GitHub - MinaKh/bcpnn-mt: Model of MT using BCPNN to self-organize

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Model of MT using BCPNN to self-organize

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Name		Name	Last commit message	Last commit date
Latest commit History 232 Commits
.gitignore		.gitignore
Analyser.py		Analyser.py
Bcpnn.py		Bcpnn.py
CheckDelayScale.py		CheckDelayScale.py
CreateConnections.py		CreateConnections.py
CreateStimuli.py		CreateStimuli.py
MeasureInputOutputCurve.py		MeasureInputOutputCurve.py
NetworkSimModule.py		NetworkSimModule.py
NetworkSimModuleOnlyExc.py		NetworkSimModuleOnlyExc.py
PlotConductances.py		PlotConductances.py
PlotPrediction.py		PlotPrediction.py
PlotSpikes.py		PlotSpikes.py
PlotWeightsAndProbabilities.py		PlotWeightsAndProbabilities.py
Plotter.py		Plotter.py
Prepare.py		Prepare.py
README		README
ResultsCollector.py		ResultsCollector.py
SimulationManager.py		SimulationManager.py
SweepAdExNeuronParameters.py		SweepAdExNeuronParameters.py
SweepNeuronParameters.py		SweepNeuronParameters.py
abstract_learning.py		abstract_learning.py
abstract_network.py		abstract_network.py
abstract_training.py		abstract_training.py
analyse_connectivity.py		analyse_connectivity.py
analyse_input.py		analyse_input.py
analyse_input_rates.py		analyse_input_rates.py
analyse_simple.py		analyse_simple.py
analyse_sweep_sigmaX_sigmaV_with_SimManager.py		analyse_sweep_sigmaX_sigmaV_with_SimManager.py
animate_bcpnn_traces.py		animate_bcpnn_traces.py
animate_stimuli.py		animate_stimuli.py
balance_connlist.py		balance_connlist.py
bcpnn_offline.py		bcpnn_offline.py
bootstrap.sh		bootstrap.sh
bootstrap_frioul.sh		bootstrap_frioul.sh
calculate_conductances.py		calculate_conductances.py
call_plot_scripts.py		call_plot_scripts.py
check_delay_scale.py		check_delay_scale.py
check_pij.py		check_pij.py
check_pij_triangular_probdist.py		check_pij_triangular_probdist.py
check_torus_movement.py		check_torus_movement.py
collect_plots.py		collect_plots.py
compare_conn_lists.py		compare_conn_lists.py
compare_delayScale.sh		compare_delayScale.sh
compare_scaleLatency.sh		compare_scaleLatency.sh
cut_spike_file.py		cut_spike_file.py
dynamic_image.py		dynamic_image.py
figure_sizes.py		figure_sizes.py
get_conductance_matrix.py		get_conductance_matrix.py
get_gids_to_record.py		get_gids_to_record.py
get_input_scaling_factor.py		get_input_scaling_factor.py
get_log_pconn.py		get_log_pconn.py
get_number_of_hypercolumns.py		get_number_of_hypercolumns.py
get_target_weights_and_delays.py		get_target_weights_and_delays.py
integrate_bcpnn.py		integrate_bcpnn.py
main.py		main.py
make_movie.py		make_movie.py
measure_tuning_curve_abstract.py		measure_tuning_curve_abstract.py
measure_tuning_curve_one_run.py		measure_tuning_curve_one_run.py
measure_tuning_curves.py		measure_tuning_curves.py
merge_abstract_input_files.py		merge_abstract_input_files.py
merge_abstract_output_files.py		merge_abstract_output_files.py
merge_abstract_training_files.py		merge_abstract_training_files.py
merge_connlists.py		merge_connlists.py
merge_input_spikefiles.py		merge_input_spikefiles.py
network_sim.py		network_sim.py
plot_3D_scatter.py		plot_3D_scatter.py
plot_Lt_rate_envelope.py		plot_Lt_rate_envelope.py
plot_abstract_activation.py		plot_abstract_activation.py
plot_abstract_input_single_cell.py		plot_abstract_input_single_cell.py
plot_activity_as_colormap.py		plot_activity_as_colormap.py
plot_activity_as_quiver_plot.py		plot_activity_as_quiver_plot.py
plot_all_pij.py		plot_all_pij.py
plot_ann_activity_as_cms_quiver_plot_one_stimulus.py		plot_ann_activity_as_cms_quiver_plot_one_stimulus.py
plot_ann_activity_as_quiver_plot.py		plot_ann_activity_as_quiver_plot.py
plot_ann_activity_as_quiver_plot_full_stimulus.py		plot_ann_activity_as_quiver_plot_full_stimulus.py
plot_ann_activity_as_quiver_plot_one_stimulus.py		plot_ann_activity_as_quiver_plot_one_stimulus.py
plot_ann_output_activity.py		plot_ann_output_activity.py
plot_bcpnn_traces.py		plot_bcpnn_traces.py
plot_bcpnn_weight_traces.py		plot_bcpnn_weight_traces.py
plot_blur_sweep_rates.py		plot_blur_sweep_rates.py
plot_cell_responses_and_properties.py		plot_cell_responses_and_properties.py
plot_colormaps.py		plot_colormaps.py
plot_conductances.py		plot_conductances.py
plot_connection_histograms.py		plot_connection_histograms.py
plot_connectivity_profile.py		plot_connectivity_profile.py
plot_connectivity_profile_abstract.py		plot_connectivity_profile_abstract.py
plot_connlist_as_colormap.py		plot_connlist_as_colormap.py
plot_connlist_difference_as_colormap.py		plot_connlist_difference_as_colormap.py
plot_connprobabilities.py		plot_connprobabilities.py
plot_grid_example.py		plot_grid_example.py
plot_hexgrid.py		plot_hexgrid.py
plot_hist.py		plot_hist.py
plot_input.py		plot_input.py
plot_input_colormap.py		plot_input_colormap.py
plot_input_spiketrains.py		plot_input_spiketrains.py
plot_matrix_as_histogram.py		plot_matrix_as_histogram.py
plot_merged_bcpnn_traces.py		plot_merged_bcpnn_traces.py
plot_multiple_results.py		plot_multiple_results.py
plot_paper_figure_readout_comparison.py		plot_paper_figure_readout_comparison.py
plot_peff.py		plot_peff.py

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# # # # # # # # # # # # #
#     bcppn-mt          #
# # # # # # # # # # # # #

Requirements:
    pyNN
    Brian, NEST or another pyNN supported simulator

Run:
    python main_noColumns.py

    or 

    mpirun -np [number_of_processes] python main_noColumns.py


installation on (neuro)debian(virtual machine on MacOsX)
--------------------------------------------------------

   sudo aptitude install ffmpeg 

#PyNN+NeuroTools
   sudo aptitude install python-pynn
   sudo aptitude install python-pip
   sudo aptitude install python-imaging
   sudo pip install NeuroTools
#NEST dependencies
   sudo aptitude install gsl-bin libgsl0-dev
   sudo aptitude install python-dev
   sudo aptitude install libncurses-dev
   sudo aptitude install libreadline-dev
#NEST
   wget http://www.nest-initiative.org/download/yHTCUpeiTsCr/nest-2.0.0.tar.gz
   tar zxvf nest-2.0.0.tar.gz
   cd nest-2.0.0
   ./configure
   make
   sudo make install