Wiki » History » Version 21
Vitor Chaud, 30 Apr 2014 14:57
| 1 | 1 | Padraig Gleeson | Introduction |
|---|---|---|---|
| 2 | 7 | Padraig Gleeson | ------------ |
| 3 | 1 | Padraig Gleeson | |
| 4 | 7 | Padraig Gleeson | This project will contain examples of the Izhikevich spiking neuron model. |
| 5 | 1 | Padraig Gleeson | |
| 6 | 8 | Padraig Gleeson | ### Installation |
| 7 | 7 | Padraig Gleeson | |
| 8 | 1 | Padraig Gleeson | To get local clone of this project… |
| 9 | 7 | Padraig Gleeson | |
| 10 | 8 | Padraig Gleeson | ### Versions of the project |
| 11 | 7 | Padraig Gleeson | |
| 12 | 7 | Padraig Gleeson | The original model in [MATLAB format](http://izhikevich.org/publications/figure1.m) has been converted to a number of other formats. |
| 13 | 7 | Padraig Gleeson | |
| 14 | 8 | Padraig Gleeson | #### PyNN |
| 15 | 1 | Padraig Gleeson | |
| 16 | 20 | Vitor Chaud | Install [PyNN](http://neuralensemble.org/trac/PyNN/wiki/Installation). Preferably, use the latest v0.8 version from [GitHub](https://github.com/NeuralEnsemble/PyNN). Note: NEURON is the only supported simulator for this model at the moment. |
| 17 | 1 | Padraig Gleeson | |
| 18 | 20 | Vitor Chaud | [Install Git](http://www.opensourcebrain.org/projects/gitintro/wiki/Wiki) and type: |
| 19 | 20 | Vitor Chaud | |
| 20 | 20 | Vitor Chaud | > git clone https://github.com/OpenSourceBrain/IzhikevichModel.git |
| 21 | 20 | Vitor Chaud | |
| 22 | 21 | Vitor Chaud | > cd IzhikevichModel/PyNN/ |
| 23 | 20 | Vitor Chaud | |
| 24 | 20 | Vitor Chaud | To run a simulation type: |
| 25 | 20 | Vitor Chaud | |
| 26 | 20 | Vitor Chaud | > python izhikevich2004.py neuron |
| 27 | 7 | Padraig Gleeson | |
| 28 | 8 | Padraig Gleeson | #### NeuroML 2 |
| 29 | 7 | Padraig Gleeson | |
| 30 | 7 | Padraig Gleeson | … |
| 31 | 7 | Padraig Gleeson | |
| 32 | 7 | Padraig Gleeson | The XML for an Izhikevich model in NeuroML v2.0 is below: |
| 33 | 7 | Padraig Gleeson | |
| 34 | 1 | Padraig Gleeson | <code class="xml"> |
| 35 | 1 | Padraig Gleeson | <izhikevichCell id="TonicSpiking" v0 = "-70mV" thresh = "30mV" a ="0.02" b = "0.2" c = "-65.0" d = "6" Iamp="0" Idel="0ms" Idur="2000ms"/></code> |
| 36 | 1 | Padraig Gleeson | |
| 37 | 1 | Padraig Gleeson | For full examples of single cells see [TonicSpiking](/projects/izhikevichmodel/repository/entry/neuroConstruct/cellMechanisms/TonicSpiking/TonicSpiking.nml) or [PhasicBursting](/projects/izhikevichmodel/repository/entry/neuroConstruct/cellMechanisms/PhasicBursting/PhasicBursting.nml) |
| 38 | 1 | Padraig Gleeson | |
| 39 | 1 | Padraig Gleeson | Tested with simulators: … |
| 40 | 8 | Padraig Gleeson | |
| 41 | 8 | Padraig Gleeson | ### Comparison to original model behaviour |
| 42 | 8 | Padraig Gleeson | |
| 43 | 8 | Padraig Gleeson | table{border:1px solid black}. |
| 44 | 15 | Vitor Chaud | {background:\#ddd}. |**Model**| **Label** | **PyNN** | **NeuroML** | |
| 45 | 15 | Vitor Chaud | |Tonic spiking | A |(a) | (a) | |
| 46 | 15 | Vitor Chaud | |Phasic spiking| B |(a) | (a) | |
| 47 | 15 | Vitor Chaud | |Tonic bursting| C |(b) | (b) | |
| 48 | 15 | Vitor Chaud | |Phasic bursting| D |(a) | (a) | |
| 49 | 15 | Vitor Chaud | |Mixed mode| E |(a) | (a) | |
| 50 | 15 | Vitor Chaud | |Spike freq. adapt.| F |(a) | (a) | |
| 51 | 15 | Vitor Chaud | |Class 1 excitable| G |(d, e)| (a, e) | |
| 52 | 15 | Vitor Chaud | |Class 2 excitable| H |(d)| © | |
| 53 | 15 | Vitor Chaud | |Spike latency | I |(b)| (b) | |
| 54 | 15 | Vitor Chaud | |Subthresh. osc.| J |(a)| (a) | |
| 55 | 15 | Vitor Chaud | |Resonator| K |(a)| (a) | |
| 56 | 15 | Vitor Chaud | |Integrator| L |(e)| (a, e) | |
| 57 | 15 | Vitor Chaud | |Rebound spike| M |(a)| (a) | |
| 58 | 15 | Vitor Chaud | |Rebound burst| N |(a)| (a) | |
| 59 | 15 | Vitor Chaud | |Threshold variability| O |(a)| (a) | |
| 60 | 15 | Vitor Chaud | |Bistability| P |(b)| (b) | |
| 61 | 15 | Vitor Chaud | |Depolarizing after-potential| Q |(b)| (b) | |
| 62 | 18 | Vitor Chaud | |Accomodation| R |(d)| (a, f)| |
| 63 | 15 | Vitor Chaud | |Inhibition-induced spiking| S |(a)| ©| |
| 64 | 17 | Vitor Chaud | |Inhibition-induced bursting| T |(b) | (b)| |
| 65 | 16 | Vitor Chaud | |
| 66 | 16 | Vitor Chaud | (a) Same behaviour |
| 67 | 16 | Vitor Chaud | (b) Similar behaviour when slightly modifying parameters |
| 68 | 16 | Vitor Chaud | © Similar but not identical behaviour (different number of spikes in the stimulus time frame) |
| 69 | 19 | Vitor Chaud | (d) Not yet implemented. Need ramp injected current. See https://github.com/NeuralEnsemble/PyNN/issues/257 |
| 70 | 18 | Vitor Chaud | (e) Requires an alternative model implementation since the model parameterization is different in the original Matlab code. In NeuroML new ComponentType [generalizedIzhikevichCell](https://github.com/OpenSourceBrain/IzhikevichModel/blob/master/NeuroML2/GeneralizedIzhikevichCell.xml) was created. |
| 71 | 18 | Vitor Chaud | (f) Requires an alternative model implementation since the model parameterization is different in the original Matlab code. In NeuroML new ComponentType [accomodationIzhikevichCell](https://github.com/OpenSourceBrain/IzhikevichModel/blob/master/NeuroML2/GeneralizedIzhikevichCell.xml) was created. |