Wiki » History » Version 36
Vitor Chaud, 30 Apr 2014 14:57
1 | 1 | Padraig Gleeson | Introduction |
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2 | 7 | Padraig Gleeson | ------------ |
3 | 1 | Padraig Gleeson | |
4 | 25 | Vitor Chaud | This project deals with the re-implementation of Izhikevich’s spiking neuron model (See [here](http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=1257420)). Currently, this model is supported by NeuroML 2 and PyNN (Neuron and NEST backends). Simulation results are in general equal or similar to those shown in the original publication (see Fig. 1 of [Izhikevich 2004](http://www.izhikevich.org/publications/whichmod.htm)). However, few model features are difficult to reproduce due to particularities regarding model description and/or backend implementations, as further described below. |
5 | 1 | Padraig Gleeson | |
6 | 8 | Padraig Gleeson | ### Installation |
7 | 7 | Padraig Gleeson | |
8 | 22 | Vitor Chaud | 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: |
9 | 1 | Padraig Gleeson | |
10 | 22 | Vitor Chaud | > git clone https://github.com/OpenSourceBrain/IzhikevichModel.git |
11 | 22 | Vitor Chaud | |
12 | 30 | Vitor Chaud | In order to install PyNN see http://neuralensemble.org/trac/PyNN/wiki/Installation. Preferably, use the latest v0.8 version from [GitHub](https://github.com/NeuralEnsemble/PyNN). At the moment, the model is supported by Neuron and NEST backend simulators. |
13 | 30 | Vitor Chaud | |
14 | 31 | Vitor Chaud | To perform simulations using [NeuroML2](https://github.com/NeuroML/jNeuroML) and [LEMS](https://github.com/LEMS/jLEMS) you may install a pre-compiled package named jNeuroML as described [here](http://sourceforge.net/mailarchive/forum.php?thread_name=51C96757.8090601%40ucl.ac.uk&forum_name=neuroml-technology). |
15 | 31 | Vitor Chaud | |
16 | 8 | Padraig Gleeson | ### Versions of the project |
17 | 7 | Padraig Gleeson | |
18 | 7 | Padraig Gleeson | The original model in [MATLAB format](http://izhikevich.org/publications/figure1.m) has been converted to a number of other formats. |
19 | 7 | Padraig Gleeson | |
20 | 20 | Vitor Chaud | #### PyNN |
21 | 1 | Padraig Gleeson | |
22 | 30 | Vitor Chaud | ##### Simulating Fig. 1 protocol in PyNN |
23 | 1 | Padraig Gleeson | |
24 | 28 | Vitor Chaud | First, go to the PyNN subdirectory in your working directory: |
25 | 28 | Vitor Chaud | |
26 | 1 | Padraig Gleeson | > cd IzhikevichModel/PyNN/ |
27 | 20 | Vitor Chaud | |
28 | 29 | Vitor Chaud | Then, type the following command to run a simulation using Neuron: |
29 | 1 | Padraig Gleeson | |
30 | 1 | Padraig Gleeson | > python izhikevich2004.py neuron |
31 | 28 | Vitor Chaud | |
32 | 29 | Vitor Chaud | … or to run a simulation using NEST: |
33 | 28 | Vitor Chaud | |
34 | 28 | Vitor Chaud | > python izhikevich2004.py nest |
35 | 7 | Padraig Gleeson | |
36 | 36 | Vitor Chaud | The figure below shows the result obtained when running the current version of izhikevich2004.py with NEST. Note that subplots G, H, L and R are not in accordance with the original published results (see Comparison to original model behavior). |
37 | 35 | Vitor Chaud | |
38 | 35 | Vitor Chaud | ![](fig1_pyNN_nest.png) |
39 | 35 | Vitor Chaud | |
40 | 7 | Padraig Gleeson | #### NeuroML 2 |
41 | 1 | Padraig Gleeson | |
42 | 31 | Vitor Chaud | First, go to the NeuroML2 subdirectory in your working directory: |
43 | 1 | Padraig Gleeson | |
44 | 31 | Vitor Chaud | > cd IzhikevichModel/NeuroML2/ |
45 | 31 | Vitor Chaud | |
46 | 31 | Vitor Chaud | Then, type the following command to run a simulation using LEMS: |
47 | 31 | Vitor Chaud | |
48 | 31 | Vitor Chaud | > ../../jNeuroMLJar/jnml LEMS_WhichModel.xml |
49 | 31 | Vitor Chaud | |
50 | 1 | Padraig Gleeson | The XML for an Izhikevich model in NeuroML v2.0 is below: |
51 | 1 | Padraig Gleeson | |
52 | 1 | Padraig Gleeson | <code class="xml"> |
53 | 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> |
54 | 1 | Padraig Gleeson | |
55 | 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) |
56 | 8 | Padraig Gleeson | |
57 | 32 | Vitor Chaud | Comparison to original model behavior |
58 | 32 | Vitor Chaud | ------------------------------------- |
59 | 8 | Padraig Gleeson | |
60 | 8 | Padraig Gleeson | table{border:1px solid black}. |
61 | 26 | Vitor Chaud | {background:\#ddd}. |**Model**|**Label** | **NeuroML 2** |**pyNN.neuron**| **pyNN.nest**| |
62 | 26 | Vitor Chaud | |Tonic spiking | A |(a) | (a) | (a) | |
63 | 26 | Vitor Chaud | |Phasic spiking| B |(a) | (a) | (a) | |
64 | 26 | Vitor Chaud | |Tonic bursting| C |(b) | (b) | (b) | |
65 | 26 | Vitor Chaud | |Phasic bursting| D |(a) | (a) | (a) | |
66 | 26 | Vitor Chaud | |Mixed mode| E |(a) | (a) | (a) | |
67 | 26 | Vitor Chaud | |Spike freq. adapt.| F |(a) | (a) | (a) | |
68 | 26 | Vitor Chaud | |Class 1 excitable| G |(a, e)| (d, e) | (e) | |
69 | 26 | Vitor Chaud | |Class 2 excitable| H |©| (d) | (g) | |
70 | 26 | Vitor Chaud | |Spike latency | I |(b)| (b) | (b) | |
71 | 26 | Vitor Chaud | |Subthresh. osc.| J |(a)| (a) | (a) | |
72 | 26 | Vitor Chaud | |Resonator| K |(a)| (a) | (a) | |
73 | 26 | Vitor Chaud | |Integrator| L |(a, e)| (e) | (e) | |
74 | 26 | Vitor Chaud | |Rebound spike| M |(a)| (a) | (a) | |
75 | 26 | Vitor Chaud | |Rebound burst| N |(a)| (a) | (a) | |
76 | 26 | Vitor Chaud | |Threshold variability| O |(a)| (a) | (a) | |
77 | 26 | Vitor Chaud | |Bistability| P |(b)| (b) | (b) | |
78 | 26 | Vitor Chaud | |Depolarizing after-potential| Q |(b)| (b) | (b) | |
79 | 26 | Vitor Chaud | |Accomodation| R |(a, f)| (d)| (f)| |
80 | 26 | Vitor Chaud | |Inhibition-induced spiking| S |(b)| (b)| (b)| |
81 | 26 | Vitor Chaud | |Inhibition-induced bursting| T |(b) | (b)| (b)| |
82 | 16 | Vitor Chaud | |
83 | 26 | Vitor Chaud | (a) Same behavior |
84 | 26 | Vitor Chaud | (b) Similar behavior when slightly modifying parameters. See the table below. |
85 | 26 | Vitor Chaud | © Similar but not identical behavior (different number of spikes in the stimulus time frame) |
86 | 19 | Vitor Chaud | (d) Not yet implemented. Need ramp injected current. See https://github.com/NeuralEnsemble/PyNN/issues/257 |
87 | 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. |
88 | 1 | Padraig Gleeson | (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. |
89 | 1 | Padraig Gleeson | (g) Could not reproduce model behavior |
90 | 27 | Vitor Chaud | |
91 | 32 | Vitor Chaud | ### Parameter changes to adequate model behavior |
92 | 24 | Vitor Chaud | |
93 | 24 | Vitor Chaud | table{border:1px solid black}. |
94 | 24 | Vitor Chaud | {background:\#ddd}. |**Model**| **Label** | **Parameter**|**Original value**|**New value**| |
95 | 24 | Vitor Chaud | |Spike latency | I | Amplitude of pulse current | 7.04 | 6.71 | |
96 | 24 | Vitor Chaud | |Bistability | P | Initial time of 2nd pulse | 216 | 208 | |
97 | 24 | Vitor Chaud | |Depolarizing after-potential | Q | b | 0.2 | 0.18 | |
98 | 1 | Padraig Gleeson | |Inhibition-induced spiking | S | Inhibition ending | 250 | 220 | |
99 | 1 | Padraig Gleeson | |Inhibition-induced bursting | T | d | ~~2.0 |~~0.7 | |
100 | 32 | Vitor Chaud | |
101 | 32 | Vitor Chaud | Alternative implementations |
102 | 32 | Vitor Chaud | --------------------------- |
103 | 32 | Vitor Chaud | |
104 | 32 | Vitor Chaud | An alternative implementation of the Izhikevich model was created using [Moose](http://moose.sourceforge.net/). The code can be found [here](http://sourceforge.net/p/moose/code/4733/tree/moose/branches/buildQ/Demos/izhikevich/). There is a GUI in which the user chooses the model parameterization an visualizes the simulation results (see the figure below). |
105 | 33 | Vitor Chaud | |
106 | 34 | Vitor Chaud | ![](moose_gui.png) |