in stimuli, which can then be detected by postsynaptic neurons. The required neural circuitry can spontaneously emerge with spike-timing-dependent plasticity. Using examples in different sensory modalities, I show that this allows simple neural circuits to extract relevant information from realistic sensory stimuli, for example to identify a fluctuating odor in the presence of distractors. ..." |
| 3. |
Duration-tuned neurons from the inferior colliculus of the big brown bat (Aubie et al. 2009)
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dtnet is a generalized neural network simulator written in C++ with an easy to use XML description language to generate arbitrary neural networks and then run simulations covering many different parameter values. For example, you can specify ranges of parameter values for several different connection weights and then automatically run simulations over all possible parameters. Graphing ability is built in as long as the free, open-source, graphing application GLE (http://glx.sourceforge.net/) is installed.
Included in the examples folder are simulation descriptions that were used to generate the results in Aubie et al. (2009). Refer to the README file for instructions on compiling and running these examples.
The most recent source code can be obtained from GitHub: <a href="https://github.com/baubie/dtnet">https://github.com/baubie/dtnet</a>
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| 4. |
Norns - Neural Network Studio (Visser & Van Gils 2014)
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The Norns - Neural Network Studio is a software package for designing, simulation and analyzing networks of spiking neurons. It consists of three parts:
1. "Urd": a Matlab frontend with high-level functions for quickly defining networks
2. "Verdandi": an optimized C++ simulation environment which runs the simulation defined by Urd
3. "Skuld": an advanced Matlab graphical user interface (GUI) for visual inspection of simulated data. |
| 5. |
Roles of subthalamic nucleus and DBS in reinforcement conflict-based decision making (Frank 2006)
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Deep brain stimulation (DBS) of the subthalamic nucleus dramatically improves the motor symptoms of Parkinson's disease, but causes cognitive side effects such as impulsivity. This model from Frank (2006) simulates the role of the subthalamic nucleus (STN) within the basal ganglia circuitry in decision making. The STN dynamically modulates network decision thresholds in proportion to decision conflict. The STN ``hold your horses'' signal adaptively allows the system more time to settle on the best choice when multiple options are valid. The model also replicates effects in Parkinson's patients on and off DBS in experiments designed to test the model (Frank et al, 2007). |
| 6. |
Spiking neuron model of the basal ganglia (Humphries et al 2006)
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A spiking neuron model of the basal ganglia (BG) circuit (striatum, STN, GP, SNr). Includes: parallel anatomical channels; tonic dopamine; dopamine receptors in striatum, STN, and GP; burst-firing in STN; GABAa, AMPA, and NMDA currents; effects of synaptic location. Model demonstrates selection and switching of input signals. Replicates experimental data on changes in slow-wave (<1 Hz) and gamma-band oscillations within BG nuclei following lesions and pharmacological manipulations. |
