Difference between revisions of "Fundamentals of Computational Neuroscience (2nd Edition): Programs"

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The second edition of ''Fundamentals of Computational Neuroscience'' is now available at [http://www.oup.com/us/catalog/general/subject/Medicine/Neuroscience/?view=usa&ci=9780199568413 Oxford University Press] and [http://www.amazon.ca/Fundamentals-Computational-Neuroscience-Thomas-Trappenberg/dp/0199568413/ref=sr_1_1?ie=UTF8&s=books&qid=1260376141&sr=8-1 Amazon.ca].
 
The second edition of ''Fundamentals of Computational Neuroscience'' is now available at [http://www.oup.com/us/catalog/general/subject/Medicine/Neuroscience/?view=usa&ci=9780199568413 Oxford University Press] and [http://www.amazon.ca/Fundamentals-Computational-Neuroscience-Thomas-Trappenberg/dp/0199568413/ref=sr_1_1?ie=UTF8&s=books&qid=1260376141&sr=8-1 Amazon.ca].
 +
== Zipfiles ==
 +
Zipfiles containing all programs from the book are available for [[Media:FCN-MATLAB.zip|MATLAB]], [[Media:FCN-SCILAB.zip|Scilab]], and [[Media:FCN-OCTAVE.zip|Octave]]. Alternatively, individual programs are available for download as below.
  
 
== Appendices ==
 
== Appendices ==
−
=== Programs ===
 
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:app_numinte.m|app_numinte.m]]||[[Media:app_numinte.sce|app_numinte.sce]]
+
|[[Media:app_numinte.m|app_numinte.m]]||[[Media:app_numinte.sce|app_numinte.sce]]||[[Media:Oct_Appendices.zip|Oct_Appendices.zip]]
 
|-
 
|-
 
|[[Media:creature_state.m|creature_state.m]]||[[Media:creature_state.sce|creature_state.sce]]
 
|[[Media:creature_state.m|creature_state.m]]||[[Media:creature_state.sce|creature_state.sce]]
Line 16: Line 17:
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
 
−
[[Media:MATLABfirst.pdf|MATLABfirst.pdf]]<br />
 
−
[[Media:MATLABfirstColor.pdf|MATLABfirstColor.pdf]]<br />
 
−
[[Media:MatlabDesktop.pdf|MatlabDesktop.pdf]]<br />
 
−
[[Media:MatlabDesktopColor.pdf|MatlabDesktopColor.pdf]]<br />
 
−
[[Media:MatlabFigure.pdf|MatlabFigure.pdf]]<br />
 
−
[[Media:MatlabFigureColor.pdf|MatlabFigureColor.pdf]]<br />
 
−
[[Media:Octave.pdf|Octave.pdf]]<br />
 
−
[[Media:SciLab.pdf|SciLab.pdf]]<br />
 
−
[[Media:Appendix_math1.pdf|appendix_math1.pdf]]<br />
 
−
[[Media:Appendix_math2.pdf|appendix_math2.pdf]]<br />
 
−
[[Media:Appendix_numinte.pdf|appendix_numinte.pdf]]<br />
 
−
[[Media:Appendix_numinte_color.pdf|appendix_numinte_color.pdf]]<br />
 
−
[[Media:Comm_channel.pdf|comm_channel.pdf]]<br />
 
−
[[Media:Dis_arbitrary.pdf|dis_arbitrary.pdf]]<br />
 
−
[[Media:Dis_binomial.pdf|dis_binomial.pdf]]<br />
 
−
[[Media:Dis_chisquare.pdf|dis_chisquare.pdf]]<br />
 
−
[[Media:Dis_exponential.pdf|dis_exponential.pdf]]<br />
 
−
[[Media:Dis_lognormal.pdf|dis_lognormal.pdf]]<br />
 
−
[[Media:Dis_poisson.pdf|dis_poisson.pdf]]<br />
 
−
[[Media:Dis_transformation.pdf|dis_transformation.pdf]]<br />
 
−
[[Media:Dis_uniform.pdf|dis_uniform.pdf]]<br />
 
−
[[Media:FigHisto.pdf|figHisto.pdf]]<br />
 
−
[[Media:Info_hand.pdf|info_hand.pdf]]<br />
 
−
[[Media:Info_hand2.pdf|info_hand2.pdf]]<br />
 
−
[[Media:Info_it1.pdf|info_it1.pdf]]<br />
 
−
[[Media:Info_spiketrain.pdf|info_spiketrain.pdf]]<br />
 
−
[[Media:Info_spiketrain2.pdf|info_spiketrain2.pdf]]<br />
 
−
[[Media:Info_surprise.pdf|info_surprise.pdf]]<br />
 
−
[[Media:Sparseness.pdf|sparseness.pdf]]<br />
 
−
 
−
== Chapter 1 ==
 
−
=== Figures ===
 
−
[[Media:AnticipatingBrain1.pdf|anticipatingBrain1.pdf]]<br />
 
−
[[Media:Deco2.pdf|deco2.pdf]]<br />
 
−
[[Media:Levels_of_org2.pdf|levels_of_org2.pdf]]<br />
 
−
[[Media:Model1.pdf|model1.pdf]]<br />
 
−
[[Media:Model2.pdf|model2.pdf]]<br />
 
  
 
== Chapter 2 ==
 
== Chapter 2 ==
−
=== Programs ===
 
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:EPSP.m|EPSP.m]]||[[Media:EPSP.sce|EPSP.sce]]
+
|[[Media:EPSP.m|EPSP.m]]||[[Media:EPSP.sce|EPSP.sce]]||[[Media:Oct_Chapter2.zip|Chapter2.zip]]
 
|-
 
|-
 
|[[Media:hh.m|hh.m]]||[[Media:hh.sce|hh.sce]]
 
|[[Media:hh.m|hh.m]]||[[Media:hh.sce|hh.sce]]
Line 69: Line 31:
 
|[[Media:wilson_euler.m|wilson_euler.m]]||[[Media:wilson_euler.sce|wilson_euler.sce]]
 
|[[Media:wilson_euler.m|wilson_euler.m]]||[[Media:wilson_euler.sce|wilson_euler.sce]]
 
|-
 
|-
−
|[[Media:wilson_ode.m|wilson_ode.m]]||[[Media:wilson_ode.sce|wilson_ode.sce]]
+
|[[Media:wilson_ode.m|wilson_ode.m]]
 
|-
 
|-
 
|[[Media:wilson.m|wilson.m]]||[[Media:wilson.sce|wilson.sce]]
 
|[[Media:wilson.m|wilson.m]]||[[Media:wilson.sce|wilson.sce]]
Line 75: Line 37:
 
|}
 
|}
  
−
=== Figures ===
+
== Chapter 3 ==
−
[[Media:Action_potential.pdf|action_potential.pdf]]<br />
 
−
[[Media:Circuit_hh.pdf|circuit_hh.pdf]]<br />
 
−
[[Media:Circuit_syn.pdf|circuit_syn.pdf]]<br />
 
−
[[Media:Compartment.pdf|compartment.pdf]]<br />
 
−
[[Media:Hh1.pdf|hh1.pdf]]<br />
 
−
[[Media:Hh2A.pdf|hh2A.pdf]]<br />
 
−
[[Media:Hh2B.pdf|hh2B.pdf]]<br />
 
−
[[Media:Hh_ion.pdf|hh_ion.pdf]]<br />
 
−
[[Media:Ion_channels.pdf|ion_channels.pdf]]<br />
 
−
[[Media:Matlab_hh.pdf|matlab_hh.pdf]]<br />
 
−
[[Media:Matlab_wilson.pdf|matlab_wilson.pdf]]<br />
 
−
[[Media:Neuron.pdf|neuron.pdf]]<br />
 
−
[[Media:Neuron_sim.pdf|neuron_sim.pdf]]<br />
 
−
[[Media:Neuron_sim2.pdf|neuron_sim2.pdf]]<br />
 
−
[[Media:Synapse1.pdf|synapse1.pdf]]<br />
 
−
[[Media:Synapse2.pdf|synapse2.pdf]]<br />
 
−
[[Media:Wilson.pdf|wilson.pdf]]<br />
 
  
−
== Chapter 3 ==
 
−
=== Programs ===
 
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:if_sim.m|if_sim.m]]||[[Media:if_sim.sce|if_sim.sce]]
+
|[[Media:if_sim.m|if_sim.m]]||[[Media:if_sim.sce|if_sim.sce]]||[[Media:Oct_Chapter3.zip|Oct_Chapter3.zip]]
 
|-
 
|-
 
|[[Media:poisson_spiketrain.m|poisson_spiketrain.m]]||[[Media:poisson_spiketrain.sce|poisson_spiketrain.sce]]
 
|[[Media:poisson_spiketrain.m|poisson_spiketrain.m]]||[[Media:poisson_spiketrain.sce|poisson_spiketrain.sce]]
Line 109: Line 52:
  
  
−
 
−
=== Figures ===
 
 
== Chapter 4 ==
 
== Chapter 4 ==
−
=== Programs ===
 
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:normal.m|normal.m]]||[[Media:normal.sce|normal.sce]]
+
|[[Media:normal.m|normal.m]]||||[[Media:Oct_Chapter4.zip|Oct_Chapter4.zip]]
 
|-
 
|-
 
|[[Media:oja.m|oja.m]]||[[Media:oja.sce|oja.sce]]
 
|[[Media:oja.m|oja.m]]||[[Media:oja.sce|oja.sce]]
Line 127: Line 67:
 
|}
 
|}
  
−
=== Figures ===
 
 
== Chapter 5 ==
 
== Chapter 5 ==
−
=== Programs ===
+
 
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:anninos.m|anninos.m]]||[[Media:anninos.sce|anninos.sce]]
+
|[[Media:anninos.m|anninos.m]]||[[Media:anninos.sce|anninos.sce]]||[[Media:Oct_Chapter5.zip|Oct_Chapter5.zip]]
 
|-
 
|-
 
|[[Media:IzhikevichRanNet.m|IzhikevichRanNet.m]]||[[Media:IzhikevichRanNet.sce|IzhikevichRanNet.sce]]
 
|[[Media:IzhikevichRanNet.m|IzhikevichRanNet.m]]||[[Media:IzhikevichRanNet.sce|IzhikevichRanNet.sce]]
Line 143: Line 82:
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
 
 
== Chapter 6 ==
 
== Chapter 6 ==
−
=== Programs ===
+
'''Important Note:''' After downloading '''pattern1.txt''' and/or '''pattern2.txt''', remove the ".txt" extension before running the program. In all zipfiles, this has already been done.
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:displayLetter.m|displayLetter.m]]||[[Media:displayLetter.sce|displayLetter.sce]]
+
|[[Media:displayLetter.m|displayLetter.m]]||[[Media:displayLetter.sce|displayLetter.sce]]||[[Media:Oct_Chapter6.zip|Oct_Chapter6.zip]]
 
|-
 
|-
 
|[[Media:mlp.m|mlp.m]]||[[Media:mlp.sce|mlp.sce]]
 
|[[Media:mlp.m|mlp.m]]||[[Media:mlp.sce|mlp.sce]]
Line 160: Line 98:
 
|[[Media:perceptronTrain.m|perceptronTrain.m]]||[[Media:perceptronTrain.sce|perceptronTrain.sce]]
 
|[[Media:perceptronTrain.m|perceptronTrain.m]]||[[Media:perceptronTrain.sce|perceptronTrain.sce]]
 
|-
 
|-
−
|[[Media:randomFlipMatrix.m|randomFlipMatrix.m]]||[[Media:randomFlipMatrix.sce|randomFlipMatrix.sce]]
+
|[[Media:randomFlipMatrix.m|randomFlipMatrix.m]]
 
|-
 
|-
 
|[[Media:svmOverlap.m|svmOverlap.m]]||[[Media:svmOverlap.sce|svmOverlap.sce]]
 
|[[Media:svmOverlap.m|svmOverlap.m]]||[[Media:svmOverlap.sce|svmOverlap.sce]]
 
|-
 
|-
 
|[[Media:svmXOR.m|svmXOR.m]]||[[Media:svmXOR.sce|svmXOR.sce]]
 
|[[Media:svmXOR.m|svmXOR.m]]||[[Media:svmXOR.sce|svmXOR.sce]]
 +
|-
 +
|[[Media:pattern1.txt|pattern1.txt]]||[[Media:pattern1.txt|pattern1.txt]]
 +
|-
 +
|[[Media:pattern2.txt|pattern2.txt]]||[[Media:pattern2.txt|pattern2.txt]]
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
+
 
 
== Chapter 7 ==
 
== Chapter 7 ==
−
=== Programs ===
+
 
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:dnf.m|dnf.m]]||[[Media:dnf.sce|dnf.sce]]
+
|[[Media:dnf.m|dnf.m]]||[[Media:dnf.sce|dnf.sce]]||[[Media:Oct_Chapter7.zip|Oct_Chapter7.zip]]
 
|-
 
|-
−
|[[Media:rnn_ode.m|rnn_ode.m]]||[[Media:rnn_ode.sce|rnn_ode.sce]]
+
|[[Media:rnn_ode.m|rnn_ode.m]]
 
|-
 
|-
 
|[[Media:som.m|som.m]]||[[Media:som.sce|som.sce]]
 
|[[Media:som.m|som.m]]||[[Media:som.sce|som.sce]]
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
+
 
 +
[http://web.cs.dal.ca/~tt/CSCI650809/noisySignal.mat noisySignal.mat]
 +
 
 
== Chapter 8 ==
 
== Chapter 8 ==
−
=== Programs ===
 
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (.zipfile)
 
|-
 
|-
−
|[[Media:ann_chaos.m|ann_chaos.m]]||[[Media:ann_chaos.sce|ann_chaos.sce]]
+
|[[Media:ann_chaos.m|ann_chaos.m]]||[[Media:ann_chaos.sce|ann_chaos.sce]]||[[Media:Oct_Chapter8.zip|Oct_Chapter8.zip]]
 
|-
 
|-
 
|[[Media:ann_cont.m|ann_cont.m]]||[[Media:ann_cont.sce|ann_cont.sce]]
 
|[[Media:ann_cont.m|ann_cont.m]]||[[Media:ann_cont.sce|ann_cont.sce]]
Line 200: Line 143:
 
|[[Media:ann_sparse.m|ann_sparse.m]]||[[Media:ann_sparse.sce|ann_sparse.sce]]
 
|[[Media:ann_sparse.m|ann_sparse.m]]||[[Media:ann_sparse.sce|ann_sparse.sce]]
 
|-
 
|-
−
|[[Media:lorenz_ode.m|lorenz_ode.m]]||[[Media:lorenz_ode.sce|lorenz_ode.sce]]
+
|[[Media:lorenz_ode.m|lorenz_ode.m]]
 
|-
 
|-
 
|[[Media:lorenz.m|lorenz.m]]||[[Media:lorenz.sce|lorenz.sce]]
 
|[[Media:lorenz.m|lorenz.m]]||[[Media:lorenz.sce|lorenz.sce]]
 
|-
 
|-
−
|[[Media:rnn_ode.m|rnn_ode.m]]||[[Media:rnn_ode.sce|rnn_ode.sce]]
+
|[[Media:rnn_ode.m|rnn_ode.m]]
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
+
 
 
== Chapter 9 ==
 
== Chapter 9 ==
−
=== Programs ===
+
 
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:experts.m|experts.m]]||[[Media:experts.sce|experts.sce]]
+
|[[Media:experts.m|experts.m]]||[[Media:experts.sce|experts.sce]]||[[Media:Oct_Chapter9.zip|Oct_Chapter9.zip]]
 
|-
 
|-
 
|[[Media:TDlearning.m|TDlearning.m]]||[[Media:TDlearning.sce|TDlearning.sce]]
 
|[[Media:TDlearning.m|TDlearning.m]]||[[Media:TDlearning.sce|TDlearning.sce]]
Line 223: Line 166:
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
 
 
== Chapter 10 ==
 
== Chapter 10 ==
−
=== Programs ===
+
'''Important Note:''' After downloading pattern1.txt, remove the ".txt" extension before running the program. In all zipfiles, this has already been done.
 
{|cellpadding="4"
 
{|cellpadding="4"
 
|-
 
|-
 
!scope="col"|MATLAB (.m)
 
!scope="col"|MATLAB (.m)
−
!scope="col"|SciLab (.sce)
+
!scope="col"|Scilab (.sce)
−
!scope="col"|Octave (.*)
+
!scope="col"|Octave (zipfile)
 
|-
 
|-
−
|[[Media:ART1.m|ART1.m]]||[[Media:ART1.sce|ART1.sce]]
+
|[[Media:ART1.m|ART1.m]]||[[Media:ART1.sce|ART1.sce]]||[[Media:Oct_Chapter10.zip|Oct_Chapter10.zip]]
 
|-
 
|-
 
|[[Media:ExpectationMaximization.m|ExpectationMaximization.m]]||[[Media:ExpectationMaximization.sce|ExpectationMaximization.sce]]
 
|[[Media:ExpectationMaximization.m|ExpectationMaximization.m]]||[[Media:ExpectationMaximization.sce|ExpectationMaximization.sce]]
 +
|-
 +
|[[Media:pattern1.txt|pattern1.txt]]||[[Media:pattern1.txt|pattern1.txt]]
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
+
 
 +
== MATLAB GUIs ==
 +
(Available for MATLAB only.) [[Media:MATLABGUIs.zip|MATLABGUIs.zip]]

Latest revision as of 18:42, 14 March 2013

The second edition of Fundamentals of Computational Neuroscience is now available at Oxford University Press and Amazon.ca.

Zipfiles

Zipfiles containing all programs from the book are available for MATLAB, Scilab, and Octave. Alternatively, individual programs are available for download as below.

Appendices

MATLAB (.m) Scilab (.sce) Octave (zipfile)
app_numinte.m app_numinte.sce Oct_Appendices.zip
creature_state.m creature_state.sce
main.m main.sce

Chapter 2

MATLAB (.m) Scilab (.sce) Octave (zipfile)
EPSP.m EPSP.sce Chapter2.zip
hh.m hh.sce
wilson_euler.m wilson_euler.sce
wilson_ode.m
wilson.m wilson.sce

Chapter 3

MATLAB (.m) Scilab (.sce) Octave (zipfile)
if_sim.m if_sim.sce Oct_Chapter3.zip
poisson_spiketrain.m poisson_spiketrain.sce


Chapter 4

MATLAB (.m) Scilab (.sce) Octave (zipfile)
normal.m Oct_Chapter4.zip
oja.m oja.sce
weightDistribution.m weightDistribution.sce

Chapter 5

MATLAB (.m) Scilab (.sce) Octave (zipfile)
anninos.m anninos.sce Oct_Chapter5.zip
IzhikevichRanNet.m IzhikevichRanNet.sce
PowerSpectrum.m PowerSpectrum.sce

Chapter 6

Important Note: After downloading pattern1.txt and/or pattern2.txt, remove the ".txt" extension before running the program. In all zipfiles, this has already been done.

MATLAB (.m) Scilab (.sce) Octave (zipfile)
displayLetter.m displayLetter.sce Oct_Chapter6.zip
mlp.m mlp.sce
perceptronTest.m perceptronTest.sce
perceptronTrain.m perceptronTrain.sce
randomFlipMatrix.m
svmOverlap.m svmOverlap.sce
svmXOR.m svmXOR.sce
pattern1.txt pattern1.txt
pattern2.txt pattern2.txt

Chapter 7

MATLAB (.m) Scilab (.sce) Octave (zipfile)
dnf.m dnf.sce Oct_Chapter7.zip
rnn_ode.m
som.m som.sce

noisySignal.mat

Chapter 8

MATLAB (.m) Scilab (.sce) Octave (.zipfile)
ann_chaos.m ann_chaos.sce Oct_Chapter8.zip
ann_cont.m ann_cont.sce
ann_fixpoint.m ann_fixpoint.sce
ann_sparse.m ann_sparse.sce
lorenz_ode.m
lorenz.m lorenz.sce
rnn_ode.m

Chapter 9

MATLAB (.m) Scilab (.sce) Octave (zipfile)
experts.m experts.sce Oct_Chapter9.zip
TDlearning.m TDlearning.sce
TDlearning2.m TDlearning2.sce

Chapter 10

Important Note: After downloading pattern1.txt, remove the ".txt" extension before running the program. In all zipfiles, this has already been done.

MATLAB (.m) Scilab (.sce) Octave (zipfile)
ART1.m ART1.sce Oct_Chapter10.zip
ExpectationMaximization.m ExpectationMaximization.sce
pattern1.txt pattern1.txt

MATLAB GUIs

(Available for MATLAB only.) MATLABGUIs.zip

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