Ave. neuron model for slow-wave sleep in cortex Tatsuki 2016 Yoshida 2018 Rasmussen 2017 (all et al)

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Accession:264519
Averaged neuron(AN) model is a conductance-based (Hodgkin-Huxley type) neuron model which includes a mean-field approximation of a population of neurons. You can simulate previous models (AN model: Tatsuki et al., 2016 and SAN model: Yoshida et al., 2018), and various models with 'X model' based on channel and parameter modules. Also, intracellular and extracellular ion concentration can be taken into consideration using the Nernst equation (See Ramussen et al., 2017).
References:
1 . Tatsuki F, Sunagawa GA, Shi S, Susaki EA, Yukinaga H, Perrin D, Sumiyama K, Ukai-Tadenuma M, Fujishima H, Ohno R, Tone D, Ode KL, Matsumoto K, Ueda HR (2016) Involvement of Ca(2+)-Dependent Hyperpolarization in Sleep Duration in Mammals. Neuron 90:70-85 [PubMed]
2 . Yoshida K, Shi S, Ukai-Tadenuma M, Fujishima H, Ohno RI, Ueda HR (2018) Leak potassium channels regulate sleep duration. Proc Natl Acad Sci U S A 115:E9459-E9468 [PubMed]
3 . Rasmussen R, Jensen MH, Heltberg ML (2017) Chaotic Dynamics Mediate Brain State Transitions, Driven by Changes in Extracellular Ion Concentrations. Cell Syst 5:591-603.e4 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Mouse; Neocortex;
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Neocortex layer 5 interneuron;
Channel(s): I Potassium; Ca pump; I A; I Calcium; I K,Ca; I K,leak; I Na,p; I Sodium; Kir; IK Bkca; IK Skca;
Gap Junctions:
Receptor(s): NMDA; AMPA; GabaA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: Python;
Model Concept(s): Sleep; Bifurcation; Activity Patterns; Action Potentials; Bursting; Calcium dynamics; Persistent activity; Brain Rhythms; Sleep-Wake transition;
Implementer(s): Tatsuki, Fumiya [tatsuki-tky at umin.ac.jp]; Yoshida, Kensuke [kensuyoshida-tky at umin.ac.jp]; Yamada, Tetsuya ; Katsumata, Takahiro [alextfkd at m.u-tokyo.ac.jp]; Shi, Shoi [sshoi0322-tky at umin.ac.jp] ; Ueda, R, Hiroki [hiroki.ueda at nifty.com];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; GabaA; AMPA; NMDA; I Na,p; I A; I K,leak; I K,Ca; I Sodium; I Calcium; I Potassium; Ca pump; Kir; IK Bkca; IK Skca; Gaba; Glutamate;
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averaged_neuron
anmodel
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README.md
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# Averaged Neuron (AN) model

## Overview
AN model is a conductance-based (Hodgkin-Huxley type) neuron model performed mean-field approximation of a population of neurons.

## Dependencies
The following packages need to be installed to use AN model:
- Python >= 3.5
- Numpy >= 1.10
- Scipy >= 1.0.0

## Usage
``` python
import matplotlib.pyplot as plt
import anmodel
an = anmodel.models.ANmodel()
an.set_sws_params()
s, _ = an.run_odeint()
plt.plot(s[4999:, 0])
```
![SWS firing (example)](images/sws_firing.png)

## References
- [Tatsuki et al., Neuron, 2016](https://www.cell.com/neuron/fulltext/S0896-6273(16)00169-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627316001690%3Fshowall%3Dtrue)
- [Rasmussen et al., Cell Systems, 2017](https://www.sciencedirect.com/science/article/pii/S2405471217305392)
- [Yoshida et al., PNAS, 2018](https://www.pnas.org/content/115/40/E9459.short)

## Authors
- Fumiya Tatsuki
- Kensuke Yoshida
- Tetsuya Yamada
- Takahiro Katsumata
- Shoi Shi
- Hiroki R. Ueda

## License
This project is licensed under the MIT License - see the [LICENSE.txt](LICENSE.txt) file for details.

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