├── .gitignore ├── Doxyfile ├── ForExtCurrent ├── Adam_stimulus_mean_curr.m └── ImageProcess_DOG.m ├── LICENSE.md ├── README.md ├── configure.ac ├── cpp.supp ├── cpp_sources ├── ChemSyn.cpp ├── ChemSyn.h ├── MyIO.cpp ├── MyIO.h ├── NeuroNet.cpp ├── NeuroNet.h ├── NeuroPop.cpp ├── NeuroPop.h ├── SimuInterface.cpp ├── SimuInterface.h ├── main.cpp └── mpi_stuff │ ├── mpi_pseudocode │ └── toymodel_mpi.cpp ├── documentation ├── SpikeNet_Documentation.bib ├── SpikeNet_Documentation.pdf ├── SpikeNet_Documentation.tex ├── work_flow.png └── work_flow_white.png ├── m4 ├── ax_cxx_compile_stdcxx.m4 └── ax_lib_hdf5.m4 ├── main_demo.m ├── makefile.in ├── matlab_interface ├── DiscardTransientData.m ├── ReadH5.m ├── ReadYG.m ├── Read_and_save_YGSamp.m ├── ReduceResolution.m ├── ReformatSpikeHistory.m ├── SaveRYG.m ├── appendThisMatlabFileHDF5_example.m ├── new_ygin_files_and_randseedHDF5.m ├── read_syn_h5.m ├── read_ygin_syn.m ├── shuffle_K_common_neighbour.m ├── try_h5read.m ├── writeBasicParaHDF5.m ├── writeChemicalConnectionHDF5.m ├── writeELIFNeuronModelHDF5.m ├── writeExplVarHDF5.m ├── writeExtConductanceSettingsHDF5.m ├── writeExtConductanceTimeVariantSettingsHDF5.m ├── writeExtCurrentPopHDF5.m ├── writeExtCurrentSettingsHDF5.m ├── writeExtCurrentTimeVariantSettingsHDF5.m ├── writeExtCurrentTimeVariantSettingsMultiGroupHDF5.m ├── writeExtInitVHDF5.m ├── writeExtSpikeSettingsHDF5.m ├── writeExtSpikeTinvSettingsHDF5.m ├── writeHeterSpikeFreqAdptHDF5.m ├── writeInhSTDPHDF5.m ├── writeInitCondHDF5.m ├── writeInitVHDF5.m ├── writeJHLearnDirectionHDF5.m ├── writeJHLearnHDF5.m ├── writeLFPRecordHDF5.m ├── writeNeuronSamplingHDF5.m ├── writePerturbationHDF5.m ├── writePoissonPopHDF5.m ├── writePopCovRecordHDF5.m ├── writePopParaHDF5.m ├── writePopSeedHDF5.m ├── writePopStatsRecordHDF5.m ├── writeRealTimeCOMHDF5.m ├── writeRunawayKillerHDF5.m ├── writeSTDHDF5.m ├── writeSpikeFileInputPopHDF5.m ├── writeSpikeFreqAdptHDF5.m ├── writeSynCovRecordHDF5.m ├── writeSynParaHDF5.m ├── writeSynSamplingHDF5.m ├── writeSynStatsRecordHDF5.m └── writeSynapseModelChoiceHDF5.m ├── models ├── generate_learning_config.m ├── main_Chen_and_Gong_2019.m ├── main_Chen_and_Gong_2021.m ├── main_GU_et_al_2018.m ├── main_Keane_and_Gong_2015.m └── main_Qi_and_Gong_2022.m ├── post_processing ├── AnalyseGC_ELIF.m ├── AnalyseYG.m ├── CorrCoefYG.m ├── GCplotSpike_onegrid.m ├── GCplotV_onegrid.m ├── PostProcessGC_ELIF.m ├── PostProcessYG.m ├── RasterGC_ELIF.m ├── SpikeNet2SpikeGrid_spikehist.m ├── SpikeTrainConvolve.m ├── convolve2.m ├── fit_bayesian_bump_2_spikes_circular.m ├── fminsearchbnd.m ├── fminsearchcon.m ├── g_EPSP_conversion.m ├── g_pool_generator.m ├── generate_comments.m ├── generate_commentsGC_ELIF.m ├── get_CC_network.m ├── get_CC_pop.m ├── get_CN_prob.m ├── get_ISI.m ├── get_combinedSpikeHist.m ├── get_g_spike_triggered.m ├── get_grid_firing_centre.m ├── get_initialV.m ├── get_motif.m ├── get_rate.m ├── get_rate_spon_evoked.m ├── get_rich_club.m ├── get_rich_club_stPR_coupling.m ├── get_seg.m ├── get_stPR.m ├── get_stru_var_decomp.m ├── get_structural_variance.m ├── get_susceptibility.m ├── get_triplet_sequence.m ├── get_triplet_sequence_no_latency.m ├── get_up_and_down.m ├── my_logn_rand.m ├── num_spikes_plot.m ├── pairs_sample_from_network.m ├── peak_height_requirement.m ├── persistence_requirement.m ├── raster_marginals_shuffling.m ├── raster_plot.m ├── seq_postprocess.m ├── seq_postprocess_p3.m ├── spike_train_kernel_YG.m └── window_spike_hist_compressed.m ├── shell_scripts ├── GC_all_in_one.sh ├── YG_all_in_one.sh ├── all_in_one.sh.bak ├── ppmat.sh.bak └── repeat_simulations.sh.bak └── simu_config_tools ├── ARBITRARY_DEGREE_NEWMAN.m ├── ARBITRARY_DEGREE_NEWMAN_PRE_POST.m ├── Brian_connectivity_toolbox ├── Koetter_chapter_modified.pdf ├── Measurements │ ├── Modularity │ │ ├── modularity_finetune_dir.m │ │ ├── modularity_finetune_und.m │ │ ├── modularity_louvain_dir.m │ │ ├── modularity_louvain_und.m │ │ ├── modularity_newman_dir.m │ │ └── modularity_newman_und.m │ ├── assortativity_wei.m │ ├── charpath.m │ ├── clustering_coef_wd.m │ ├── degrees_dir.m │ ├── density_dir.m │ ├── distance_wei.m │ ├── jdegree.m │ ├── make_motif34lib.m │ ├── motif3struct_bin.m │ ├── motif3struct_wei.m │ ├── motif4struct_wei.m │ ├── rich_club_wd.m │ └── strengths_dir.m ├── Node Reorder │ ├── align_matrices.m │ ├── reorderMAT.m │ ├── reorder_matrix.m │ └── reorder_mod.m ├── backbone_wu.m ├── breadth.m ├── grid_communities.m ├── makefractalCIJ.m ├── makerandCIJdegreesfixed.m └── rich_club_bd.m ├── GenerateAjacencyMatrix.m ├── GridDM.m ├── Lattice2Lattice.m ├── MIT_Network_Toolbox ├── documentational │ ├── MIT Network toolbox.htm │ └── MIT Network toolbox_files │ │ ├── NGexample.png │ │ ├── circle_draw_example.png │ │ ├── continentalUS.png │ │ ├── dot_matrix_example.png │ │ ├── ga.js │ │ ├── header04.jpg │ │ ├── hexlattice.jpg │ │ ├── logo.gif │ │ ├── radial_plot_example.jpg │ │ ├── random_modular_graph.png │ │ ├── spectral_partitioning_example.png │ │ └── style.css └── original code │ ├── BFS.m │ ├── DoddsWattsSabel.m │ ├── PriceModel.m │ ├── add_edge_weights.m │ ├── adj2adjL.m │ ├── adj2dl.m │ ├── adj2edgeL.m │ ├── adj2inc.m │ ├── adj2pajek.m │ ├── adj2simple.m │ ├── adj2str.m │ ├── adjL2adj.m │ ├── adjL2edgeL.m │ ├── algebraic_connectivity.m │ ├── ave_neighbor_deg.m │ ├── ave_path_length.m │ ├── average_degree.m │ ├── build_smax_graph.m │ ├── canonical_nets.m │ ├── closeness.m │ ├── clust_coeff.m │ ├── degrees.m │ ├── diameter.m │ ├── dijkstra.m │ ├── distance_distribution.m │ ├── dot_matrix_plot.m │ ├── draw_circ_graph.m │ ├── edgeL2adj.m │ ├── edgeL2adjL.m │ ├── edgeL2cyto.m │ ├── edgeL2pajek.m │ ├── edgeL2simple.m │ ├── edge_betweenness.m │ ├── edgelist2dl.m │ ├── eigencentrality.m │ ├── el2geom.m │ ├── exponential_growth_model.m │ ├── fabrikant_model.m │ ├── fiedler_vector.m │ ├── find_conn_comp.m │ ├── forestFireModel.m │ ├── getEdges.m │ ├── getNodes.m │ ├── giant_component.m │ ├── graph_complement.m │ ├── graph_dual.m │ ├── graph_energy.m │ ├── graph_from_degree_sequence.m │ ├── graph_radius.m │ ├── graph_similarity.m │ ├── graph_spectrum.m │ ├── inc2adj.m │ ├── inc2edgeL.m │ ├── isbipartite.m │ ├── iscomplete.m │ ├── isconnected.m │ ├── isdirected.m │ ├── iseulerian.m │ ├── isgraphic.m │ ├── isregular.m │ ├── issimple.m │ ├── istree.m │ ├── isweighted.m │ ├── kmin_neighbors.m │ ├── kneighbors.m │ ├── kregular.m │ ├── laplacian_matrix.m │ ├── leaf_edges.m │ ├── leaf_nodes.m │ ├── license.txt │ ├── link_density.m │ ├── loops3.m │ ├── loops4.m │ ├── louvain_community_finding.m │ ├── master_equation_growth_model.m │ ├── min_span_tree.m │ ├── modularity_metric.m │ ├── multiedges.m │ ├── nested_hierarchies_model.m │ ├── newman_comm_fast.m │ ├── newman_eigenvector_method.m │ ├── newmangastner.m │ ├── newmangirvan.m │ ├── node_betweenness_faster.m │ ├── node_betweenness_slow.m │ ├── num_conn_comp.m │ ├── num_conn_triples.m │ ├── num_loops.m │ ├── num_star_motifs.m │ ├── numedges.m │ ├── numnodes.m │ ├── pajek2adj.m │ ├── pajek2edgeL.m │ ├── pajek2xyz.m │ ├── pdf_cdf_rank.m │ ├── pearson.m │ ├── preferential_attachment.m │ ├── purge.m │ ├── radial_plot.m │ ├── random_directed_graph.m │ ├── random_graph.m │ ├── random_modular_graph.m │ ├── rewire.m │ ├── rewire_assort.m │ ├── rewire_disassort.m │ ├── rich_club_metric.m │ ├── s_metric.m │ ├── selfloops.m │ ├── shortest_pathDP.m │ ├── simple_dijkstra.m │ ├── simple_spectral_partitioning.m │ ├── smooth_diameter.m │ ├── sort_nodes_by_max_neighbor_degree.m │ ├── sort_nodes_by_sum_neighbor_degrees.m │ ├── str2adj.m │ ├── subgraph.m │ ├── symmetrize.m │ ├── symmetrize_edgeL.m │ ├── tarjan.m │ ├── test_all_functions.m │ ├── vertex_eccentricity.m │ └── weighted_clust_coeff.m ├── MyRandomGraphGenerator.m ├── degree2stub.m ├── dirclustercoeffs.m ├── generate_IJ_2D.m ├── generate_graph_given_in_out_degree.m ├── hybrid_degree.m ├── inverse_pool.m ├── lattice_nD.m ├── lattice_nD_find_dist.m ├── poissrnd_2D.m ├── 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