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Vitor Chaud, 30 Apr 2014 14:57

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Introduction
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This project contains examples of the Izhikevich spiking neuron model. Most of the behaviours seem in Fig. 1 of [Izhikevich 2004](http://www.izhikevich.org/publications/whichmod.htm) are reproduced in PyNN and NeuroML 2 implementations.





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### Installation





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To get local clone of this project [Install Git](http://www.opensourcebrain.org/projects/gitintro/wiki/Wiki), go to the directory in which the project will be cloned and type:





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    > git clone https://github.com/OpenSourceBrain/IzhikevichModel.git





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### Versions of the project





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The original model in [MATLAB format](http://izhikevich.org/publications/figure1.m) has been converted to a number of other formats.





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#### PyNN





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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.





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    > cd IzhikevichModel/PyNN/





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To run a simulation type:





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    > python izhikevich2004.py neuron





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#### NeuroML 2





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…





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The XML for an Izhikevich model in NeuroML v2.0 is below:





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    <code class="xml">





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    <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>





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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)





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Tested with simulators: …





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### Comparison to original model behaviour





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table{border:1px solid black}.





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{background:\#ddd}. |**Model**|&nbsp;&nbsp;&nbsp;&nbsp; **Label** &nbsp;&nbsp;&nbsp;&nbsp; |&nbsp;&nbsp;&nbsp;&nbsp; **PyNN** &nbsp;&nbsp;&nbsp;&nbsp; | &nbsp;&nbsp;&nbsp;&nbsp; **NeuroML** &nbsp;&nbsp;&nbsp;&nbsp; |





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|Tonic spiking | &nbsp;&nbsp;&nbsp;A |(a) | &nbsp;&nbsp;&nbsp;(a) |





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|Phasic spiking| &nbsp;&nbsp;&nbsp;B |(a) | &nbsp;&nbsp;&nbsp;(a) |





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|Tonic bursting| &nbsp;&nbsp;&nbsp;C |(b) | &nbsp;&nbsp;&nbsp;(b) |





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|Phasic bursting| &nbsp;&nbsp;&nbsp;D |(a) | &nbsp;&nbsp;&nbsp;(a) |





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|Mixed mode| &nbsp;&nbsp;&nbsp;E |(a) | &nbsp;&nbsp;&nbsp;(a) |





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|Spike freq. adapt.| &nbsp;&nbsp;&nbsp;F |(a) | &nbsp;&nbsp;&nbsp;(a) |





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|Class 1 excitable| &nbsp;&nbsp;&nbsp;G |(d, e)| &nbsp;&nbsp;&nbsp;(a, e) |





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|Class 2 excitable| &nbsp;&nbsp;&nbsp;H |(d)| &nbsp;&nbsp;&nbsp;© |





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|Spike latency | &nbsp;&nbsp;&nbsp;I |(b)| &nbsp;&nbsp;&nbsp;(b) |





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|Subthresh. osc.| &nbsp;&nbsp;&nbsp;J |(a)| &nbsp;&nbsp;&nbsp;(a) |





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|Resonator| &nbsp;&nbsp;&nbsp;K |(a)| &nbsp;&nbsp;&nbsp;(a) |





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|Integrator| &nbsp;&nbsp;&nbsp;L |(e)| &nbsp;&nbsp;&nbsp;(a, e) |





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|Rebound spike| &nbsp;&nbsp;&nbsp;M |(a)| &nbsp;&nbsp;&nbsp;(a) |





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|Rebound burst| &nbsp;&nbsp;&nbsp;N |(a)| &nbsp;&nbsp;&nbsp;(a) |





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|Threshold variability| &nbsp;&nbsp;&nbsp;O |(a)| &nbsp;&nbsp;&nbsp;(a) |





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|Bistability| &nbsp;&nbsp;&nbsp;P |(b)| &nbsp;&nbsp;&nbsp;(b) |





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|Depolarizing after-potential| &nbsp;&nbsp;&nbsp;Q |(b)| &nbsp;&nbsp;&nbsp;(b) |





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|Accomodation| &nbsp;&nbsp;&nbsp;R |(d)| &nbsp;&nbsp;&nbsp;(a, f)|





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|Inhibition-induced spiking| &nbsp;&nbsp;&nbsp;S |(a)| &nbsp;&nbsp;&nbsp;©|





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|Inhibition-induced bursting| &nbsp;&nbsp;&nbsp;T |(b) | &nbsp;&nbsp;&nbsp;(b)|





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(a) Same behaviour





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(b) Similar behaviour when slightly modifying parameters





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© Similar but not identical behaviour (different number of spikes in the stimulus time frame)





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(d) Not yet implemented. Need ramp injected current. See https://github.com/NeuralEnsemble/PyNN/issues/257





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(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.





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(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.