diff --git a/cann/index.rst b/cann/index.rst new file mode 100644 index 0000000..e4010c2 --- /dev/null +++ b/cann/index.rst @@ -0,0 +1,4 @@ +.. toctree:: + :maxdepth: 1 + + Wu_2008_CANN.ipynb diff --git a/decision_making/index.rst b/decision_making/index.rst new file mode 100644 index 0000000..88814e6 --- /dev/null +++ b/decision_making/index.rst @@ -0,0 +1,6 @@ +.. toctree:: + :maxdepth: 1 + + Wang_2002_decision_making_spiking.ipynb + Wang_2006_decision_making_rate.ipynb + diff --git a/dynamics_analysis/index.rst b/dynamics_analysis/index.rst new file mode 100644 index 0000000..70aebb2 --- /dev/null +++ b/dynamics_analysis/index.rst @@ -0,0 +1,11 @@ +.. toctree:: + :maxdepth: 1 + + 1d_simple_systems.ipynb + 2d_decision_making_model.ipynb + ../decision_making/Wang_2006_decision_making_rate.ipynb + 2d_NaK_model.ipynb + 3d_hindmarsh_rose_model.ipynb + highdim_CANN.ipynb + highdim_gj_coupled_fhn.ipynb + ../recurrent_networks/Yang_2020_RNN_Analysis.ipynb \ No newline at end of file diff --git a/ei_nets/index.rst b/ei_nets/index.rst new file mode 100644 index 0000000..a9db01d --- /dev/null +++ b/ei_nets/index.rst @@ -0,0 +1,8 @@ +.. toctree:: + :maxdepth: 1 + + Vreeswijk_1996_EI_net.ipynb + Brette_2007_COBA.ipynb + Brette_2007_CUBA.ipynb + Brette_2007_COBAHH.ipynb + Tian_2020_EI_net_for_fast_response.ipynb diff --git a/gj_nets/index.rst b/gj_nets/index.rst new file mode 100644 index 0000000..29a70b2 --- /dev/null +++ b/gj_nets/index.rst @@ -0,0 +1,4 @@ +.. toctree:: + :maxdepth: 1 + + Sherman_1992_gj_antisynchrony.ipynb \ No newline at end of file diff --git a/index.rst b/index.rst index dad88a1..f42cc9a 100644 --- a/index.rst +++ b/index.rst @@ -10,17 +10,14 @@ to implement various neuron models or network models. :maxdepth: 1 :caption: Neuron Models - neurons/Izhikevich_2003_Izhikevich_model.ipynb - neurons/Romain_2004_LIF_phase_locking.ipynb - neurons/Gerstner_2005_AdExIF_model.ipynb - neurons/Niebur_2009_GIF.ipynb + neurons/index.rst .. toctree:: :maxdepth: 1 :caption: Continuous-attractor Network - cann/Wu_2008_CANN.ipynb + cann/index.rst @@ -28,8 +25,7 @@ to implement various neuron models or network models. :maxdepth: 1 :caption: Decision Making Model - decision_making/Wang_2002_decision_making_spiking.ipynb - decision_making/Wang_2006_decision_making_rate.ipynb + decision_making/index.rst @@ -37,11 +33,7 @@ to implement various neuron models or network models. :maxdepth: 1 :caption: E/I Balanced Network - ei_nets/Vreeswijk_1996_EI_net.ipynb - ei_nets/Brette_2007_COBA.ipynb - ei_nets/Brette_2007_CUBA.ipynb - ei_nets/Brette_2007_COBAHH.ipynb - ei_nets/Tian_2020_EI_net_for_fast_response.ipynb + ei_nets/index.rst @@ -49,7 +41,7 @@ to implement various neuron models or network models. :maxdepth: 1 :caption: Gap Junction Network - gj_nets/Sherman_1992_gj_antisynchrony.ipynb + gj_nets/index.rst @@ -57,9 +49,7 @@ to implement various neuron models or network models. :maxdepth: 1 :caption: Oscillation and Synchronization - oscillation_synchronization/Wang_1996_gamma_oscillation.ipynb - oscillation_synchronization/Brunel_Hakim_1999_fast_oscillation.ipynb - oscillation_synchronization/Diesmann_1999_synfire_chains.ipynb + oscillation_synchronization/index.rst .. toctree:: @@ -71,13 +61,7 @@ to implement various neuron models or network models. :maxdepth: 1 :caption: Recurrent Neural Network - recurrent_networks/Sussillo_Abbott_2009_FORCE_Learning.ipynb - recurrent_networks/Laje_Buonomano_2013_robust_timing_rnn.ipynb - recurrent_networks/integrator_rnn.ipynb - recurrent_networks/ParametricWorkingMemory.ipynb - recurrent_networks/Song_2016_EI_RNN.ipynb - recurrent_networks/Masse_2019_STP_RNN.ipynb - recurrent_networks/Yang_2020_RNN_Analysis.ipynb + recurrent_networks/index.rst @@ -85,25 +69,14 @@ to implement various neuron models or network models. :maxdepth: 1 :caption: Working Memory Model - working_memory/Mi_2017_working_memory_capacity.ipynb - working_memory/Bouchacourt_2019_Flexible_working_memory.ipynb - ../recurrent_networks/Masse_2019_STP_RNN.ipynb - + working_memory/index.rst .. toctree:: :maxdepth: 1 :caption: Dynamics Analysis - dynamics_analysis/1d_simple_systems.ipynb - dynamics_analysis/2d_decision_making_model.ipynb - ../decision_making/Wang_2006_decision_making_rate.ipynb - dynamics_analysis/2d_fitzhugh_nagumo_model.ipynb - dynamics_analysis/2d_NaK_model.ipynb - dynamics_analysis/3d_hindmarsh_rose_model.ipynb - dynamics_analysis/highdim_CANN.ipynb - dynamics_analysis/highdim_gj_coupled_fhn.ipynb - ../recurrent_networks/Yang_2020_RNN_Analysis.ipynb + dynamics_analysis/index.rst diff --git a/neurons/index.rst b/neurons/index.rst new file mode 100644 index 0000000..de2340a --- /dev/null +++ b/neurons/index.rst @@ -0,0 +1,7 @@ +.. toctree:: + :maxdepth: 1 + + Izhikevich_2003_Izhikevich_model.ipynb + Romain_2004_LIF_phase_locking.ipynb + Gerstner_2005_AdExIF_model.ipynb + Niebur_2009_GIF.ipynb diff --git a/oscillation_synchronization/index.rst b/oscillation_synchronization/index.rst new file mode 100644 index 0000000..959ef55 --- /dev/null +++ b/oscillation_synchronization/index.rst @@ -0,0 +1,6 @@ +.. toctree:: + :maxdepth: 1 + + Wang_1996_gamma_oscillation.ipynb + Brunel_Hakim_1999_fast_oscillation.ipynb + Diesmann_1999_synfire_chains.ipynb diff --git a/recurrent_networks/index.rst b/recurrent_networks/index.rst new file mode 100644 index 0000000..e38ccf5 --- /dev/null +++ b/recurrent_networks/index.rst @@ -0,0 +1,10 @@ +.. toctree:: + :maxdepth: 1 + + Sussillo_Abbott_2009_FORCE_Learning.ipynb + Laje_Buonomano_2013_robust_timing_rnn.ipynb + integrator_rnn.ipynb + ParametricWorkingMemory.ipynb + Song_2016_EI_RNN.ipynb + Masse_2019_STP_RNN.ipynb + Yang_2020_RNN_Analysis.ipynb diff --git a/working_memory/index.rst b/working_memory/index.rst new file mode 100644 index 0000000..a7fbc7b --- /dev/null +++ b/working_memory/index.rst @@ -0,0 +1,6 @@ +.. toctree:: + :maxdepth: 1 + + Bouchacourt_2019_Flexible_working_memory.ipynb + Mi_2017_working_memory_capacity.ipynb + ../recurrent_networks/Masse_2019_STP_RNN.ipynb