.. _pynest_examples:

PyNEST examples
===============

.. grid:: 1 1 2 3
    :gutter: 1

    .. grid-item-card:: Simple networks
           :img-top: ../static/img/pynest/mc_neuron.png

           * :doc:`../auto_examples/one_neuron`
           * :doc:`../auto_examples/one_neuron_with_noise`
           * :doc:`../auto_examples/twoneurons`
           * :doc:`../auto_examples/balancedneuron`
           * :doc:`../auto_examples/aeif_cond_beta_multisynapse`
           * :doc:`../auto_examples/testiaf`
           * :doc:`../auto_examples/vinit_example`
           * :doc:`../auto_examples/mc_neuron`


    .. grid-item-card:: 2D Spatially-structured networks
           :img-top: ../static/img/pynest/layer4.png

           * :doc:`../auto_examples/spatial/conncomp`
           * :doc:`../auto_examples/spatial/conncon_sources`
           * :doc:`../auto_examples/spatial/conncon_targets`
           * :doc:`../auto_examples/spatial/connex`
           * :doc:`../auto_examples/spatial/connex_ew`
           * :doc:`../auto_examples/spatial/ctx_2n`
           * :doc:`../auto_examples/spatial/gaussex`
           * :doc:`../auto_examples/spatial/grid_iaf`
           * :doc:`../auto_examples/spatial/grid_iaf_irr`
           * :doc:`../auto_examples/spatial/grid_iaf_oc`

    .. grid-item-card:: 3D Spatially-structured networks
           :img-top: ../static/img/pynest/spatial_test3d.png

           * :doc:`../auto_examples/spatial/test_3d`
           * :doc:`../auto_examples/spatial/test_3d_exp`
           * :doc:`../auto_examples/spatial/test_3d_gauss`


.. grid:: 1 1 2 3

    .. grid-item-card:: NEST Sudoku solver
           :img-top: ../static/img/sudoku_solution.gif

           * :doc:`../auto_examples/sudoku/sudoku_solver`
           * :doc:`../auto_examples/sudoku/plot_progress`

    .. grid-item-card:: NEST Pong game
           :img-top: ../static/img/pong_sim.gif

           * :doc:`../auto_examples/pong/run_simulations`
           * :doc:`../auto_examples/pong/generate_gif`

    .. grid-item-card:: Astrocytes
           :img-top: ../static/img/astrocyte_interaction.png

           * :doc:`../auto_examples/astrocytes/astrocyte_single`
           * :doc:`../auto_examples/astrocytes/astrocyte_interaction`
           * :doc:`../auto_examples/astrocytes/astrocyte_small_network`
           * :doc:`../auto_examples/astrocytes/astrocyte_brunel_bernoulli`
           * :doc:`../auto_examples/astrocytes/astrocyte_brunel_fixed_indegree`


.. grid:: 1 1 2 3

    .. grid-item-card:: Random balanced networks (Brunel)
           :img-top: ../static/img/pynest/brunel_alpha.png

           * :doc:`../auto_examples/brunel_alpha_nest`
           * :doc:`../auto_examples/brunel_delta_nest`
           * :doc:`../auto_examples/brunel_siegert_nest`
           * :doc:`../auto_examples/brunel_exp_multisynapse_nest`
           * :doc:`../auto_examples/brunel_alpha_evolution_strategies`


    .. grid-item-card::  Large scale cortical network models
           :img-top: ../static/img/network_model_sketch_mesocircuit.png

           * :doc:`../auto_examples/Potjans_2014/index` (Potjans and Diesmann 2014)
           * `The mesocircuit model <https://mesocircuit-model.readthedocs.io/en/latest/>`_: A layered cortical network with distance-dependent connectivity
           * `The multi-area model <https://inm-6.github.io/multi-area-model/>`_: A network model of the visual cortex of the macaque monkey
           * `The HuMAM model <https://github.com/INM-6/human-multi-area-model>`_: Multi-Scale Spiking Network Model of Human Cerebral Cortex


    .. grid-item-card:: EI clustered network (Rostami et al)
           :img-top: ../auto_examples/EI_clustered_network/EI_clustered_network_schematic.png

           :doc:`../auto_examples/EI_clustered_network/index`



.. grid:: 1 1 2 3

    .. grid-item-card:: GLIF (from Allen institute)
           :img-top: ../static/img/pynest/glif_cond.png

           * :doc:`../auto_examples/glif_cond_neuron`
           * :doc:`../auto_examples/glif_psc_neuron`
           * :doc:`../auto_examples/glif_psc_double_alpha_neuron`

    .. grid-item-card:: Compartmental neurons
           :img-top: ../static/img/pynest/dendritic_synapse_conductances.png

           * :doc:`../auto_examples/compartmental_model/receptors_and_current`
           * :doc:`../auto_examples/compartmental_model/two_comps`



    .. grid-item-card:: GIF (from Gerstner lab)
           :img-top: ../static/img/pynest/gif_pop.png

           * :doc:`../auto_examples/gif_cond_exp_multisynapse`
           * :doc:`../auto_examples/gif_population`
           * :doc:`../auto_examples/gif_pop_psc_exp`


.. grid:: 1 1 2 3

    .. grid-item-card:: Rate neurons
           :img-top: ../static/img/pynest/rate_neuron.png

           * :doc:`../auto_examples/lin_rate_ipn_network`
           * :doc:`../auto_examples/rate_neuron_dm`


    .. grid-item-card:: Hodgkin-Huxley
           :img-top: ../static/img/pynest/hh_phase.png

           * :doc:`../auto_examples/hh_psc_alpha`
           * :doc:`../auto_examples/hh_phaseplane`

    .. grid-item-card:: Brody Hopfield
           :img-top: ../static/img/nest_logo-faded.png

           * :doc:`../auto_examples/BrodyHopfield`

.. grid:: 1 1 2 3

    .. grid-item-card:: Brette and Gerstner
           :img-top: ../static/img/pynest/brette_gerstner2c.png

           * :doc:`../auto_examples/brette_gerstner_fig_2c`
           * :doc:`../auto_examples/brette_gerstner_fig_3d`


    .. grid-item-card:: Precise spiking
           :img-top: ../static/img/pynest/precisespiking.png

           * :doc:`../auto_examples/precise_spiking`

    .. grid-item-card:: Campbell Siegert
           :img-top: ../static/img/nest_logo-faded.png

           * :doc:`../auto_examples/CampbellSiegert`

.. grid:: 1 1 2 3

      .. grid-item-card:: Decision making in recurrent network (after Wang 2002)
           :img-top: ../static/img/nest_logo-faded.png

           * :doc:`../auto_examples/wang_decision_making`


.. grid:: 1 1 2 3

    .. grid-item-card:: Gap junctions
           :img-top: ../static/img/pynest/gap_junctioninhib.png


           * :doc:`../auto_examples/gap_junctions_two_neurons`
           * :doc:`../auto_examples/gap_junctions_inhibitory_network`


    .. grid-item-card:: Structural plasticity
           :img-top: ../static/img/pynest/structuralplasticity.png

           * :doc:`../auto_examples/structural_plasticity`

    .. grid-item-card:: Synapse collection
           :img-top: ../static/img/pynest/synapsecollection.png

           * :doc:`../auto_examples/synapsecollection`

.. grid:: 1 1 2 3

    .. grid-item-card:: Urbanczik
           :img-top: ../static/img/pynest/urbanczik_syn.png

           * :doc:`../auto_examples/urbanczik_synapse_example`



    .. grid-item-card:: Clopath
           :img-top: ../static/img/pynest/clopath.png


           * :doc:`../auto_examples/clopath_synapse_spike_pairing`
           * :doc:`../auto_examples/clopath_synapse_small_network`



    .. grid-item-card:: Short-term plasticity
           :img-top: ../static/img/pynest/tsodyks_dep.png

           * :doc:`../auto_examples/iaf_tum_2000_short_term_depression`
           * :doc:`../auto_examples/iaf_tum_2000_short_term_facilitation`
           * :doc:`../auto_examples/evaluate_tsodyks2_synapse`


.. grid:: 1 1 2 3

    .. grid-item-card:: :doc:`../auto_examples/eprop_plasticity/index`
           :img-top: ../static/img/pynest/eprop_supervised_classification_infrastructure.png

           * :doc:`/auto_examples/eprop_plasticity/eprop_supervised_classification_evidence-accumulation_bsshslm_2020`
           * :doc:`/auto_examples/eprop_plasticity/eprop_supervised_regression_sine-waves_bsshslm_2020`
           * :doc:`/auto_examples/eprop_plasticity/eprop_supervised_regression_handwriting_bsshslm_2020`
           * :doc:`/auto_examples/eprop_plasticity/eprop_supervised_regression_lemniscate_bsshslm_2020`
           * :doc:`/auto_examples/eprop_plasticity/eprop_supervised_regression_sine-waves`
           * :doc:`/auto_examples/eprop_plasticity/eprop_supervised_classification_neuromorphic_mnist`


.. grid:: 1 1 2 3

    .. grid-item-card:: Recording and analyzing networks
           :img-top: ../static/img/pynest/correlospinmatrix.png

           * :doc:`../auto_examples/multimeter_file`
           * :doc:`../auto_examples/plot_weight_matrices`
           * :doc:`../auto_examples/if_curve`
           * :doc:`../auto_examples/pulsepacket`
           * :doc:`../auto_examples/correlospinmatrix_detector_two_neuron`
           * :doc:`../auto_examples/cross_check_mip_corrdet`

    .. grid-item-card:: Stimulating networks
           :img-top: ../static/img/pynest/sensitivitypertubation.png

           * :doc:`../auto_examples/sinusoidal_poisson_generator`
           * :doc:`../auto_examples/sinusoidal_gamma_generator`
           * :doc:`../auto_examples/repeated_stimulation`
           * :doc:`../auto_examples/sensitivity_to_perturbation`
           * :doc:`../auto_examples/intrinsic_currents_spiking`
           * :doc:`../auto_examples/intrinsic_currents_subthreshold`

    .. grid-item-card:: Handling output
           :img-top: ../static/img/pynest/store_restore.png


           * :doc:`../auto_examples/recording_demo`
           * :doc:`../auto_examples/store_restore_network`
           * :doc:`../auto_examples/music_cont_out_proxy_example/nest_script`


.. grid:: 1 1 2 3

    .. grid-item-card:: SONATA network
           :img-top: ../static/img/300_pointneurons.png

           * :doc:`../auto_examples/sonata_example/sonata_network`

    .. grid-item-card:: HPC benchmark
           :img-top: ../auto_examples/hpc_benchmark_connectivity.svg

           * :doc:`../auto_examples/hpc_benchmark`


    .. grid-item-card:: Connection set algebra
           :img-top: ../static/img/nest_logo-faded.png

           * :doc:`../auto_examples/csa_example`
           * :doc:`../auto_examples/csa_spatial_example`

.. toctree::
   :hidden:

   running_notebooks
   ../auto_examples/sudoku/index
   ../auto_examples/pong/index
   ../auto_examples/spatial/index
   ../auto_examples/music_cont_out_proxy_example/index
   ../auto_examples/compartmental_model/index
   ../auto_examples/Potjans_2014/index
   ../auto_examples/one_neuron
   ../auto_examples/one_neuron_with_noise
   ../auto_examples/twoneurons
   ../auto_examples/balancedneuron
   ../auto_examples/aeif_cond_beta_multisynapse
   ../auto_examples/gif_cond_exp_multisynapse
   ../auto_examples/brette_gerstner_fig_2c
   ../auto_examples/brette_gerstner_fig_3d
   ../auto_examples/hh_psc_alpha
   ../auto_examples/hh_phaseplane
   ../auto_examples/BrodyHopfield
   ../auto_examples/gif_population
   ../auto_examples/gif_pop_psc_exp
   ../auto_examples/mc_neuron
   ../auto_examples/glif_cond_neuron
   ../auto_examples/glif_psc_neuron
   ../auto_examples/glif_psc_double_alpha_neuron
   ../auto_examples/precise_spiking
   ../auto_examples/CampbellSiegert
   ../auto_examples/vinit_example
   ../auto_examples/recording_demo
   ../auto_examples/store_restore_network
   ../auto_examples/synapsecollection
   ../auto_examples/structural_plasticity
   ../auto_examples/gap_junctions_two_neurons
   ../auto_examples/gap_junctions_inhibitory_network
   ../auto_examples/evaluate_tsodyks2_synapse
   ../auto_examples/evaluate_quantal_stp_synapse
   ../auto_examples/clopath_synapse_spike_pairing
   ../auto_examples/clopath_synapse_small_network
   ../auto_examples/urbanczik_synapse_example
   ../auto_examples/iaf_tum_2000_short_term_depression
   ../auto_examples/iaf_tum_2000_short_term_facilitation
   ../auto_examples/lin_rate_ipn_network
   ../auto_examples/rate_neuron_dm
   ../auto_examples/brunel_alpha_nest
   ../auto_examples/brunel_delta_nest
   ../auto_examples/brunel_siegert_nest
   ../auto_examples/brunel_exp_multisynapse_nest
   ../auto_examples/brunel_alpha_evolution_strategies
   ../auto_examples/sonata_example/index
   ../auto_examples/testiaf
   ../auto_examples/repeated_stimulation
   ../auto_examples/multimeter_file
   ../auto_examples/sensitivity_to_perturbation
   ../auto_examples/plot_weight_matrices
   ../auto_examples/if_curve
   ../auto_examples/pulsepacket
   ../auto_examples/correlospinmatrix_detector_two_neuron
   ../auto_examples/sinusoidal_poisson_generator
   ../auto_examples/sinusoidal_gamma_generator
   ../auto_examples/cross_check_mip_corrdet
   ../auto_examples/intrinsic_currents_spiking
   ../auto_examples/intrinsic_currents_subthreshold
   ../auto_examples/csa_example
   ../auto_examples/csa_spatial_example
   ../auto_examples/hpc_benchmark
   ../auto_examples/astrocytes/index
   ../auto_examples/EI_clustered_network/index
   ../auto_examples/eprop_plasticity/index
   ../auto_examples/wang_decision_making