├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── MANIFEST.in ├── Makefile ├── README.rst ├── doc ├── Makefile ├── _build │ ├── doctrees │ │ ├── contents.doctree │ │ ├── environment.pickle │ │ ├── exercises │ │ │ ├── adex-model.doctree │ │ │ ├── brunel-network.doctree │ │ │ ├── exponential-integrate-and-fire.doctree │ │ │ ├── hodgkin-huxley.doctree │ │ │ ├── hopfield-network.doctree │ │ │ ├── index.doctree │ │ │ ├── leaky-integrate-and-fire.doctree │ │ │ ├── neuron-type.doctree │ │ │ ├── ojas-rule.doctree │ │ │ ├── passive-cable.doctree │ │ │ ├── perceptual-decision-making.doctree │ │ │ ├── phase-plane-analysis.doctree │ │ │ └── spatial-working-memory.doctree │ │ ├── index.doctree │ │ ├── intro.doctree │ │ ├── licence.doctree │ │ ├── modules │ │ │ ├── modules.doctree │ │ │ ├── neurodynex3.adex_model.doctree │ │ │ ├── neurodynex3.brunel_model.doctree │ │ │ ├── neurodynex3.cable_equation.doctree │ │ │ ├── neurodynex3.competing_populations.doctree │ │ │ ├── neurodynex3.doctree │ │ │ ├── neurodynex3.exponential_integrate_fire.doctree │ │ │ ├── neurodynex3.hodgkin_huxley.doctree │ │ │ ├── neurodynex3.hopfield_network.doctree │ │ │ ├── neurodynex3.leaky_integrate_and_fire.doctree │ │ │ ├── neurodynex3.neuron_type.doctree │ │ │ ├── neurodynex3.ojas_rule.doctree │ │ │ ├── neurodynex3.phase_plane_analysis.doctree │ │ │ ├── neurodynex3.test.doctree │ │ │ ├── neurodynex3.tools.doctree │ │ │ └── neurodynex3.working_memory_network.doctree │ │ └── setup.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _images │ │ ├── AdaptiveExponential_Init_burst.png │ │ ├── Brunel_SIfast_PSpop.png │ │ ├── Brunel_SIfast_PSsingle.png │ │ ├── Brunel_SIfast_activity.png │ │ ├── Brunel_Spiking_LIF.png │ │ ├── Brunel_Synchronization.png │ │ ├── DecisionMaking_NetworkStructureAll.png │ │ ├── DecisionMaking_NetworkStructureDetail.png │ │ ├── DecisionMaking_PhasePlane_3.png │ │ ├── HF_CheckerboardAndPatterns.png │ │ ├── HF_CheckerboardRecovered2.png │ │ ├── HF_LetterAandOverlap.png │ │ ├── HH_getting_started.png │ │ ├── LIF_getting_started.png │ │ ├── Oja_3D.png │ │ ├── Oja_cloud.png │ │ ├── Oja_setup.png │ │ ├── WorkingMemory_Demo.png │ │ ├── WorkingMemory_NetworkStructure.png │ │ ├── WorkingMemory_PopulationVector2048.png │ │ ├── anaconda-prompt.png │ │ ├── cable_equation_pulse.png │ │ ├── exp_IF_min_current.png │ │ ├── passive_cable_ABC.png │ │ ├── run-code.png │ │ └── start-notebook.png │ │ ├── _modules │ │ ├── index.html │ │ └── neurodynex3 │ │ │ ├── hopfield_network │ │ │ ├── network.html │ │ │ └── pattern_tools.html │ │ │ ├── test.html │ │ │ └── test │ │ │ ├── test_cable_equation.html │ │ │ ├── test_hopfield.html │ │ │ ├── test_nagumo.html │ │ │ ├── test_neuron_type.html │ │ │ ├── test_oja.html │ │ │ └── test_spike_tools.html │ │ ├── _sources │ │ ├── contents.rst.txt │ │ ├── exercises │ │ │ ├── adex-model.rst.txt │ │ │ ├── brunel-network.rst.txt │ │ │ ├── exponential-integrate-and-fire.rst.txt │ │ │ ├── hodgkin-huxley.rst.txt │ │ │ ├── hopfield-network.rst.txt │ │ │ ├── index.rst.txt │ │ │ ├── leaky-integrate-and-fire.rst.txt │ │ │ ├── neuron-type.rst.txt │ │ │ ├── ojas-rule.rst.txt │ │ │ ├── passive-cable.rst.txt │ │ │ ├── perceptual-decision-making.rst.txt │ │ │ ├── phase-plane-analysis.rst.txt │ │ │ └── spatial-working-memory.rst.txt │ │ ├── index.rst.txt │ │ ├── intro.rst.txt │ │ ├── licence.rst.txt │ │ ├── modules │ │ │ ├── modules.rst.txt │ │ │ ├── neurodynex3.adex_model.rst.txt │ │ │ ├── neurodynex3.brunel_model.rst.txt │ │ │ ├── neurodynex3.cable_equation.rst.txt │ │ │ ├── neurodynex3.competing_populations.rst.txt │ │ │ ├── neurodynex3.exponential_integrate_fire.rst.txt │ │ │ ├── neurodynex3.hodgkin_huxley.rst.txt │ │ │ ├── neurodynex3.hopfield_network.rst.txt │ │ │ ├── neurodynex3.leaky_integrate_and_fire.rst.txt │ │ │ ├── neurodynex3.neuron_type.rst.txt │ │ │ ├── neurodynex3.ojas_rule.rst.txt │ │ │ ├── neurodynex3.phase_plane_analysis.rst.txt │ │ │ ├── neurodynex3.rst.txt │ │ │ ├── neurodynex3.test.rst.txt │ │ │ ├── neurodynex3.tools.rst.txt │ │ │ └── neurodynex3.working_memory_network.rst.txt │ │ └── setup.rst.txt │ │ ├── _static │ │ ├── basic.css │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Inconsolata.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ │ ├── jquery-3.4.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── contents.html │ │ ├── exercises │ │ ├── adex-model.html │ │ ├── brunel-network.html │ │ ├── exponential-integrate-and-fire.html │ │ ├── hodgkin-huxley.html │ │ ├── hopfield-network.html │ │ ├── index.html │ │ ├── leaky-integrate-and-fire.html │ │ ├── neuron-type.html │ │ ├── ojas-rule.html │ │ ├── passive-cable.html │ │ ├── perceptual-decision-making.html │ │ ├── phase-plane-analysis.html │ │ ├── setup.html │ │ └── spatial-working-memory.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── intro.html │ │ ├── licence.html │ │ ├── modules │ │ ├── modules.html │ │ ├── neurodynex3.adex_model.html │ │ ├── neurodynex3.brunel_model.html │ │ ├── neurodynex3.cable_equation.html │ │ ├── neurodynex3.competing_populations.html │ │ ├── neurodynex3.exponential_integrate_fire.html │ │ ├── neurodynex3.hodgkin_huxley.html │ │ ├── neurodynex3.hopfield_network.html │ │ ├── neurodynex3.html │ │ ├── neurodynex3.leaky_integrate_and_fire.html │ │ ├── neurodynex3.neuron_type.html │ │ ├── neurodynex3.ojas_rule.html │ │ ├── neurodynex3.phase_plane_analysis.html │ │ ├── neurodynex3.test.html │ │ ├── neurodynex3.tools.html │ │ └── neurodynex3.working_memory_network.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── setup.html ├── conf.py ├── contents.rst ├── exercises │ ├── adex-model.rst │ ├── brunel-network.rst │ ├── exc_images │ │ ├── AdaptiveExponential_Init_burst.png │ │ ├── Brunel_SIfast_PSpop.png │ │ ├── Brunel_SIfast_PSsingle.png │ │ ├── Brunel_SIfast_activity.png │ │ ├── Brunel_Spiking_LIF.png │ │ ├── Brunel_Synchronization.png │ │ ├── DecisionMaking_NetworkStructure.key │ │ ├── DecisionMaking_NetworkStructureAll.png │ │ ├── DecisionMaking_NetworkStructureDetail.png │ │ ├── DecisionMaking_PhasePlane.png │ │ ├── DecisionMaking_PhasePlane_3.png │ │ ├── HF_CheckerboardAndPatterns.png │ │ ├── HF_CheckerboardRecovered2.png │ │ ├── HF_LetterAandOverlap.png │ │ ├── HH_getting_started.png │ │ ├── LIF_getting_started.png │ │ ├── Oja_3D.png │ │ ├── Oja_cloud.png │ │ ├── Oja_setup.png │ │ ├── WorkingMemory_Demo.png │ │ ├── WorkingMemory_Demo.psd │ │ ├── WorkingMemory_NetworkStructure.key │ │ ├── WorkingMemory_NetworkStructure.png │ │ ├── WorkingMemory_PopulationVector2048.png │ │ ├── cable_equation_pulse.png │ │ ├── exp_IF_min_current.png │ │ └── passive_cable_ABC.png │ ├── exponential-integrate-and-fire.rst │ ├── hodgkin-huxley.rst │ ├── hopfield-network.rst │ ├── index.rst │ ├── leaky-integrate-and-fire.rst │ ├── neuron-type.rst │ ├── ojas-rule.rst │ ├── passive-cable.rst │ ├── perceptual-decision-making.rst │ ├── phase-plane-analysis.rst │ └── spatial-working-memory.rst ├── index.rst ├── intro.rst ├── licence.rst ├── modules │ ├── modules.rst │ ├── neurodynex3.adex_model.rst │ ├── neurodynex3.brunel_model.rst │ ├── neurodynex3.cable_equation.rst │ ├── neurodynex3.competing_populations.rst │ ├── neurodynex3.exponential_integrate_fire.rst │ ├── neurodynex3.hodgkin_huxley.rst │ ├── neurodynex3.hopfield_network.rst │ ├── neurodynex3.leaky_integrate_and_fire.rst │ ├── neurodynex3.neuron_type.rst │ ├── neurodynex3.ojas_rule.rst │ ├── neurodynex3.phase_plane_analysis.rst │ ├── neurodynex3.rst │ ├── neurodynex3.test.rst │ ├── neurodynex3.tools.rst │ └── neurodynex3.working_memory_network.rst ├── requirements.txt ├── setup.rst └── setup_images │ ├── StartJupyter.png │ ├── StartJupyter_2.png │ ├── anaconda-prompt.png │ ├── run-code.png │ └── start-notebook.png ├── neurodynex3.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── requires.txt └── top_level.txt ├── neurodynex3 ├── __init__.py ├── adex_model │ ├── AdEx.py │ └── __init__.py ├── brunel_model │ ├── LIF_spiking_network.py │ └── __init__.py ├── cable_equation │ ├── __init__.py │ └── passive_cable.py ├── competing_populations │ ├── __init__.py │ └── decision_making.py ├── data │ └── alphabet.pickle.gz ├── exponential_integrate_fire │ ├── __init__.py │ └── exp_IF.py ├── hodgkin_huxley │ ├── HH.py │ └── __init__.py ├── hopfield_network │ ├── __init__.py │ ├── demo.py │ ├── network.py │ ├── pattern_tools.py │ └── plot_tools.py ├── leaky_integrate_and_fire │ ├── LIF.py │ └── __init__.py ├── neuron_type │ ├── __init__.py │ └── neurons.py ├── ojas_rule │ ├── __init__.py │ └── oja.py ├── phase_plane_analysis │ ├── 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