Examples
========

.. toctree::
   :maxdepth: 1

   COBAHH <COBAHH>
   CUBA <CUBA>
   IF_curve_Hodgkin_Huxley <IF_curve_Hodgkin_Huxley>
   IF_curve_LIF <IF_curve_LIF>
   adaptive_threshold <adaptive_threshold>
   coupled_oscillators <coupled_oscillators>
   network_operation_stop <network_operation_stop>
   non_reliability <non_reliability>
   phase_locking <phase_locking>
   reliability <reliability>

.. _advanced:


advanced
--------

.. toctree::
   :maxdepth: 1

   COBAHH_approximated <advanced.COBAHH_approximated>
   Ornstein_Uhlenbeck <advanced.Ornstein_Uhlenbeck>
   compare_GSL_to_conventional <advanced.compare_GSL_to_conventional>
   custom_events <advanced.custom_events>
   exprel_function <advanced.exprel_function>
   float_32_64_benchmark <advanced.float_32_64_benchmark>
   modelfitting_sbi <advanced.modelfitting_sbi>
   opencv_movie <advanced.opencv_movie>
   stochastic_odes <advanced.stochastic_odes>

.. _compartmental:


compartmental
-------------

.. toctree::
   :maxdepth: 1

   bipolar_cell <compartmental.bipolar_cell>
   bipolar_with_inputs <compartmental.bipolar_with_inputs>
   bipolar_with_inputs2 <compartmental.bipolar_with_inputs2>
   cylinder <compartmental.cylinder>
   hh_with_spikes <compartmental.hh_with_spikes>
   hodgkin_huxley_1952 <compartmental.hodgkin_huxley_1952>
   infinite_cable <compartmental.infinite_cable>
   lfp <compartmental.lfp>
   morphotest <compartmental.morphotest>
   rall <compartmental.rall>
   spike_initiation <compartmental.spike_initiation>

.. _frompapers:


frompapers
----------

.. toctree::
   :maxdepth: 1

   Brette_2004 <frompapers.Brette_2004>
   Brette_Gerstner_2005 <frompapers.Brette_Gerstner_2005>
   Brette_Guigon_2003 <frompapers.Brette_Guigon_2003>
   Brunel_2000 <frompapers.Brunel_2000>
   Brunel_Hakim_1999 <frompapers.Brunel_Hakim_1999>
   Brunel_Wang_2001 <frompapers.Brunel_Wang_2001>
   Clopath_et_al_2010_homeostasis <frompapers.Clopath_et_al_2010_homeostasis>
   Clopath_et_al_2010_no_homeostasis <frompapers.Clopath_et_al_2010_no_homeostasis>
   Destexhe_et_al_1998 <frompapers.Destexhe_et_al_1998>
   Diehl_Cook_2015 <frompapers.Diehl_Cook_2015>
   Diesmann_et_al_1999 <frompapers.Diesmann_et_al_1999>
   Graupner_Brunel_2012 <frompapers.Graupner_Brunel_2012>
   Hindmarsh_Rose_1984 <frompapers.Hindmarsh_Rose_1984>
   Izhikevich_2003 <frompapers.Izhikevich_2003>
   Izhikevich_2007 <frompapers.Izhikevich_2007>
   Jansen_Rit_1995_single_column <frompapers.Jansen_Rit_1995_single_column>
   Kremer_et_al_2011_barrel_cortex <frompapers.Kremer_et_al_2011_barrel_cortex>
   Maass_Natschlaeger_Markram_2002 <frompapers.Maass_Natschlaeger_Markram_2002>
   Morris_Lecar_1981 <frompapers.Morris_Lecar_1981>
   Naud_et_al_2008_adex_firing_patterns <frompapers.Naud_et_al_2008_adex_firing_patterns>
   Nicola_Clopath_2017 <frompapers.Nicola_Clopath_2017>
   Platkiewicz_Brette_2011 <frompapers.Platkiewicz_Brette_2011>
   Rossant_et_al_2011bis <frompapers.Rossant_et_al_2011bis>
   Rothman_Manis_2003 <frompapers.Rothman_Manis_2003>
   Sturzl_et_al_2000 <frompapers.Sturzl_et_al_2000>
   Tetzlaff_2015 <frompapers.Tetzlaff_2015>
   Touboul_Brette_2008 <frompapers.Touboul_Brette_2008>
   Tsodyks_Pawelzik_Markram_1998 <frompapers.Tsodyks_Pawelzik_Markram_1998>
   Tsodyks_Uziel_Markram_2000 <frompapers.Tsodyks_Uziel_Markram_2000>
   Vogels_et_al_2011 <frompapers.Vogels_et_al_2011>
   Wang_2002 <frompapers.Wang_2002>
   Wang_Buszaki_1996 <frompapers.Wang_Buszaki_1996>

.. _frompapers.brette_2012:


frompapers/Brette_2012
----------------------

.. toctree::
   :maxdepth: 1

   Fig1 <frompapers.Brette_2012.Fig1>
   Fig3AB <frompapers.Brette_2012.Fig3AB>
   Fig3CF <frompapers.Brette_2012.Fig3CF>
   Fig4 <frompapers.Brette_2012.Fig4>
   Fig5A <frompapers.Brette_2012.Fig5A>
   params <frompapers.Brette_2012.params>
   README.txt <frompapers.Brette_2012.README.txt.rst>

.. _frompapers.spreizer_et_al_2019:


frompapers/Spreizer_et_al_2019
------------------------------

.. toctree::
   :maxdepth: 1

   Spreizer_et_al_2019 <frompapers.Spreizer_et_al_2019.Spreizer_et_al_2019>
   perlin1.npy <frompapers.Spreizer_et_al_2019.perlin1.npy.rst>
   perlin2.npy <frompapers.Spreizer_et_al_2019.perlin2.npy.rst>
   perlin3.npy <frompapers.Spreizer_et_al_2019.perlin3.npy.rst>
   perlin4.npy <frompapers.Spreizer_et_al_2019.perlin4.npy.rst>
   perlin5.npy <frompapers.Spreizer_et_al_2019.perlin5.npy.rst>

.. _frompapers.stimberg_et_al_2018:


frompapers/Stimberg_et_al_2018
------------------------------

.. toctree::
   :maxdepth: 1

   example_1_COBA <frompapers.Stimberg_et_al_2018.example_1_COBA>
   example_2_gchi_astrocyte <frompapers.Stimberg_et_al_2018.example_2_gchi_astrocyte>
   example_3_io_synapse <frompapers.Stimberg_et_al_2018.example_3_io_synapse>
   example_4_rsmean <frompapers.Stimberg_et_al_2018.example_4_rsmean>
   example_4_synrel <frompapers.Stimberg_et_al_2018.example_4_synrel>
   example_5_astro_ring <frompapers.Stimberg_et_al_2018.example_5_astro_ring>
   example_6_COBA_with_astro <frompapers.Stimberg_et_al_2018.example_6_COBA_with_astro>
   plot_utils <frompapers.Stimberg_et_al_2018.plot_utils>
   README.md <frompapers.Stimberg_et_al_2018.README.md.rst>
   figures.mplstyle <frompapers.Stimberg_et_al_2018.figures.mplstyle.rst>

.. _frompapers.stimberg_et_al_2019:


frompapers/Stimberg_et_al_2019
------------------------------

.. toctree::
   :maxdepth: 1

   example_3_bisection <frompapers.Stimberg_et_al_2019.example_3_bisection>
   example_3_bisection_standalone <frompapers.Stimberg_et_al_2019.example_3_bisection_standalone>

.. _multiprocessing:


multiprocessing
---------------

.. toctree::
   :maxdepth: 1

   01_using_cython <multiprocessing.01_using_cython>
   02_using_standalone <multiprocessing.02_using_standalone>
   03_standalone_joblib <multiprocessing.03_standalone_joblib>

.. _standalone:


standalone
----------

.. toctree::
   :maxdepth: 1

   STDP_standalone <standalone.STDP_standalone>
   cuba_openmp <standalone.cuba_openmp>
   simple_case <standalone.simple_case>
   simple_case_build <standalone.simple_case_build>
   standalone_multiple_processes <standalone.standalone_multiple_processes>
   standalone_multiplerun <standalone.standalone_multiplerun>

.. _synapses:


synapses
--------

.. toctree::
   :maxdepth: 1

   STDP <synapses.STDP>
   continuous_interaction <synapses.continuous_interaction>
   efficient_gaussian_connectivity <synapses.efficient_gaussian_connectivity>
   gapjunctions <synapses.gapjunctions>
   homeostatic_stdp_at_inhibitory_synapes <synapses.homeostatic_stdp_at_inhibitory_synapes>
   jeffress <synapses.jeffress>
   licklider <synapses.licklider>
   nonlinear <synapses.nonlinear>
   spatial_connections <synapses.spatial_connections>
   spike_based_homeostasis <synapses.spike_based_homeostasis>
   state_variables <synapses.state_variables>
   synapses <synapses.synapses>