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 108: Line 51:
 
|}
 
|}
  
−
 
−
 
−
=== Figures ===
 
−
[[Media:Adrian.pdf|adrian.pdf]]<br />
 
−
[[Media:Alpha1.pdf|alpha1.pdf]]<br />
 
−
[[Media:Alpha2.pdf|alpha2.pdf]]<br />
 
−
[[Media:Alpha2.pdf|alpha2.pdf]]<br />
 
−
[[Media:Buracas.pdf|buracas.pdf]]<br />
 
−
[[Media:Decharms_merzenich.pdf|decharms_merzenich.pdf]]<br />
 
−
[[Media:Epsilon1.pdf|epsilon1.pdf]]<br />
 
−
[[Media:Epsilon2.pdf|epsilon2.pdf]]<br />
 
−
[[Media:Epsilon3.pdf|epsilon3.pdf]]<br />
 
−
[[Media:If_fast.pdf|if_fast.pdf]]<br />
 
−
[[Media:If_gauss.pdf|if_gauss.pdf]]<br />
 
−
[[Media:If_isi.pdf|if_isi.pdf]]<br />
 
−
[[Media:If_node.pdf|if_node.pdf]]<br />
 
−
[[Media:If_poisson.pdf|if_poisson.pdf]]<br />
 
−
[[Media:Inte_coincidence.pdf|inte_coincidence.pdf]]<br />
 
−
[[Media:Isi_hist.pdf|isi_hist.pdf]]<br />
 
−
[[Media:Izhikevich_neuron.pdf|izhikevich_neuron.pdf]]<br />
 
−
[[Media:Leaky_if.pdf|leaky_if.pdf]]<br />
 
−
[[Media:Mean_firing_if.pdf|mean_firing_if.pdf]]<br />
 
−
[[Media:Modulation.pdf|modulation.pdf]]<br />
 
−
[[Media:Noise_models.pdf|noise_models.pdf]]<br />
 
−
[[Media:Phys_gain.pdf|phys_gain.pdf]]<br />
 
−
[[Media:Rate_population.pdf|rate_population.pdf]]<br />
 
−
[[Media:Rate_temporal.pdf|rate_temporal.pdf]]<br />
 
−
[[Media:Table_transf.pdf|table_transf.pdf]]<br />
 
−
[[Media:Tuning.pdf|tuning.pdf]]<br />
 
  
 
== 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 154: Line 67:
 
|}
 
|}
  
−
=== Figures ===
+
== Chapter 5 ==
−
[[Media:Asso2.pdf|asso2.pdf]]<br />
 
−
[[Media:Associative_learning.pdf|associative_learning.pdf]]<br />
 
−
[[Media:Associative_net.pdf|associative_net.pdf]]<br />
 
−
[[Media:Associative_node.pdf|associative_node.pdf]]<br />
 
−
[[Media:Calcium.pdf|calcium.pdf]]<br />
 
−
[[Media:F_prepost.pdf|f_prepost.pdf]]<br />
 
−
[[Media:F_prepost2.pdf|f_prepost2.pdf]]<br />
 
−
[[Media:Hebb1_distribution.pdf|hebb1_distribution.pdf]]<br />
 
−
[[Media:Hebb_stdp.pdf|hebb_stdp.pdf]]<br />
 
−
[[Media:If_STDP_Song.pdf|if_STDP_Song.pdf]]<br />
 
−
[[Media:If_crosscorr.pdf|if_crosscorr.pdf]]<br />
 
−
[[Media:Oja.pdf|oja.pdf]]<br />
 
−
[[Media:Oja_node.pdf|oja_node.pdf]]<br />
 
−
[[Media:Plasticity1.pdf|plasticity1.pdf]]<br />
 
−
[[Media:Plasticity2.pdf|plasticity2.pdf]]<br />
 
−
[[Media:Signaling.pdf|signaling.pdf]]<br />
 
  
−
== 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 187: Line 82:
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
 
−
[[Media:Abeles.pdf|abeles.pdf]]<br />
 
−
[[Media:Asyn_gain.pdf|asyn_gain.pdf]]<br />
 
−
[[Media:Brain.pdf|brain.pdf]]<br />
 
−
[[Media:Cortex_column.pdf|cortex_column.pdf]]<br />
 
−
[[Media:Cortex_layers.pdf|cortex_layers.pdf]]<br />
 
−
[[Media:IzhikevichNet.pdf|izhikevichNet.pdf]]<br />
 
−
[[Media:Layers_schematic1.pdf|layers_schematic1.pdf]]<br />
 
−
[[Media:Layers_schematic2.pdf|layers_schematic2.pdf]]<br />
 
−
[[Media:Module_cortex.pdf|module_cortex.pdf]]<br />
 
−
[[Media:Netlets.pdf|netlets.pdf]]<br />
 
−
[[Media:Netlets2.pdf|netlets2.pdf]]<br />
 
−
[[Media:Thorpe.pdf|thorpe.pdf]]<br />
 
−
 
 
== 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 217: 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 ===
 
−
[[Media:A_binarization.pdf|A_binarization.pdf]]<br />
 
−
[[Media:A_letter.pdf|A_letter.pdf]]<br />
 
−
[[Media:Boolean.pdf|boolean.pdf]]<br />
 
−
[[Media:Elman.pdf|elman.pdf]]<br />
 
−
[[Media:Gradient_decent.pdf|gradient_descent.pdf]]<br />
 
−
[[Media:Mlp.pdf|mlp.pdf]]<br />
 
−
[[Media:Mlp_XOR.pdf|mlp_XOR.pdf]]<br />
 
−
[[Media:Mlp_XOR2.pdf|mlp_XOR2.pdf]]<br />
 
−
[[Media:Mlp_comp.pdf|mlp_comp.pdf]]<br />
 
−
[[Media:Mlp_comp2.pdf|mlp_comp2.pdf]]<br />
 
−
[[Media:Mlp_sine.pdf|mlp_sine.pdf]]<br />
 
−
[[Media:Node_creation.pdf|node_creation.pdf]]<br />
 
−
[[Media:Overfit.pdf|overfit.pdf]]<br />
 
−
[[Media:PerceptronExample.pdf|perceptronExample.pdf]]<br />
 
−
[[Media:RbfNet.pdf|rbfNet.pdf]]<br />
 
−
[[Media:RbfTrans.pdf|rbfTrans.pdf]]<br />
 
−
[[Media:Sigma_node2.pdf|sigma_node2.pdf]]<br />
 
−
[[Media:Surface1.pdf|surface1.pdf]]<br />
 
−
[[Media:Svm1.pdf|svm1.pdf]]<br />
 
−
[[Media:Svm1map.pdf|svm1map.pdf]]<br />
 
−
[[Media:Svm1nl.pdf|svm1nl.pdf]]<br />
 
−
[[Media:Svm2.pdf|svm2.pdf]]<br />
 
−
[[Media:Svm2Color.pdf|svm2Color.pdf]]<br />
 
  
 
== 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 ===
+
 
−
[[Media:DNFexamplePlaceField.pdf|DNFexamplePlaceField.pdf]]<br />
+
[http://web.cs.dal.ca/~tt/CSCI650809/noisySignal.mat noisySignal.mat]
−
[[Media:DNFexampleWM.pdf|DNFexampleWM.pdf]]<br />
 
−
[[Media:DNFexamples.pdf|DNFexamples.pdf]]<br />
 
−
[[Media:DNFheadDirections.pdf|DNFheadDirections.pdf]]<br />
 
−
[[Media:DNFpiModel.pdf|DNFpiModel.pdf]]<br />
 
−
[[Media:DNFpiSim2.pdf|DNFpiSim2.pdf]]<br />
 
−
[[Media:DNFpiSim2.pdf|DNFpiSim2.pdf]]<br />
 
−
[[Media:DNFpopulationDecoding.pdf|DNFpopulationDecoding.pdf]]<br />
 
−
[[Media:DNFweightkernel.pdf|DNFweightkernel.pdf]]<br />
 
−
[[Media:DNFweightkernelSC.pdf|DNFweightkernelSC.pdf]]<br />
 
−
[[Media:Cann_drift.pdf|cann_drift.pdf]]<br />
 
−
[[Media:Cann_sim1.pdf|cann_sim1.pdf]]<br />
 
−
[[Media:Cann_sim1b.pdf|cann_sim1b.pdf]]<br />
 
−
[[Media:Cann_theory.pdf|cann_theory.pdf]]<br />
 
−
[[Media:Cann_theory2.pdf|cann_theory2.pdf]]<br />
 
−
[[Media:Hd_model.pdf|hd_model.pdf]]<br />
 
−
[[Media:Pop_decoding.pdf|pop_decoding.pdf]]<br />
 
−
[[Media:Som_a1.pdf|som_a1.pdf]]<br />
 
−
[[Media:Som_model1.pdf|som_model1.pdf]]<br />
 
−
[[Media:Som_model2.pdf|som_model2.pdf]]<br />
 
−
[[Media:Som_sim1b.pdf|som_sim1b.pdf]]<br />
 
−
[[Media:Som_sim2b.pdf|som_sim2b.pdf]]<br />
 
−
[[Media:TuningCurve.pdf|tuningCurve.pdf]]<br />
 
−
[[Media:Tuning_curve2.pdf|tuning_curve2.pdf]]<br />
 
  
 
== 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 306: 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 ===
 
−
[[Media:GH_phasediagram.pdf|GH_phasediagram.pdf]]<br />
 
−
[[Media:Ann.pdf|ann.pdf]]<br />
 
−
[[Media:Ann_asym.pdf|ann_asym.pdf]]<br />
 
−
[[Media:Ann_diluted.pdf|ann_diluted.pdf]]<br />
 
−
[[Media:Ann_retrieval.pdf|ann_retrieval.pdf]]<br />
 
−
[[Media:Ann_sim.pdf|ann_sim.pdf]]<br />
 
−
[[Media:Ann_sim_color.pdf|ann_sim_color.pdf]]<br />
 
−
[[Media:Expansion_recoding.pdf|expansion_recoding.pdf]]<br />
 
−
[[Media:Gradient_decent1.pdf|gradient_descent1.pdf]]<br />
 
−
[[Media:Hippo.pdf|hippo.pdf]]<br />
 
−
[[Media:Lorenz.pdf|lorenz.pdf]]<br />
 
−
[[Media:MemoryClassification.pdf|memoryClassification.pdf]]<br />
 
−
[[Media:Signoise.pdf|signoise.pdf]]<br />
 
−
[[Media:Sparse1.pdf|sparse1.pdf]]<br />
 
−
[[Media:Sparse2.pdf|sparse2.pdf]]<br />
 
  
 
== 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 345: Line 166:
 
|-
 
|-
 
|}
 
|}
−
=== Figures ===
 
−
[[Media:DNFmemoryLimit.pdf|DNFmemoryLimit.pdf]]<br />
 
−
[[Media:TDlearning.pdf|TDlearning.pdf]]<br />
 
−
[[Media:Ann_sequence.pdf|ann_sequence.pdf]]<br />
 
−
[[Media:Basal_ganglia2.pdf|basal_ganglia2.pdf]]<br />
 
−
[[Media:Basal_ganglia2.pdf|basal_ganglia2.pdf]]<br />
 
−
[[Media:Basal_ganglia3.pdf|basal_ganglia3.pdf]]<br />
 
−
[[Media:Basal_ganglia4.pdf|basal_ganglia4.pdf]]<br />
 
−
[[Media:Cerebellum.pdf|cerebellum.pdf]]<br />
 
−
[[Media:Conditioning.pdf|conditioning.pdf]]<br />
 
−
[[Media:Control_critic.pdf|control_critic.pdf]]<br />
 
−
[[Media:Control_forward.pdf|control_forward.pdf]]<br />
 
−
[[Media:Control_forward_inverse.pdf|control_forward_inverse.pdf]]<br />
 
−
[[Media:Control_inverse.pdf|control_inverse.pdf]]<br />
 
−
[[Media:Control_negative.pdf|control_negative.pdf]]<br />
 
−
[[Media:Coupled_ann.pdf|coupled_ann.pdf]]<br />
 
−
[[Media:Coupled_ann2.pdf|coupled_ann2.pdf]]<br />
 
−
[[Media:Experts.pdf|experts.pdf]]<br />
 
−
[[Media:Mixture_experts.pdf|mixture_experts.pdf]]<br />
 
−
[[Media:Modular_function.pdf|modular_function.pdf]]<br />
 
−
[[Media:Td.pdf|td.pdf]]<br />
 
−
[[Media:What_where.pdf|what_where.pdf]]<br />
 
−
[[Media:Wm_limit.pdf|wm_limit.pdf]]<br />
 
−
[[Media:Wm_randy.pdf|wm_randy.pdf]]<br />
 
−
 
 
== 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 ===
+
 
−
[[Media:ART.pdf|ART.pdf]]<br />
+
== MATLAB GUIs ==
−
[[Media:ARTletter.pdf|ARTletter.pdf]]<br />
+
(Available for MATLAB only.) [[Media:MATLABGUIs.zip|MATLABGUIs.zip]]
−
[[Media:Boltzmann1.pdf|Boltzmann1.pdf]]<br />
 
−
[[Media:Boltzmann2.pdf|Boltzmann2.pdf]]<br />
 
−
[[Media:Boltzmann3.pdf|Boltzmann3.pdf]]<br />
 
−
[[Media:EM.pdf|EM.pdf]]<br />
 
−
[[Media:EMcolor.pdf|EMcolor.pdf]]<br />
 
−
[[Media:FRistonTT.pdf|FRistonTT.pdf]]<br />
 
−
[[Media:Helmholtz.pdf|Helmholtz.pdf]]<br />
 
−
[[Media:Hinton.pdf|Hinton.pdf]]<br />
 
−
[[Media:HintonColour.pdf|HintonColour.pdf]]<br />
 
−
[[Media:BayesianNetworks2.pdf|bayesianNetworks2.pdf]]<br />
 
−
[[Media:BayesianNetworks2.pdf|bayesianNetworks2.pdf]]<br />
 
−
[[Media:Deco_model.pdf|deco_model.pdf]]<br />
 
−
[[Media:Deco_res.pdf|deco_res.pdf]]<br />
 
−
[[Media:Deco_where_what.pdf|deco_where_what.pdf]]<br />
 
−
[[Media:Dehaene.pdf|dehaene.pdf]]<br />
 
−
[[Media:Dehaene2.pdf|dehaene2.pdf]]<br />
 
−
[[Media:Rec_fiels.pdf|rec_fiels.pdf]]<br />
 
−
[[Media:Stroop.pdf|stroop.pdf]]<br />
 
−
[[Media:Visnet.pdf|visnet.pdf]]<br />
 

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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