diff --git a/doc/models_library/aeif_cond_alpha_characterisation.rst b/doc/models_library/aeif_cond_alpha_characterisation.rst deleted file mode 100644 index c88e62822..000000000 --- a/doc/models_library/aeif_cond_alpha_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[aeif_cond_alpha]_synaptic_response.png - :alt: aeif_cond_alpha_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[aeif_cond_alpha]_f-I_curve.png - :alt: aeif_cond_alpha_neuron - diff --git a/doc/models_library/aeif_cond_alpha.rst b/doc/models_library/aeif_cond_alpha_neuron.rst similarity index 83% rename from doc/models_library/aeif_cond_alpha.rst rename to doc/models_library/aeif_cond_alpha_neuron.rst index 7a7d56913..7c55cc008 100644 --- a/doc/models_library/aeif_cond_alpha.rst +++ b/doc/models_library/aeif_cond_alpha_neuron.rst @@ -1,5 +1,5 @@ -aeif_cond_alpha -############### +aeif_cond_alpha_neuron +###################### aeif_cond_alpha - Conductance based exponential integrate-and-fire neuron model @@ -50,22 +50,22 @@ Parameters :widths: auto - "C_m", "pF", "281.0pF", "membrane parametersMembrane Capacitance" + "C_m", "pF", "281.0pF", "Membrane Capacitance" "refr_T", "ms", "2ms", "Duration of refractory period" "V_reset", "mV", "-60.0mV", "Reset Potential" "g_L", "nS", "30.0nS", "Leak Conductance" "E_L", "mV", "-70.6mV", "Leak reversal Potential (aka resting potential)" - "a", "nS", "4nS", "spike adaptation parametersSubthreshold adaptation" + "a", "nS", "4nS", "Subthreshold adaptation" "b", "pA", "80.5pA", "Spike-triggered adaptation" "Delta_T", "mV", "2.0mV", "Slope factor" "tau_w", "ms", "144.0ms", "Adaptation time constant" "V_th", "mV", "-50.4mV", "Threshold Potential" "V_peak", "mV", "0mV", "Spike detection threshold" - "E_exc", "mV", "0mV", "synaptic parametersExcitatory reversal Potential" + "E_exc", "mV", "0mV", "Excitatory reversal Potential" "tau_syn_exc", "ms", "0.2ms", "Synaptic Time Constant Excitatory Synapse" "E_inh", "mV", "-85.0mV", "Inhibitory reversal Potential" "tau_syn_inh", "ms", "2.0ms", "Synaptic Time Constant for Inhibitory Synapse" - "I_e", "pA", "0pA", "constant external input current" + "I_e", "pA", "0pA", "Constant external input current" @@ -101,14 +101,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `aeif_cond_alpha `_. +The model source code can be found in the NESTML models repository here: `aeif_cond_alpha_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: aeif_cond_alpha_characterisation.rst +.. include:: aeif_cond_alpha_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.055963 \ No newline at end of file + Generated at 2024-05-22 14:51:14.532753 \ No newline at end of file diff --git a/doc/models_library/aeif_cond_exp_characterisation.rst b/doc/models_library/aeif_cond_exp_characterisation.rst deleted file mode 100644 index 40e78bf2c..000000000 --- a/doc/models_library/aeif_cond_exp_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[aeif_cond_exp]_synaptic_response.png - :alt: aeif_cond_exp_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[aeif_cond_exp]_f-I_curve.png - :alt: aeif_cond_exp_neuron - diff --git a/doc/models_library/aeif_cond_exp.rst b/doc/models_library/aeif_cond_exp_neuron.rst similarity index 92% rename from doc/models_library/aeif_cond_exp.rst rename to doc/models_library/aeif_cond_exp_neuron.rst index bbecca498..c2978cf53 100644 --- a/doc/models_library/aeif_cond_exp.rst +++ b/doc/models_library/aeif_cond_exp_neuron.rst @@ -1,5 +1,5 @@ -aeif_cond_exp -############# +aeif_cond_exp_neuron +#################### aeif_cond_exp - Conductance based exponential integrate-and-fire neuron model @@ -102,14 +102,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `aeif_cond_exp `_. +The model source code can be found in the NESTML models repository here: `aeif_cond_exp_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: aeif_cond_exp_characterisation.rst +.. include:: aeif_cond_exp_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.284516 \ No newline at end of file + Generated at 2024-05-22 14:51:14.484055 \ No newline at end of file diff --git a/doc/models_library/aeif_cond_exp_neuron_characterisation.rst b/doc/models_library/aeif_cond_exp_neuron_characterisation.rst new file mode 100644 index 000000000..7d334b174 --- /dev/null +++ b/doc/models_library/aeif_cond_exp_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[aeif_cond_exp_neuron_nestml].png + :alt: aeif_cond_exp_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[aeif_cond_exp_neuron_nestml].png + :alt: aeif_cond_exp_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[aeif_cond_exp_neuron_nestml].png + :alt: aeif_cond_exp_neuron f-I curve + diff --git a/doc/models_library/hh_cond_exp_destexhe.rst b/doc/models_library/hh_cond_exp_destexhe_neuron.rst similarity index 94% rename from doc/models_library/hh_cond_exp_destexhe.rst rename to doc/models_library/hh_cond_exp_destexhe_neuron.rst index 1f4e535b2..572ffbeab 100644 --- a/doc/models_library/hh_cond_exp_destexhe.rst +++ b/doc/models_library/hh_cond_exp_destexhe_neuron.rst @@ -1,5 +1,5 @@ -hh_cond_exp_destexhe -#################### +hh_cond_exp_destexhe_neuron +########################### hh_cond_exp_destexhe - Hodgin Huxley based model, Traub, Destexhe and Mainen modified @@ -118,14 +118,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `hh_cond_exp_destexhe `_. +The model source code can be found in the NESTML models repository here: `hh_cond_exp_destexhe_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: hh_cond_exp_destexhe_characterisation.rst +.. include:: hh_cond_exp_destexhe_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.935360 \ No newline at end of file + Generated at 2024-05-22 14:51:14.490875 \ No newline at end of file diff --git a/doc/models_library/hh_cond_exp_traub_characterisation.rst b/doc/models_library/hh_cond_exp_traub_characterisation.rst deleted file mode 100644 index 4f5458f90..000000000 --- a/doc/models_library/hh_cond_exp_traub_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[hh_cond_exp_traub]_synaptic_response.png - :alt: hh_cond_exp_traub_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[hh_cond_exp_traub]_f-I_curve.png - :alt: hh_cond_exp_traub_neuron - diff --git a/doc/models_library/hh_cond_exp_traub.rst b/doc/models_library/hh_cond_exp_traub_neuron.rst similarity index 94% rename from doc/models_library/hh_cond_exp_traub.rst rename to doc/models_library/hh_cond_exp_traub_neuron.rst index 0656ac442..329a11c3c 100644 --- a/doc/models_library/hh_cond_exp_traub.rst +++ b/doc/models_library/hh_cond_exp_traub_neuron.rst @@ -1,5 +1,5 @@ -hh_cond_exp_traub -################# +hh_cond_exp_traub_neuron +######################## hh_cond_exp_traub - Hodgkin-Huxley model for Brette et al (2007) review @@ -122,14 +122,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `hh_cond_exp_traub `_. +The model source code can be found in the NESTML models repository here: `hh_cond_exp_traub_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: hh_cond_exp_traub_characterisation.rst +.. include:: hh_cond_exp_traub_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.801490 \ No newline at end of file + Generated at 2024-05-22 14:51:14.653714 \ No newline at end of file diff --git a/doc/models_library/hh_cond_exp_traub_neuron_characterisation.rst b/doc/models_library/hh_cond_exp_traub_neuron_characterisation.rst new file mode 100644 index 000000000..b4f1c86d0 --- /dev/null +++ b/doc/models_library/hh_cond_exp_traub_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[hh_cond_exp_traub_neuron_nestml].png + :alt: hh_cond_exp_traub_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[hh_cond_exp_traub_neuron_nestml].png + :alt: hh_cond_exp_traub_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[hh_cond_exp_traub_neuron_nestml].png + :alt: hh_cond_exp_traub_neuron f-I curve + diff --git a/doc/models_library/hh_moto_5ht.rst b/doc/models_library/hh_moto_5ht_neuron.rst similarity index 94% rename from doc/models_library/hh_moto_5ht.rst rename to doc/models_library/hh_moto_5ht_neuron.rst index e1c23e0dc..6ea66fc38 100644 --- a/doc/models_library/hh_moto_5ht.rst +++ b/doc/models_library/hh_moto_5ht_neuron.rst @@ -1,5 +1,5 @@ -hh_moto_5ht -########### +hh_moto_5ht_neuron +################## hh_moto_5ht_nestml - a motor neuron model in HH formalism with 5HT modulation @@ -126,14 +126,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `hh_moto_5ht `_. +The model source code can be found in the NESTML models repository here: `hh_moto_5ht_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: hh_moto_5ht_characterisation.rst +.. include:: hh_moto_5ht_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.883052 \ No newline at end of file + Generated at 2024-05-22 14:51:14.627082 \ No newline at end of file diff --git a/doc/models_library/hh_psc_alpha_characterisation.rst b/doc/models_library/hh_psc_alpha_characterisation.rst deleted file mode 100644 index 0d53a5593..000000000 --- a/doc/models_library/hh_psc_alpha_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[hh_psc_alpha]_synaptic_response.png - :alt: hh_psc_alpha_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[hh_psc_alpha]_f-I_curve.png - :alt: hh_psc_alpha_neuron - diff --git a/doc/models_library/hh_psc_alpha.rst b/doc/models_library/hh_psc_alpha_neuron.rst similarity index 93% rename from doc/models_library/hh_psc_alpha.rst rename to doc/models_library/hh_psc_alpha_neuron.rst index 33302469e..d21c56d83 100644 --- a/doc/models_library/hh_psc_alpha.rst +++ b/doc/models_library/hh_psc_alpha_neuron.rst @@ -1,5 +1,5 @@ -hh_psc_alpha -############ +hh_psc_alpha_neuron +################### hh_psc_alpha - Hodgkin-Huxley neuron model @@ -110,14 +110,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `hh_psc_alpha `_. +The model source code can be found in the NESTML models repository here: `hh_psc_alpha_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: hh_psc_alpha_characterisation.rst +.. include:: hh_psc_alpha_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.850147 \ No newline at end of file + Generated at 2024-05-22 14:51:14.446835 \ No newline at end of file diff --git a/doc/models_library/hh_psc_alpha_neuron_characterisation.rst b/doc/models_library/hh_psc_alpha_neuron_characterisation.rst new file mode 100644 index 000000000..6dab13d8a --- /dev/null +++ b/doc/models_library/hh_psc_alpha_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[hh_psc_alpha_neuron_nestml].png + :alt: hh_psc_alpha_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[hh_psc_alpha_neuron_nestml].png + :alt: hh_psc_alpha_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[hh_psc_alpha_neuron_nestml].png + :alt: hh_psc_alpha_neuron f-I curve + diff --git a/doc/models_library/hill_tononi.rst b/doc/models_library/hill_tononi_neuron.rst similarity index 95% rename from doc/models_library/hill_tononi.rst rename to doc/models_library/hill_tononi_neuron.rst index 93ccabbdf..586fd47d2 100644 --- a/doc/models_library/hill_tononi.rst +++ b/doc/models_library/hill_tononi_neuron.rst @@ -1,5 +1,5 @@ -hill_tononi -########### +hill_tononi_neuron +################## hill_tononi - Neuron model after Hill & Tononi (2005) @@ -142,14 +142,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `hill_tononi `_. +The model source code can be found in the NESTML models repository here: `hill_tononi_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: hill_tononi_characterisation.rst +.. include:: hill_tononi_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.143368 \ No newline at end of file + Generated at 2024-05-22 14:51:14.539823 \ No newline at end of file diff --git a/doc/models_library/iaf_chxk_2008.rst b/doc/models_library/iaf_chxk_2008_neuron.rst similarity index 91% rename from doc/models_library/iaf_chxk_2008.rst rename to doc/models_library/iaf_chxk_2008_neuron.rst index 25a207e28..191296824 100644 --- a/doc/models_library/iaf_chxk_2008.rst +++ b/doc/models_library/iaf_chxk_2008_neuron.rst @@ -1,5 +1,5 @@ -iaf_chxk_2008 -############# +iaf_chxk_2008_neuron +#################### iaf_chxk_2008 - Conductance based leaky integrate-and-fire neuron model used in Casti et al. 2008 @@ -92,14 +92,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_chxk_2008 `_. +The model source code can be found in the NESTML models repository here: `iaf_chxk_2008_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_chxk_2008_characterisation.rst +.. include:: iaf_chxk_2008_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.989187 \ No newline at end of file + Generated at 2024-05-22 14:51:14.647974 \ No newline at end of file diff --git a/doc/models_library/iaf_chxk_2008_neuron_characterisation.rst b/doc/models_library/iaf_chxk_2008_neuron_characterisation.rst new file mode 100644 index 000000000..be31432a9 --- /dev/null +++ b/doc/models_library/iaf_chxk_2008_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_chxk_2008_neuron_nestml].png + :alt: iaf_chxk_2008_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_chxk_2008_neuron_nestml].png + :alt: iaf_chxk_2008_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_chxk_2008_neuron_nestml].png + :alt: iaf_chxk_2008_neuron f-I curve + diff --git a/doc/models_library/iaf_cond_alpha_characterisation.rst b/doc/models_library/iaf_cond_alpha_characterisation.rst deleted file mode 100644 index c652ebb24..000000000 --- a/doc/models_library/iaf_cond_alpha_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_alpha]_synaptic_response.png - :alt: iaf_cond_alpha_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_alpha]_f-I_curve.png - :alt: iaf_cond_alpha_neuron - diff --git a/doc/models_library/iaf_cond_alpha.rst b/doc/models_library/iaf_cond_alpha_neuron.rst similarity index 90% rename from doc/models_library/iaf_cond_alpha.rst rename to doc/models_library/iaf_cond_alpha_neuron.rst index 3b778ce06..23fb80742 100644 --- a/doc/models_library/iaf_cond_alpha.rst +++ b/doc/models_library/iaf_cond_alpha_neuron.rst @@ -1,5 +1,5 @@ -iaf_cond_alpha -############## +iaf_cond_alpha_neuron +##################### iaf_cond_alpha - Simple conductance based leaky integrate-and-fire neuron model @@ -88,14 +88,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_cond_alpha `_. +The model source code can be found in the NESTML models repository here: `iaf_cond_alpha_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_cond_alpha_characterisation.rst +.. include:: iaf_cond_alpha_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.088874 \ No newline at end of file + Generated at 2024-05-22 14:51:14.597480 \ No newline at end of file diff --git a/doc/models_library/iaf_cond_alpha_neuron_characterisation.rst b/doc/models_library/iaf_cond_alpha_neuron_characterisation.rst new file mode 100644 index 000000000..91fb496a6 --- /dev/null +++ b/doc/models_library/iaf_cond_alpha_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_cond_alpha_neuron_nestml].png + :alt: iaf_cond_alpha_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_cond_alpha_neuron_nestml].png + :alt: iaf_cond_alpha_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_cond_alpha_neuron_nestml].png + :alt: iaf_cond_alpha_neuron f-I curve + diff --git a/doc/models_library/iaf_cond_beta_characterisation.rst b/doc/models_library/iaf_cond_beta_characterisation.rst deleted file mode 100644 index 39367c85b..000000000 --- a/doc/models_library/iaf_cond_beta_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_beta]_synaptic_response.png - :alt: iaf_cond_beta_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_beta]_f-I_curve.png - :alt: iaf_cond_beta_neuron - diff --git a/doc/models_library/iaf_cond_beta.rst b/doc/models_library/iaf_cond_beta_neuron.rst similarity index 93% rename from doc/models_library/iaf_cond_beta.rst rename to doc/models_library/iaf_cond_beta_neuron.rst index 7e4515189..c07e1c076 100644 --- a/doc/models_library/iaf_cond_beta.rst +++ b/doc/models_library/iaf_cond_beta_neuron.rst @@ -1,5 +1,5 @@ -iaf_cond_beta -############# +iaf_cond_beta_neuron +#################### iaf_cond_beta - Simple conductance based leaky integrate-and-fire neuron model @@ -104,14 +104,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_cond_beta `_. +The model source code can be found in the NESTML models repository here: `iaf_cond_beta_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_cond_beta_characterisation.rst +.. include:: iaf_cond_beta_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.839983 \ No newline at end of file + Generated at 2024-05-22 14:51:14.643932 \ No newline at end of file diff --git a/doc/models_library/iaf_cond_beta_neuron_characterisation.rst b/doc/models_library/iaf_cond_beta_neuron_characterisation.rst new file mode 100644 index 000000000..1ca6d71f9 --- /dev/null +++ b/doc/models_library/iaf_cond_beta_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_cond_beta_neuron_nestml].png + :alt: iaf_cond_beta_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_cond_beta_neuron_nestml].png + :alt: iaf_cond_beta_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_cond_beta_neuron_nestml].png + :alt: iaf_cond_beta_neuron f-I curve + diff --git a/doc/models_library/iaf_cond_exp_characterisation.rst b/doc/models_library/iaf_cond_exp_characterisation.rst deleted file mode 100644 index 215c24c67..000000000 --- a/doc/models_library/iaf_cond_exp_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_exp]_synaptic_response.png - :alt: iaf_cond_exp_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_exp]_f-I_curve.png - :alt: iaf_cond_exp_neuron - diff --git a/doc/models_library/iaf_cond_exp.rst b/doc/models_library/iaf_cond_exp_neuron.rst similarity index 89% rename from doc/models_library/iaf_cond_exp.rst rename to doc/models_library/iaf_cond_exp_neuron.rst index 2422a7bcf..9c05bf7cd 100644 --- a/doc/models_library/iaf_cond_exp.rst +++ b/doc/models_library/iaf_cond_exp_neuron.rst @@ -1,5 +1,5 @@ -iaf_cond_exp -############ +iaf_cond_exp_neuron +################### iaf_cond_exp - Simple conductance based leaky integrate-and-fire neuron model @@ -78,14 +78,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_cond_exp `_. +The model source code can be found in the NESTML models repository here: `iaf_cond_exp_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_cond_exp_characterisation.rst +.. include:: iaf_cond_exp_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.122450 \ No newline at end of file + Generated at 2024-05-22 14:51:14.600957 \ No newline at end of file diff --git a/doc/models_library/iaf_cond_exp_neuron_characterisation.rst b/doc/models_library/iaf_cond_exp_neuron_characterisation.rst new file mode 100644 index 000000000..f3c44f598 --- /dev/null +++ b/doc/models_library/iaf_cond_exp_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_cond_exp_neuron_nestml].png + :alt: iaf_cond_exp_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_cond_exp_neuron_nestml].png + :alt: iaf_cond_exp_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_cond_exp_neuron_nestml].png + :alt: iaf_cond_exp_neuron f-I curve + diff --git a/doc/models_library/iaf_cond_exp_sfa_rr.rst b/doc/models_library/iaf_cond_exp_sfa_rr_neuron.rst similarity index 92% rename from doc/models_library/iaf_cond_exp_sfa_rr.rst rename to doc/models_library/iaf_cond_exp_sfa_rr_neuron.rst index b6316329d..c1fafc1da 100644 --- a/doc/models_library/iaf_cond_exp_sfa_rr.rst +++ b/doc/models_library/iaf_cond_exp_sfa_rr_neuron.rst @@ -1,5 +1,5 @@ -iaf_cond_exp_sfa_rr -################### +iaf_cond_exp_sfa_rr_neuron +########################## iaf_cond_exp_sfa_rr - Conductance based leaky integrate-and-fire model with spike-frequency adaptation and relative refractory mechanisms @@ -100,14 +100,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_cond_exp_sfa_rr `_. +The model source code can be found in the NESTML models repository here: `iaf_cond_exp_sfa_rr_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_cond_exp_sfa_rr_characterisation.rst +.. include:: iaf_cond_exp_sfa_rr_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.920345 \ No newline at end of file + Generated at 2024-05-22 14:51:14.587435 \ No newline at end of file diff --git a/doc/models_library/iaf_cond_exp_sfa_rr_neuron_characterisation.rst b/doc/models_library/iaf_cond_exp_sfa_rr_neuron_characterisation.rst new file mode 100644 index 000000000..9cfb191df --- /dev/null +++ b/doc/models_library/iaf_cond_exp_sfa_rr_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_cond_exp_sfa_rr_neuron_nestml].png + :alt: iaf_cond_exp_sfa_rr_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_cond_exp_sfa_rr_neuron_nestml].png + :alt: iaf_cond_exp_sfa_rr_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_cond_exp_sfa_rr_neuron_nestml].png + :alt: iaf_cond_exp_sfa_rr_neuron f-I curve + diff --git a/doc/models_library/iaf_psc_alpha_characterisation.rst b/doc/models_library/iaf_psc_alpha_characterisation.rst deleted file mode 100644 index 63d414d90..000000000 --- a/doc/models_library/iaf_psc_alpha_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_alpha]_synaptic_response.png - :alt: iaf_psc_alpha_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_alpha]_f-I_curve.png - :alt: iaf_psc_alpha_neuron - diff --git a/doc/models_library/iaf_psc_alpha.rst b/doc/models_library/iaf_psc_alpha_neuron.rst similarity index 92% rename from doc/models_library/iaf_psc_alpha.rst rename to doc/models_library/iaf_psc_alpha_neuron.rst index 28e4fd532..442824c10 100644 --- a/doc/models_library/iaf_psc_alpha.rst +++ b/doc/models_library/iaf_psc_alpha_neuron.rst @@ -1,5 +1,5 @@ -iaf_psc_alpha -############# +iaf_psc_alpha_neuron +#################### iaf_psc_alpha - Leaky integrate-and-fire neuron model @@ -107,14 +107,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_psc_alpha `_. +The model source code can be found in the NESTML models repository here: `iaf_psc_alpha_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_psc_alpha_characterisation.rst +.. include:: iaf_psc_alpha_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.193173 \ No newline at end of file + Generated at 2024-05-22 14:51:14.609049 \ No newline at end of file diff --git a/doc/models_library/iaf_psc_alpha_neuron_characterisation.rst b/doc/models_library/iaf_psc_alpha_neuron_characterisation.rst new file mode 100644 index 000000000..934683581 --- /dev/null +++ b/doc/models_library/iaf_psc_alpha_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_psc_alpha_neuron_nestml].png + :alt: iaf_psc_alpha_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_psc_alpha_neuron_nestml].png + :alt: iaf_psc_alpha_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_psc_alpha_neuron_nestml].png + :alt: iaf_psc_alpha_neuron f-I curve + diff --git a/doc/models_library/iaf_psc_delta_characterisation.rst b/doc/models_library/iaf_psc_delta_characterisation.rst deleted file mode 100644 index f39cd970e..000000000 --- a/doc/models_library/iaf_psc_delta_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_delta]_synaptic_response.png - :alt: iaf_psc_delta_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_delta]_f-I_curve.png - :alt: iaf_psc_delta_neuron - diff --git a/doc/models_library/iaf_psc_delta.rst b/doc/models_library/iaf_psc_delta_neuron.rst similarity index 79% rename from doc/models_library/iaf_psc_delta.rst rename to doc/models_library/iaf_psc_delta_neuron.rst index 338dd53e9..da0283e3d 100644 --- a/doc/models_library/iaf_psc_delta.rst +++ b/doc/models_library/iaf_psc_delta_neuron.rst @@ -1,5 +1,5 @@ -iaf_psc_delta -############# +iaf_psc_delta_neuron +#################### iaf_psc_delta - Current-based leaky integrate-and-fire neuron model with delta-kernel post-synaptic currents @@ -23,15 +23,6 @@ The general framework for the consistent formulation of systems with neuron like dynamics interacting by point events is described in [1]_. A flow chart can be found in [2]_. -Critical tests for the formulation of the neuron model are the -comparisons of simulation results for different computation step -sizes. sli/testsuite/nest contains a number of such tests. - -The iaf_psc_delta is the standard model used to check the consistency -of the nest simulation kernel because it is at the same time complex -enough to exhibit non-trivial dynamics and simple enough compute -relevant measures analytically. - References ++++++++++ @@ -100,14 +91,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_psc_delta `_. - -Characterisation -++++++++++++++++ +The model source code can be found in the NESTML models repository here: `iaf_psc_delta_neuron `_. -.. include:: iaf_psc_delta_characterisation.rst +.. include:: iaf_psc_delta_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.305247 \ No newline at end of file + Generated at 2024-05-22 14:51:14.604392 \ No newline at end of file diff --git a/doc/models_library/iaf_psc_delta_neuron_characterisation.rst b/doc/models_library/iaf_psc_delta_neuron_characterisation.rst new file mode 100644 index 000000000..1b6036734 --- /dev/null +++ b/doc/models_library/iaf_psc_delta_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_psc_delta_neuron_nestml].png + :alt: iaf_psc_delta_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_psc_delta_neuron_nestml].png + :alt: iaf_psc_delta_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_psc_delta_neuron_nestml].png + :alt: iaf_psc_delta_neuron f-I curve + diff --git a/doc/models_library/iaf_psc_exp_characterisation.rst b/doc/models_library/iaf_psc_exp_characterisation.rst deleted file mode 100644 index 7605c85a7..000000000 --- a/doc/models_library/iaf_psc_exp_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_exp]_synaptic_response.png - :alt: iaf_psc_exp_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_exp]_f-I_curve.png - :alt: iaf_psc_exp_neuron - diff --git a/doc/models_library/iaf_psc_exp_dend.rst b/doc/models_library/iaf_psc_exp_dend_neuron.rst similarity index 89% rename from doc/models_library/iaf_psc_exp_dend.rst rename to doc/models_library/iaf_psc_exp_dend_neuron.rst index 5e559fde4..ce4c6f49e 100644 --- a/doc/models_library/iaf_psc_exp_dend.rst +++ b/doc/models_library/iaf_psc_exp_dend_neuron.rst @@ -1,5 +1,5 @@ -iaf_psc_exp_dend -################ +iaf_psc_exp_dend_neuron +####################### iaf_psc_exp_dend - Leaky integrate-and-fire neuron model with exponential PSCs @@ -87,14 +87,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_psc_exp_dend `_. +The model source code can be found in the NESTML models repository here: `iaf_psc_exp_dend_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_psc_exp_dend_characterisation.rst +.. include:: iaf_psc_exp_dend_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.318084 \ No newline at end of file + Generated at 2024-05-22 14:51:14.593810 \ No newline at end of file diff --git a/doc/models_library/iaf_psc_exp_htum.rst b/doc/models_library/iaf_psc_exp_htum_neuron.rst similarity index 93% rename from doc/models_library/iaf_psc_exp_htum.rst rename to doc/models_library/iaf_psc_exp_htum_neuron.rst index e044f54da..b7f48f676 100644 --- a/doc/models_library/iaf_psc_exp_htum.rst +++ b/doc/models_library/iaf_psc_exp_htum_neuron.rst @@ -1,5 +1,5 @@ -iaf_psc_exp_htum -################ +iaf_psc_exp_htum_neuron +####################### iaf_psc_exp_htum - Leaky integrate-and-fire model with separate relative and absolute refractory period @@ -102,14 +102,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_psc_exp_htum `_. +The model source code can be found in the NESTML models repository here: `iaf_psc_exp_htum_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_psc_exp_htum_characterisation.rst +.. include:: iaf_psc_exp_htum_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.874736 \ No newline at end of file + Generated at 2024-05-22 14:51:14.504836 \ No newline at end of file diff --git a/doc/models_library/iaf_psc_exp.rst b/doc/models_library/iaf_psc_exp_neuron.rst similarity index 93% rename from doc/models_library/iaf_psc_exp.rst rename to doc/models_library/iaf_psc_exp_neuron.rst index 324eeff91..292ccd395 100644 --- a/doc/models_library/iaf_psc_exp.rst +++ b/doc/models_library/iaf_psc_exp_neuron.rst @@ -1,5 +1,5 @@ -iaf_psc_exp -########### +iaf_psc_exp_neuron +################## iaf_psc_exp - Leaky integrate-and-fire neuron model @@ -111,14 +111,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `iaf_psc_exp `_. +The model source code can be found in the NESTML models repository here: `iaf_psc_exp_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: iaf_psc_exp_characterisation.rst +.. include:: iaf_psc_exp_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.130225 \ No newline at end of file + Generated at 2024-05-22 14:51:14.522280 \ No newline at end of file diff --git a/doc/models_library/iaf_psc_exp_neuron_characterisation.rst b/doc/models_library/iaf_psc_exp_neuron_characterisation.rst new file mode 100644 index 000000000..5c9f3708a --- /dev/null +++ b/doc/models_library/iaf_psc_exp_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_psc_exp_neuron_nestml].png + :alt: iaf_psc_exp_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_psc_exp_neuron_nestml].png + :alt: iaf_psc_exp_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_psc_exp_neuron_nestml].png + :alt: iaf_psc_exp_neuron f-I curve + diff --git a/doc/models_library/ignore_and_fire.rst b/doc/models_library/ignore_and_fire_neuron.rst similarity index 89% rename from doc/models_library/ignore_and_fire.rst rename to doc/models_library/ignore_and_fire_neuron.rst index 15bba03fd..ce902ab39 100644 --- a/doc/models_library/ignore_and_fire.rst +++ b/doc/models_library/ignore_and_fire_neuron.rst @@ -1,5 +1,5 @@ -ignore_and_fire -############### +ignore_and_fire_neuron +###################### ignore_and_fire - Neuron generating spikes at fixed intervals irrespective of inputs @@ -60,14 +60,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `ignore_and_fire `_. +The model source code can be found in the NESTML models repository here: `ignore_and_fire_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: ignore_and_fire_characterisation.rst +.. include:: ignore_and_fire_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.002509 \ No newline at end of file + Generated at 2024-05-22 14:51:14.532290 \ No newline at end of file diff --git a/doc/models_library/index.rst b/doc/models_library/index.rst index f95ca9a89..8f67ba68e 100644 --- a/doc/models_library/index.rst +++ b/doc/models_library/index.rst @@ -5,319 +5,452 @@ Neuron models ~~~~~~~~~~~~~ -:doc:`iaf_psc_delta ` ------------------------------------- +:doc:`aeif_cond_alpha_neuron ` +------------------------------------------------------ -Current-based leaky integrate-and-fire neuron model with delta-kernel post-synaptic currents +aeif_cond_alpha - Conductance based exponential integrate-and-fire neuron model -Source file: `iaf_psc_delta_neuron.nestml `_ +Source file: `aeif_cond_alpha_neuron.nestml `_ + + +:doc:`aeif_cond_exp_neuron ` +-------------------------------------------------- + +aeif_cond_exp - Conductance based exponential integrate-and-fire neuron model + +Source file: `aeif_cond_exp_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_delta]_synaptic_response_small.png - :alt: iaf_psc_delta + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[aeif_cond_exp_neuron_nestml]_small.png + :alt: aeif_cond_exp_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_delta]_f-I_curve_small.png - :alt: iaf_psc_delta + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[aeif_cond_exp_neuron_nestml]_small.png + :alt: aeif_cond_exp_neuron -:doc:`iaf_psc_exp ` --------------------------------- + Step current response -Leaky integrate-and-fire neuron model + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[aeif_cond_exp_neuron_nestml]_small.png + :alt: aeif_cond_exp_neuron -Source file: `iaf_psc_exp_neuron.nestml `_ + Firing rate vs. current -.. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_exp]_synaptic_response_small.png - :alt: iaf_psc_exp +:doc:`hh_cond_exp_destexhe_neuron ` +---------------------------------------------------------------- - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_exp]_f-I_curve_small.png - :alt: iaf_psc_exp +hh_cond_exp_destexhe - Hodgin Huxley based model, Traub, Destexhe and Mainen modified +Source file: `hh_cond_exp_destexhe_neuron.nestml `_ -:doc:`iaf_psc_alpha ` ------------------------------------- -Leaky integrate-and-fire neuron model +:doc:`hh_cond_exp_traub_neuron ` +---------------------------------------------------------- -Source file: `iaf_psc_alpha_neuron.nestml `_ +hh_cond_exp_traub - Hodgkin-Huxley model for Brette et al (2007) review + +Source file: `hh_cond_exp_traub_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_alpha]_synaptic_response_small.png - :alt: iaf_psc_alpha + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[hh_cond_exp_traub_neuron_nestml]_small.png + :alt: hh_cond_exp_traub_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_psc_alpha]_f-I_curve_small.png - :alt: iaf_psc_alpha + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[hh_cond_exp_traub_neuron_nestml]_small.png + :alt: hh_cond_exp_traub_neuron -:doc:`iaf_cond_exp ` ----------------------------------- + Step current response -Simple conductance based leaky integrate-and-fire neuron model + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[hh_cond_exp_traub_neuron_nestml]_small.png + :alt: hh_cond_exp_traub_neuron -Source file: `iaf_cond_exp_neuron.nestml `_ + Firing rate vs. current -.. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_exp]_synaptic_response_small.png - :alt: iaf_cond_exp +:doc:`hh_moto_5ht_neuron ` +---------------------------------------------- + +hh_moto_5ht_nestml - a motor neuron model in HH formalism with 5HT modulation - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_exp]_f-I_curve_small.png - :alt: iaf_cond_exp +Source file: `hh_moto_5ht_neuron.nestml `_ -:doc:`iaf_cond_alpha ` --------------------------------------- +:doc:`hh_psc_alpha_neuron ` +------------------------------------------------ -Simple conductance based leaky integrate-and-fire neuron model +hh_psc_alpha - Hodgkin-Huxley neuron model -Source file: `iaf_cond_alpha_neuron.nestml `_ +Source file: `hh_psc_alpha_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_alpha]_synaptic_response_small.png - :alt: iaf_cond_alpha + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[hh_psc_alpha_neuron_nestml]_small.png + :alt: hh_psc_alpha_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_alpha]_f-I_curve_small.png - :alt: iaf_cond_alpha + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[hh_psc_alpha_neuron_nestml]_small.png + :alt: hh_psc_alpha_neuron -:doc:`iaf_cond_beta ` ------------------------------------- + Step current response -Simple conductance based leaky integrate-and-fire neuron model + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[hh_psc_alpha_neuron_nestml]_small.png + :alt: hh_psc_alpha_neuron -Source file: `iaf_cond_beta_neuron.nestml `_ + Firing rate vs. current + + +:doc:`hill_tononi_neuron ` +---------------------------------------------- + +hill_tononi - Neuron model after Hill & Tononi (2005) + +Source file: `hill_tononi_neuron.nestml `_ + + +:doc:`iaf_chxk_2008_neuron ` +-------------------------------------------------- + +iaf_chxk_2008 - Conductance based leaky integrate-and-fire neuron model used in Casti et al. 2008 + +Source file: `iaf_chxk_2008_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_beta]_synaptic_response_small.png - :alt: iaf_cond_beta + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_chxk_2008_neuron_nestml]_small.png + :alt: iaf_chxk_2008_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[iaf_cond_beta]_f-I_curve_small.png - :alt: iaf_cond_beta + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_chxk_2008_neuron_nestml]_small.png + :alt: iaf_chxk_2008_neuron -:doc:`izhikevich ` ------------------------------- + Step current response -Izhikevich neuron model + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_chxk_2008_neuron_nestml]_small.png + :alt: iaf_chxk_2008_neuron -Source file: `izhikevich_neuron.nestml `_ + Firing rate vs. current + + +:doc:`iaf_cond_alpha_neuron ` +---------------------------------------------------- + +iaf_cond_alpha - Simple conductance based leaky integrate-and-fire neuron model + +Source file: `iaf_cond_alpha_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[izhikevich]_synaptic_response_small.png - :alt: izhikevich + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_cond_alpha_neuron_nestml]_small.png + :alt: iaf_cond_alpha_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[izhikevich]_f-I_curve_small.png - :alt: izhikevich + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_cond_alpha_neuron_nestml]_small.png + :alt: iaf_cond_alpha_neuron -:doc:`hh_psc_alpha ` ----------------------------------- + Step current response -Hodgkin-Huxley neuron model + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_cond_alpha_neuron_nestml]_small.png + :alt: iaf_cond_alpha_neuron -Source file: `hh_psc_alpha_neuron.nestml `_ + Firing rate vs. current + + +:doc:`iaf_cond_beta_neuron ` +-------------------------------------------------- + +iaf_cond_beta - Simple conductance based leaky integrate-and-fire neuron model + +Source file: `iaf_cond_beta_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[hh_psc_alpha]_synaptic_response_small.png - :alt: hh_psc_alpha + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_cond_beta_neuron_nestml]_small.png + :alt: iaf_cond_beta_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[hh_psc_alpha]_f-I_curve_small.png - :alt: hh_psc_alpha + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_cond_beta_neuron_nestml]_small.png + :alt: iaf_cond_beta_neuron -:doc:`hh_cond_exp_traub ` --------------------------------------------- + Step current response -Hodgkin-Huxley model for Brette et al (2007) review + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_cond_beta_neuron_nestml]_small.png + :alt: iaf_cond_beta_neuron -Source file: `hh_cond_exp_traub_neuron.nestml `_ + Firing rate vs. current + + +:doc:`iaf_cond_exp_neuron ` +------------------------------------------------ + +iaf_cond_exp - Simple conductance based leaky integrate-and-fire neuron model + +Source file: `iaf_cond_exp_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[hh_cond_exp_traub]_synaptic_response_small.png - :alt: hh_cond_exp_traub + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_cond_exp_neuron_nestml]_small.png + :alt: iaf_cond_exp_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[hh_cond_exp_traub]_f-I_curve_small.png - :alt: hh_cond_exp_traub + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_cond_exp_neuron_nestml]_small.png + :alt: iaf_cond_exp_neuron -:doc:`aeif_cond_exp ` ------------------------------------- + Step current response -Conductance based exponential integrate-and-fire neuron model + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_cond_exp_neuron_nestml]_small.png + :alt: iaf_cond_exp_neuron -Source file: `aeif_cond_exp_neuron.nestml `_ + Firing rate vs. current + + +:doc:`iaf_cond_exp_sfa_rr_neuron ` +-------------------------------------------------------------- + +iaf_cond_exp_sfa_rr - Conductance based leaky integrate-and-fire model with spike-frequency adaptation and relative refractory mechanisms + +Source file: `iaf_cond_exp_sfa_rr_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[aeif_cond_exp]_synaptic_response_small.png - :alt: aeif_cond_exp + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_cond_exp_sfa_rr_neuron_nestml]_small.png + :alt: iaf_cond_exp_sfa_rr_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[aeif_cond_exp]_f-I_curve_small.png - :alt: aeif_cond_exp + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_cond_exp_sfa_rr_neuron_nestml]_small.png + :alt: iaf_cond_exp_sfa_rr_neuron -:doc:`aeif_cond_alpha ` ----------------------------------------- + Step current response -Conductance based exponential integrate-and-fire neuron model + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_cond_exp_sfa_rr_neuron_nestml]_small.png + :alt: iaf_cond_exp_sfa_rr_neuron -Source file: `aeif_cond_alpha_neuron.nestml `_ + Firing rate vs. current + + +:doc:`iaf_psc_alpha_neuron ` +-------------------------------------------------- + +iaf_psc_alpha - Leaky integrate-and-fire neuron model + +Source file: `iaf_psc_alpha_neuron.nestml `_ .. list-table:: - * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[aeif_cond_alpha]_synaptic_response_small.png - :alt: aeif_cond_alpha + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_psc_alpha_neuron_nestml]_small.png + :alt: iaf_psc_alpha_neuron - - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[aeif_cond_alpha]_f-I_curve_small.png - :alt: aeif_cond_alpha + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_psc_alpha_neuron_nestml]_small.png + :alt: iaf_psc_alpha_neuron -:doc:`mat2_psc_exp ` ----------------------------------- + Step current response -Non-resetting leaky integrate-and-fire neuron model with exponential PSCs and adaptive threshold + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_psc_alpha_neuron_nestml]_small.png + :alt: iaf_psc_alpha_neuron -Source file: `mat2_psc_exp_neuron.nestml `_ + Firing rate vs. current -:doc:`izhikevich_psc_alpha ` +:doc:`iaf_psc_delta_neuron ` -------------------------------------------------- -Detailed Izhikevich neuron model with alpha-kernel post-synaptic current +iaf_psc_delta - Current-based leaky integrate-and-fire neuron model with delta-kernel post-synaptic currents -Source file: `izhikevich_psc_alpha_neuron.nestml `_ +Source file: `iaf_psc_delta_neuron.nestml `_ +.. list-table:: -:doc:`iaf_psc_exp_htum ` ------------------------------------------- + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_psc_delta_neuron_nestml]_small.png + :alt: iaf_psc_delta_neuron -Leaky integrate-and-fire model with separate relative and absolute refractory period + Post-synaptic potential -Source file: `iaf_psc_exp_htum_neuron.nestml `_ + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_psc_delta_neuron_nestml]_small.png + :alt: iaf_psc_delta_neuron + Step current response -:doc:`hh_moto_5ht ` --------------------------------- + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_psc_delta_neuron_nestml]_small.png + :alt: iaf_psc_delta_neuron -_nestml - a motor neuron model in HH formalism with 5HT modulation + Firing rate vs. current -Source file: `hh_moto_5ht_neuron.nestml `_ +:doc:`iaf_psc_exp_dend_neuron ` +-------------------------------------------------------- -:doc:`iaf_cond_exp_sfa_rr ` ------------------------------------------------- +iaf_psc_exp_dend - Leaky integrate-and-fire neuron model with exponential PSCs -Conductance based leaky integrate-and-fire model with spike-frequency adaptation and relative refractory mechanisms +Source file: `iaf_psc_exp_dend_neuron.nestml `_ -Source file: `iaf_cond_exp_sfa_rr_neuron.nestml `_ +:doc:`iaf_psc_exp_htum_neuron ` +-------------------------------------------------------- -:doc:`hh_cond_exp_destexhe ` --------------------------------------------------- +iaf_psc_exp_htum - Leaky integrate-and-fire model with separate relative and absolute refractory period -Hodgin Huxley based model, Traub, Destexhe and Mainen modified +Source file: `iaf_psc_exp_htum_neuron.nestml `_ -Source file: `hh_cond_exp_destexhe_neuron.nestml `_ +:doc:`iaf_psc_exp_neuron ` +---------------------------------------------- -:doc:`wb_cond_multisyn ` ------------------------------------------- +iaf_psc_exp - Leaky integrate-and-fire neuron model -Wang-Buzsaki model with multiple synapses +Source file: `iaf_psc_exp_neuron.nestml `_ -Source file: `wb_cond_multisyn_neuron.nestml `_ +.. list-table:: + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_psc_exp_neuron_nestml]_small.png + :alt: iaf_psc_exp_neuron -:doc:`iaf_chxk_2008 ` ------------------------------------- + Post-synaptic potential -Conductance based leaky integrate-and-fire neuron model used in Casti et al. 2008 + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_psc_exp_neuron_nestml]_small.png + :alt: iaf_psc_exp_neuron -Source file: `iaf_chxk_2008_neuron.nestml `_ + Step current response + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_psc_exp_neuron_nestml]_small.png + :alt: iaf_psc_exp_neuron -:doc:`ignore_and_fire ` ----------------------------------------- + Firing rate vs. current -Neuron generating spikes at fixed intervals irrespective of inputs -Source file: `ignore_and_fire_neuron.nestml `_ +:doc:`ignore_and_fire_neuron ` +------------------------------------------------------ +ignore_and_fire - Neuron generating spikes at fixed intervals irrespective of inputs -:doc:`wb_cond_exp ` --------------------------------- +Source file: `ignore_and_fire_neuron.nestml `_ -Wang-Buzsaki model -Source file: `wb_cond_exp_neuron.nestml `_ +:doc:`izhikevich_neuron ` +-------------------------------------------- +izhikevich - Izhikevich neuron model -:doc:`terub_stn ` ----------------------------- +Source file: `izhikevich_neuron.nestml `_ -Terman Rubin neuron model +.. list-table:: -Source file: `terub_stn_neuron.nestml `_ + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[izhikevich_neuron_nestml]_small.png + :alt: izhikevich_neuron + Post-synaptic potential -:doc:`traub_psc_alpha ` ----------------------------------------- + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[izhikevich_neuron_nestml]_small.png + :alt: izhikevich_neuron -Traub model according to Borgers 2017 + Step current response -Source file: `traub_psc_alpha_neuron.nestml `_ + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[izhikevich_neuron_nestml]_small.png + :alt: izhikevich_neuron + Firing rate vs. current -:doc:`hill_tononi ` --------------------------------- -Neuron model after Hill & Tononi (2005) +:doc:`izhikevich_psc_alpha_neuron ` +---------------------------------------------------------------- -Source file: `hill_tononi_neuron.nestml `_ +izhikevich_psc_alpha - Detailed Izhikevich neuron model with alpha-kernel post-synaptic current + +Source file: `izhikevich_psc_alpha_neuron.nestml `_ -:doc:`traub_cond_multisyn ` +:doc:`mat2_psc_exp_neuron ` ------------------------------------------------ -Traub model according to Borgers 2017 +mat2_psc_exp - Non-resetting leaky integrate-and-fire neuron model with exponential PSCs and adaptive threshold -Source file: `traub_cond_multisyn_neuron.nestml `_ +Source file: `mat2_psc_exp_neuron.nestml `_ + +.. list-table:: + + * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[mat2_psc_exp_neuron_nestml]_small.png + :alt: mat2_psc_exp_neuron + + Post-synaptic potential + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[mat2_psc_exp_neuron_nestml]_small.png + :alt: mat2_psc_exp_neuron -:doc:`terub_gpe ` ----------------------------- + Step current response -Terman Rubin neuron model + - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[mat2_psc_exp_neuron_nestml]_small.png + :alt: mat2_psc_exp_neuron + + Firing rate vs. current + + +:doc:`terub_gpe_neuron ` +------------------------------------------ + +terub_gpe - Terman Rubin neuron model Source file: `terub_gpe_neuron.nestml `_ -:doc:`iaf_psc_exp_dend ` +:doc:`terub_stn_neuron ` ------------------------------------------ -Leaky integrate-and-fire neuron model with exponential PSCs +terub_stn - Terman Rubin neuron model -Source file: `iaf_psc_exp_dend_neuron.nestml `_ +Source file: `terub_stn_neuron.nestml `_ + + +:doc:`traub_cond_multisyn_neuron ` +-------------------------------------------------------------- + +traub_cond_multisyn - Traub model according to Borgers 2017 + +Source file: `traub_cond_multisyn_neuron.nestml `_ + + +:doc:`traub_psc_alpha_neuron ` +------------------------------------------------------ + +traub_psc_alpha - Traub model according to Borgers 2017 + +Source file: `traub_psc_alpha_neuron.nestml `_ + + +:doc:`wb_cond_exp_neuron ` +---------------------------------------------- + +wb_cond_exp - Wang-Buzsaki model + +Source file: `wb_cond_exp_neuron.nestml `_ + + +:doc:`wb_cond_multisyn_neuron ` +-------------------------------------------------------- + +wb_cond_multisyn - Wang-Buzsaki model with multiple synapses + +Source file: `wb_cond_multisyn_neuron.nestml `_ Synapse models ~~~~~~~~~~~~~~ -:doc:`static_synapse ` --------------------------------------- +:doc:`neuromodulated_stdp_synapse ` +---------------------------------------------------------------- -Static synapse +neuromodulated_stdp - Synapse model for spike-timing dependent plasticity modulated by a neurotransmitter such as dopamine -Source file: `static_synapse `_ +Source file: `neuromodulated_stdp_synapse.nestml `_ :doc:`noisy_synapse ` @@ -325,15 +458,15 @@ Source file: `static_synapse `_ +Source file: `noisy_synapse.nestml `_ -:doc:`stdp_synapse ` ----------------------------------- +:doc:`static_synapse ` +-------------------------------------- -stdp - Synapse model for spike-timing dependent plasticity +Static synapse -Source file: `stdp_synapse `_ +Source file: `static_synapse.nestml `_ :doc:`stdp_nn_pre_centered_synapse ` @@ -341,7 +474,7 @@ Source file: `stdp_synapse `_ +Source file: `stdp_nn_pre_centered_synapse.nestml `_ :doc:`stdp_nn_restr_symm_synapse ` @@ -349,7 +482,7 @@ Source file: `stdp_nn_pre_centered_synapse `_ +Source file: `stdp_nn_restr_symm_synapse.nestml `_ :doc:`stdp_nn_symm_synapse ` @@ -357,23 +490,23 @@ Source file: `stdp_nn_restr_symm_synapse `_ +Source file: `stdp_nn_symm_synapse.nestml `_ -:doc:`stdp_triplet_nn_synapse ` --------------------------------------------------------- +:doc:`stdp_synapse ` +---------------------------------- -stdp_triplet_nn - Synapse type with triplet spike-timing dependent plasticity +stdp - Synapse model for spike-timing dependent plasticity -Source file: `stdp_triplet_nn_synapse `_ +Source file: `stdp_synapse.nestml `_ :doc:`stdp_triplet_synapse ` -------------------------------------------------- -stdp_triplet - Synapse type with triplet spike-timing dependent plasticity +Synapse type with triplet spike-timing dependent plasticity -Source file: `stdp_triplet_synapse `_ +Source file: `stdp_triplet_synapse.nestml `_ :doc:`third_factor_stdp_synapse ` @@ -381,13 +514,5 @@ Source file: `stdp_triplet_synapse `_ - - -:doc:`neuromodulated_stdp_synapse ` ----------------------------------------------------------------- - -neuromodulated_stdp - Synapse model for spike-timing dependent plasticity modulated by a neurotransmitter such as dopamine - -Source file: `neuromodulated_stdp_synapse `_ +Source file: `third_factor_stdp_synapse.nestml `_ diff --git a/doc/models_library/izhikevich_characterisation.rst b/doc/models_library/izhikevich_characterisation.rst deleted file mode 100644 index f1f4a7c4f..000000000 --- a/doc/models_library/izhikevich_characterisation.rst +++ /dev/null @@ -1,12 +0,0 @@ -Synaptic response ------------------ - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[izhikevich]_synaptic_response.png - :alt: izhikevich_neuron - -f-I curve ---------- - -.. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library/nestml_models_library_[izhikevich]_f-I_curve.png - :alt: izhikevich_neuron - diff --git a/doc/models_library/izhikevich.rst b/doc/models_library/izhikevich_neuron.rst similarity index 91% rename from doc/models_library/izhikevich.rst rename to doc/models_library/izhikevich_neuron.rst index 87dd92726..aae8ac3a0 100644 --- a/doc/models_library/izhikevich.rst +++ b/doc/models_library/izhikevich_neuron.rst @@ -1,5 +1,5 @@ -izhikevich -########## +izhikevich_neuron +################# izhikevich - Izhikevich neuron model @@ -88,14 +88,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `izhikevich `_. +The model source code can be found in the NESTML models repository here: `izhikevich_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: izhikevich_characterisation.rst +.. include:: izhikevich_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.073555 \ No newline at end of file + Generated at 2024-05-22 14:51:14.664250 \ No newline at end of file diff --git a/doc/models_library/izhikevich_neuron_characterisation.rst b/doc/models_library/izhikevich_neuron_characterisation.rst new file mode 100644 index 000000000..d3283db35 --- /dev/null +++ b/doc/models_library/izhikevich_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[izhikevich_neuron_nestml].png + :alt: izhikevich_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[izhikevich_neuron_nestml].png + :alt: izhikevich_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[izhikevich_neuron_nestml].png + :alt: izhikevich_neuron f-I curve + diff --git a/doc/models_library/izhikevich_psc_alpha.rst b/doc/models_library/izhikevich_psc_alpha_neuron.rst similarity index 87% rename from doc/models_library/izhikevich_psc_alpha.rst rename to doc/models_library/izhikevich_psc_alpha_neuron.rst index 389b856f8..5e33a542a 100644 --- a/doc/models_library/izhikevich_psc_alpha.rst +++ b/doc/models_library/izhikevich_psc_alpha_neuron.rst @@ -1,5 +1,5 @@ -izhikevich_psc_alpha -#################### +izhikevich_psc_alpha_neuron +########################### izhikevich_psc_alpha - Detailed Izhikevich neuron model with alpha-kernel post-synaptic current @@ -48,7 +48,7 @@ Parameters "C_m", "pF", "200pF", "Membrane capacitance" - "k", "pF / (ms mV)", "8pF / mV / ms", "Spiking slope" + "k", "pF / (mV ms)", "8pF / mV / ms", "Spiking slope" "V_r", "mV", "-65mV", "Resting potential" "V_t", "mV", "-45mV", "Threshold potential" "a", "1 / ms", "0.01 / ms", "Time scale of recovery variable" @@ -95,14 +95,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `izhikevich_psc_alpha `_. +The model source code can be found in the NESTML models repository here: `izhikevich_psc_alpha_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: izhikevich_psc_alpha_characterisation.rst +.. include:: izhikevich_psc_alpha_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.824156 \ No newline at end of file + Generated at 2024-05-22 14:51:14.580406 \ No newline at end of file diff --git a/doc/models_library/lorenz_attractor.rst b/doc/models_library/lorenz_attractor.rst deleted file mode 100644 index eb6a221ba..000000000 --- a/doc/models_library/lorenz_attractor.rst +++ /dev/null @@ -1,93 +0,0 @@ -lorenz_attractor -################ - - - - -Parameters -++++++++++ - - - -.. csv-table:: - :header: "Name", "Physical unit", "Default value", "Description" - :widths: auto - - - "sigma", "real", "10", "" - "beta", "real", "8 / 3", "" - "rho", "real", "28", "" - - - - -State variables -+++++++++++++++ - -.. csv-table:: - :header: "Name", "Physical unit", "Default value", "Description" - :widths: auto - - - "x", "real", "1", "" - "y", "real", "1", "" - "z", "real", "1", "" - - - - -Equations -+++++++++ - - - - -.. math:: - \frac{ dx } { dt }= \frac{ \sigma \cdot (y - x) } { \mathrm{s} } - - -.. math:: - \frac{ dy } { dt }= \frac{ (x \cdot (\rho - z) - y) } { \mathrm{s} } - - -.. math:: - \frac{ dz } { dt }= \frac{ (x \cdot y - \beta \cdot z) } { \mathrm{s} } - - - - - -Source code -+++++++++++ - -.. code-block:: nestml - - neuron lorenz_attractor: - state: - x real = 1 - y real = 1 - z real = 1 - equations: - x'=sigma * (y - x) / s - y'=(x * (rho - z) - y) / s - z'=(x * y - beta * z) / s - - update: - integrate_odes() - - parameters: - sigma real = 10 - beta real = 8 / 3 - rho real = 28 - - - -Characterisation -++++++++++++++++ - -.. include:: lorenz_attractor_characterisation.rst - - -.. footer:: - - Generated at 2021-12-09 08:22:32.491153 \ No newline at end of file diff --git a/doc/models_library/mat2_psc_exp.rst b/doc/models_library/mat2_psc_exp_neuron.rst similarity index 92% rename from doc/models_library/mat2_psc_exp.rst rename to doc/models_library/mat2_psc_exp_neuron.rst index 16efbd86a..0748908dc 100644 --- a/doc/models_library/mat2_psc_exp.rst +++ b/doc/models_library/mat2_psc_exp_neuron.rst @@ -1,5 +1,5 @@ -mat2_psc_exp -############ +mat2_psc_exp_neuron +################### mat2_psc_exp - Non-resetting leaky integrate-and-fire neuron model with exponential PSCs and adaptive threshold @@ -98,14 +98,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `mat2_psc_exp `_. +The model source code can be found in the NESTML models repository here: `mat2_psc_exp_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: mat2_psc_exp_characterisation.rst +.. include:: mat2_psc_exp_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.782490 \ No newline at end of file + Generated at 2024-05-22 14:51:14.528325 \ No newline at end of file diff --git a/doc/models_library/mat2_psc_exp_neuron_characterisation.rst b/doc/models_library/mat2_psc_exp_neuron_characterisation.rst new file mode 100644 index 000000000..f26509f17 --- /dev/null +++ b/doc/models_library/mat2_psc_exp_neuron_characterisation.rst @@ -0,0 +1,18 @@ +Synaptic response ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[mat2_psc_exp_neuron_nestml].png + :alt: mat2_psc_exp_neuron postsynaptic response + +Response to pulse current injection ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[mat2_psc_exp_neuron_nestml].png + :alt: mat2_psc_exp_neuron current pulse response + +f-I curve ++++++++++++++++++ + +.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[mat2_psc_exp_neuron_nestml].png + :alt: mat2_psc_exp_neuron f-I curve + diff --git a/doc/models_library/nestml_current_pulse_response_[aeif_cond_exp_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[aeif_cond_exp_neuron_nestml].png new file mode 100644 index 000000000..42dd7b365 Binary files /dev/null and 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Binary files /dev/null and b/doc/models_library/nestml_psp_[mat2_psc_exp_neuron_nestml]_small.png differ diff --git a/doc/models_library/neuromodulated_stdp_synapse.rst b/doc/models_library/neuromodulated_stdp_synapse.rst index 9650c5427..e338f235b 100644 --- a/doc/models_library/neuromodulated_stdp_synapse.rst +++ b/doc/models_library/neuromodulated_stdp_synapse.rst @@ -67,12 +67,9 @@ Source code The model source code can be found in the NESTML models repository here: `neuromodulated_stdp_synapse `_. -Characterisation -++++++++++++++++ - .. include:: neuromodulated_stdp_synapse_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.345553 \ No newline at end of file + Generated at 2024-05-22 14:51:14.674282 \ No newline at end of file diff --git a/doc/models_library/noisy_synapse.rst b/doc/models_library/noisy_synapse.rst index bca1d384d..36e996c12 100644 --- a/doc/models_library/noisy_synapse.rst +++ b/doc/models_library/noisy_synapse.rst @@ -29,12 +29,9 @@ Source code The model source code can be found in the NESTML models repository here: `noisy_synapse `_. -Characterisation -++++++++++++++++ - .. include:: noisy_synapse_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.328814 \ No newline at end of file + Generated at 2024-05-22 14:51:14.673953 \ No newline at end of file diff --git a/doc/models_library/output.html b/doc/models_library/output.html new file mode 100644 index 000000000..4cf344b05 --- /dev/null +++ b/doc/models_library/output.html @@ -0,0 +1,433 @@ +

Models library

+

Neuron models

+

aeif_cond_alpha_neuron <aeif_cond_alpha_neuron>

+

aeif_cond_alpha - Conductance based exponential integrate-and-fire +neuron model

+

Source file: aeif_cond_alpha_neuron.nestml

+

aeif_cond_exp_neuron <aeif_cond_exp_neuron>

+

aeif_cond_exp - Conductance based exponential integrate-and-fire +neuron model

+

Source file: aeif_cond_exp_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

hh_cond_exp_destexhe_neuron <hh_cond_exp_destexhe_neuron>

+

hh_cond_exp_destexhe - Hodgin Huxley based model, Traub, Destexhe and +Mainen modified

+

Source file: hh_cond_exp_destexhe_neuron.nestml

+

hh_cond_exp_traub_neuron <hh_cond_exp_traub_neuron>

+

hh_cond_exp_traub - Hodgkin-Huxley model for Brette et al (2007) +review

+

Source file: hh_cond_exp_traub_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

hh_moto_5ht_neuron <hh_moto_5ht_neuron>

+

hh_moto_5ht_nestml - a motor neuron model in HH formalism with 5HT +modulation

+

Source file: hh_moto_5ht_neuron.nestml

+

hh_psc_alpha_neuron <hh_psc_alpha_neuron>

+

hh_psc_alpha - Hodgkin-Huxley neuron model

+

Source file: hh_psc_alpha_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

hill_tononi_neuron <hill_tononi_neuron>

+

hill_tononi - Neuron model after Hill & Tononi (2005)

+

Source file: hill_tononi_neuron.nestml

+

iaf_chxk_2008_neuron <iaf_chxk_2008_neuron>

+

iaf_chxk_2008 - Conductance based leaky integrate-and-fire neuron +model used in Casti et al. 2008

+

Source file: iaf_chxk_2008_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

iaf_cond_alpha_neuron <iaf_cond_alpha_neuron>

+

iaf_cond_alpha - Simple conductance based leaky integrate-and-fire +neuron model

+

Source file: iaf_cond_alpha_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

iaf_cond_beta_neuron <iaf_cond_beta_neuron>

+

iaf_cond_beta - Simple conductance based leaky integrate-and-fire +neuron model

+

Source file: iaf_cond_beta_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

iaf_cond_exp_neuron <iaf_cond_exp_neuron>

+

iaf_cond_exp - Simple conductance based leaky integrate-and-fire +neuron model

+

Source file: iaf_cond_exp_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

iaf_cond_exp_sfa_rr_neuron <iaf_cond_exp_sfa_rr_neuron>

+

iaf_cond_exp_sfa_rr - Conductance based leaky integrate-and-fire +model with spike-frequency adaptation and relative refractory +mechanisms

+

Source file: iaf_cond_exp_sfa_rr_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

iaf_psc_alpha_neuron <iaf_psc_alpha_neuron>

+

iaf_psc_alpha - Leaky integrate-and-fire neuron model

+

Source file: iaf_psc_alpha_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

iaf_psc_delta_neuron <iaf_psc_delta_neuron>

+

iaf_psc_delta - Current-based leaky integrate-and-fire neuron model +with delta-kernel post-synaptic currents

+

Source file: iaf_psc_delta_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

iaf_psc_exp_dend_neuron <iaf_psc_exp_dend_neuron>

+

iaf_psc_exp_dend - Leaky integrate-and-fire neuron model with +exponential PSCs

+

Source file: iaf_psc_exp_dend_neuron.nestml

+

iaf_psc_exp_htum_neuron <iaf_psc_exp_htum_neuron>

+

iaf_psc_exp_htum - Leaky integrate-and-fire model with separate +relative and absolute refractory period

+

Source file: iaf_psc_exp_htum_neuron.nestml

+

iaf_psc_exp_neuron <iaf_psc_exp_neuron>

+

iaf_psc_exp - Leaky integrate-and-fire neuron model

+

Source file: iaf_psc_exp_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

ignore_and_fire_neuron <ignore_and_fire_neuron>

+

ignore_and_fire - Neuron generating spikes at fixed intervals +irrespective of inputs

+

Source file: ignore_and_fire_neuron.nestml

+

izhikevich_neuron <izhikevich_neuron>

+

izhikevich - Izhikevich neuron model

+

Source file: izhikevich_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

izhikevich_psc_alpha_neuron <izhikevich_psc_alpha_neuron>

+

izhikevich_psc_alpha - Detailed Izhikevich neuron model with +alpha-kernel post-synaptic current

+

Source file: izhikevich_psc_alpha_neuron.nestml

+

mat2_psc_exp_neuron <mat2_psc_exp_neuron>

+

mat2_psc_exp - Non-resetting leaky integrate-and-fire neuron model +with exponential PSCs and adaptive threshold

+

Source file: mat2_psc_exp_neuron.nestml

+ + + + + + + + +
Post-synaptic potentialStep current responseFiring rate vs. current
+

terub_gpe_neuron <terub_gpe_neuron>

+

terub_gpe - Terman Rubin neuron model

+

Source file: terub_gpe_neuron.nestml

+

terub_stn_neuron <terub_stn_neuron>

+

terub_stn - Terman Rubin neuron model

+

Source file: terub_stn_neuron.nestml

+

traub_cond_multisyn_neuron <traub_cond_multisyn_neuron>

+

traub_cond_multisyn - Traub model according to Borgers 2017

+

Source file: traub_cond_multisyn_neuron.nestml

+

traub_psc_alpha_neuron <traub_psc_alpha_neuron>

+

traub_psc_alpha - Traub model according to Borgers 2017

+

Source file: traub_psc_alpha_neuron.nestml

+

wb_cond_exp_neuron <wb_cond_exp_neuron>

+

wb_cond_exp - Wang-Buzsaki model

+

Source file: wb_cond_exp_neuron.nestml

+

wb_cond_multisyn_neuron <wb_cond_multisyn_neuron>

+

wb_cond_multisyn - Wang-Buzsaki model with multiple synapses

+

Source file: wb_cond_multisyn_neuron.nestml

+

Synapse models

+

neuromodulated_stdp_synapse <neuromodulated_stdp_synapse>

+

neuromodulated_stdp - Synapse model for spike-timing dependent +plasticity modulated by a neurotransmitter such as dopamine

+

Source file: neuromodulated_stdp_synapse.nestml

+

noisy_synapse <noisy_synapse>

+

Static synapse with Gaussian noise

+

Source file: noisy_synapse.nestml

+

static_synapse <static_synapse>

+

Static synapse

+

Source file: static_synapse.nestml

+

stdp_nn_pre_centered_synapse <stdp_nn_pre_centered_synapse>

+

stdp_nn_pre_centered - Synapse type for spike-timing dependent +plasticity, with nearest-neighbour spike pairing

+

Source file: stdp_nn_pre_centered_synapse.nestml

+

stdp_nn_restr_symm_synapse <stdp_nn_restr_symm_synapse>

+

Synapse type for spike-timing dependent plasticity with restricted +symmetric nearest-neighbour spike pairing scheme

+

Source file: stdp_nn_restr_symm_synapse.nestml

+

stdp_nn_symm_synapse <stdp_nn_symm_synapse>

+

Synapse type for spike-timing dependent plasticity with symmetric +nearest-neighbour spike pairing scheme

+

Source file: stdp_nn_symm_synapse.nestml

+

stdp_synapse <stdp_synapse>

+

stdp - Synapse model for spike-timing dependent plasticity

+

Source file: stdp_synapse.nestml

+

stdp_triplet_synapse <stdp_triplet_synapse>

+

Synapse type with triplet spike-timing dependent plasticity

+

Source file: stdp_triplet_synapse.nestml

+

third_factor_stdp_synapse <third_factor_stdp_synapse>

+

Synapse model for spike-timing dependent plasticity with postsynaptic +third-factor modulation

+

Source file: third_factor_stdp_synapse.nestml

diff --git a/doc/models_library/static_synapse.rst b/doc/models_library/static_synapse.rst index 1927bfdd0..76c65eb7b 100644 --- a/doc/models_library/static_synapse.rst +++ b/doc/models_library/static_synapse.rst @@ -27,12 +27,9 @@ Source code The model source code can be found in the NESTML models repository here: `static_synapse `_. -Characterisation -++++++++++++++++ - .. include:: static_synapse_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.329827 \ No newline at end of file + Generated at 2024-05-22 14:51:14.678237 \ No newline at end of file diff --git a/doc/models_library/stdp_nn_pre_centered_synapse.rst b/doc/models_library/stdp_nn_pre_centered_synapse.rst index a7abafb84..4cf3a69fb 100644 --- a/doc/models_library/stdp_nn_pre_centered_synapse.rst +++ b/doc/models_library/stdp_nn_pre_centered_synapse.rst @@ -91,12 +91,9 @@ Source code The model source code can be found in the NESTML models repository here: `stdp_nn_pre_centered_synapse `_. -Characterisation -++++++++++++++++ - .. include:: stdp_nn_pre_centered_synapse_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.333803 \ No newline at end of file + Generated at 2024-05-22 14:51:14.672063 \ No newline at end of file diff --git a/doc/models_library/stdp_nn_restr_symm_synapse.rst b/doc/models_library/stdp_nn_restr_symm_synapse.rst index cbbb77eb7..f4c0e056c 100644 --- a/doc/models_library/stdp_nn_restr_symm_synapse.rst +++ b/doc/models_library/stdp_nn_restr_symm_synapse.rst @@ -84,12 +84,9 @@ Source code The model source code can be found in the NESTML models repository here: `stdp_nn_restr_symm_synapse `_. -Characterisation -++++++++++++++++ - .. include:: stdp_nn_restr_symm_synapse_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.336464 \ No newline at end of file + Generated at 2024-05-22 14:51:14.675341 \ No newline at end of file diff --git a/doc/models_library/stdp_nn_symm_synapse.rst b/doc/models_library/stdp_nn_symm_synapse.rst index 26b601728..10534f11c 100644 --- a/doc/models_library/stdp_nn_symm_synapse.rst +++ b/doc/models_library/stdp_nn_symm_synapse.rst @@ -88,12 +88,9 @@ Source code The model source code can be found in the NESTML models repository here: `stdp_nn_symm_synapse `_. -Characterisation -++++++++++++++++ - .. include:: stdp_nn_symm_synapse_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.341467 \ No newline at end of file + Generated at 2024-05-22 14:51:14.676315 \ No newline at end of file diff --git a/doc/models_library/stdp_synapse.rst b/doc/models_library/stdp_synapse.rst index 147e56810..96dc34982 100644 --- a/doc/models_library/stdp_synapse.rst +++ b/doc/models_library/stdp_synapse.rst @@ -74,12 +74,9 @@ Source code The model source code can be found in the NESTML models repository here: `stdp_synapse `_. -Characterisation -++++++++++++++++ - .. include:: stdp_synapse_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.343488 \ No newline at end of file + Generated at 2024-05-22 14:51:14.671094 \ No newline at end of file diff --git a/doc/models_library/stdp_triplet_nn_synapse.rst b/doc/models_library/stdp_triplet_nn_synapse.rst deleted file mode 100644 index e69d0b8bb..000000000 --- a/doc/models_library/stdp_triplet_nn_synapse.rst +++ /dev/null @@ -1,72 +0,0 @@ -stdp_triplet_nn_synapse -####################### - - -stdp_triplet_nn - Synapse type with triplet spike-timing dependent plasticity - -Description -+++++++++++ - -A connection with spike time dependent plasticity accounting for spike triplet effects (as defined in [1]_). - -Nearest-neighbour variant of pre- and postsynaptic spike coupling. - - -References -++++++++++ -.. [1] Pfister JP, Gerstner W (2006). Triplets of spikes in a model - of spike timing-dependent plasticity. The Journal of Neuroscience - 26(38):9673-9682. DOI: https://doi.org/10.1523/JNEUROSCI.1425-06.2006 - - - -Parameters -++++++++++ - - -.. csv-table:: - :header: "Name", "Physical unit", "Default value", "Description" - :widths: auto - - - "d", "ms", "1ms", "Synaptic transmission delay" - "tau_plus", "ms", "16.8ms", "time constant for tr_r1" - "tau_x", "ms", "101ms", "time constant for tr_r2" - "tau_minus", "ms", "33.7ms", "time constant for tr_o1" - "tau_y", "ms", "125ms", "time constant for tr_o2" - "A2_plus", "real", "7.5e-10", "" - "A3_plus", "real", "0.0093", "" - "A2_minus", "real", "0.007", "" - "A3_minus", "real", "0.00023", "" - "Wmax", "nS", "100nS", "" - "Wmin", "nS", "0nS", "" - - -State variables -+++++++++++++++ - -.. csv-table:: - :header: "Name", "Physical unit", "Default value", "Description" - :widths: auto - - - "w", "nS", "1nS", "Synaptic weight" - "tr_r1", "real", "0.0", "" - "tr_r2", "real", "0.0", "" - "tr_o1", "real", "0.0", "" - "tr_o2", "real", "0.0", "" -Source code -+++++++++++ - -The model source code can be found in the NESTML models repository here: `stdp_triplet_nn_synapse `_. - - -Characterisation -++++++++++++++++ - -.. include:: stdp_triplet_nn_synapse_characterisation.rst - - -.. footer:: - - Generated at 2023-11-16 11:40:54.338858 \ No newline at end of file diff --git a/doc/models_library/stdp_triplet_synapse.rst b/doc/models_library/stdp_triplet_synapse.rst new file mode 100644 index 000000000..2f04cc9d7 --- /dev/null +++ b/doc/models_library/stdp_triplet_synapse.rst @@ -0,0 +1,69 @@ +stdp_triplet_synapse +#################### + + +stdp_triplet_synapse - Synapse type with triplet spike-timing dependent plasticity + +Description ++++++++++++ + +A connection with spike time dependent plasticity accounting for spike triplet effects (as defined in [1]_). + +Nearest-neighbour variant of pre- and postsynaptic spike coupling. + + +References +++++++++++ +.. [1] Pfister JP, Gerstner W (2006). Triplets of spikes in a model + of spike timing-dependent plasticity. The Journal of Neuroscience + 26(38):9673-9682. DOI: https://doi.org/10.1523/JNEUROSCI.1425-06.2006 + + + +Parameters +++++++++++ + + +.. csv-table:: + :header: "Name", "Physical unit", "Default value", "Description" + :widths: auto + + + "d", "ms", "1ms", "Synaptic transmission delay" + "tau_plus", "ms", "16.8ms", "time constant for tr_r1" + "tau_x", "ms", "101ms", "time constant for tr_r2" + "tau_minus", "ms", "33.7ms", "time constant for tr_o1" + "tau_y", "ms", "125ms", "time constant for tr_o2" + "A2_plus", "real", "7.5e-10", "" + "A3_plus", "real", "0.0093", "" + "A2_minus", "real", "0.007", "" + "A3_minus", "real", "0.00023", "" + "Wmax", "nS", "100nS", "" + "Wmin", "nS", "0nS", "" + + +State variables ++++++++++++++++ + +.. csv-table:: + :header: "Name", "Physical unit", "Default value", "Description" + :widths: auto + + + "w", "nS", "1nS", "Synaptic weight" + "tr_r1", "real", "0.0", "" + "tr_r2", "real", "0.0", "" + "tr_o1", "real", "0.0", "" + "tr_o2", "real", "0.0", "" +Source code ++++++++++++ + +The model source code can be found in the NESTML models repository here: `stdp_triplet_synapse `_. + + +.. include:: stdp_triplet_synapse_characterisation.rst + + +.. footer:: + + Generated at 2024-05-22 14:51:14.677173 \ No newline at end of file diff --git a/doc/models_library/terub_gpe.rst b/doc/models_library/terub_gpe_neuron.rst similarity index 93% rename from doc/models_library/terub_gpe.rst rename to doc/models_library/terub_gpe_neuron.rst index 4273d7086..28e335d7c 100644 --- a/doc/models_library/terub_gpe.rst +++ b/doc/models_library/terub_gpe_neuron.rst @@ -1,5 +1,5 @@ -terub_gpe -######### +terub_gpe_neuron +################ terub_gpe - Terman Rubin neuron model @@ -104,14 +104,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `terub_gpe `_. +The model source code can be found in the NESTML models repository here: `terub_gpe_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: terub_gpe_characterisation.rst +.. include:: terub_gpe_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.240311 \ No newline at end of file + Generated at 2024-05-22 14:51:14.612077 \ No newline at end of file diff --git a/doc/models_library/terub_stn.rst b/doc/models_library/terub_stn_neuron.rst similarity index 93% rename from doc/models_library/terub_stn.rst rename to doc/models_library/terub_stn_neuron.rst index afa6983be..405ebb8b4 100644 --- a/doc/models_library/terub_stn.rst +++ b/doc/models_library/terub_stn_neuron.rst @@ -1,5 +1,5 @@ -terub_stn -######### +terub_stn_neuron +################ terub_stn - Terman Rubin neuron model @@ -100,14 +100,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `terub_stn `_. +The model source code can be found in the NESTML models repository here: `terub_stn_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: terub_stn_characterisation.rst +.. include:: terub_stn_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.023572 \ No newline at end of file + Generated at 2024-05-22 14:51:14.508465 \ No newline at end of file diff --git a/doc/models_library/third_factor_stdp_synapse.rst b/doc/models_library/third_factor_stdp_synapse.rst index 19784b10b..cd8c66052 100644 --- a/doc/models_library/third_factor_stdp_synapse.rst +++ b/doc/models_library/third_factor_stdp_synapse.rst @@ -75,12 +75,9 @@ Source code The model source code can be found in the NESTML models repository here: `third_factor_stdp_synapse `_. -Characterisation -++++++++++++++++ - .. include:: third_factor_stdp_synapse_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.330550 \ No newline at end of file + Generated at 2024-05-22 14:51:14.672974 \ No newline at end of file diff --git a/doc/models_library/traub_cond_multisyn.rst b/doc/models_library/traub_cond_multisyn_neuron.rst similarity index 93% rename from doc/models_library/traub_cond_multisyn.rst rename to doc/models_library/traub_cond_multisyn_neuron.rst index ed08818ae..45953ce49 100644 --- a/doc/models_library/traub_cond_multisyn.rst +++ b/doc/models_library/traub_cond_multisyn_neuron.rst @@ -1,5 +1,5 @@ -traub_cond_multisyn -################### +traub_cond_multisyn_neuron +########################## traub_cond_multisyn - Traub model according to Borgers 2017 @@ -116,14 +116,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `traub_cond_multisyn `_. +The model source code can be found in the NESTML models repository here: `traub_cond_multisyn_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: traub_cond_multisyn_characterisation.rst +.. include:: traub_cond_multisyn_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.202921 \ No newline at end of file + Generated at 2024-05-22 14:51:14.472118 \ No newline at end of file diff --git a/doc/models_library/traub_psc_alpha.rst b/doc/models_library/traub_psc_alpha_neuron.rst similarity index 91% rename from doc/models_library/traub_psc_alpha.rst rename to doc/models_library/traub_psc_alpha_neuron.rst index 8ea51d7bb..45ad27fc0 100644 --- a/doc/models_library/traub_psc_alpha.rst +++ b/doc/models_library/traub_psc_alpha_neuron.rst @@ -1,5 +1,5 @@ -traub_psc_alpha -############### +traub_psc_alpha_neuron +###################### traub_psc_alpha - Traub model according to Borgers 2017 @@ -88,14 +88,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `traub_psc_alpha `_. +The model source code can be found in the NESTML models repository here: `traub_psc_alpha_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: traub_psc_alpha_characterisation.rst +.. include:: traub_psc_alpha_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.096671 \ No newline at end of file + Generated at 2024-05-22 14:51:14.569603 \ No newline at end of file diff --git a/doc/models_library/wb_cond_exp.rst b/doc/models_library/wb_cond_exp_neuron.rst similarity index 91% rename from doc/models_library/wb_cond_exp.rst rename to doc/models_library/wb_cond_exp_neuron.rst index 58be2a321..1bf56829c 100644 --- a/doc/models_library/wb_cond_exp.rst +++ b/doc/models_library/wb_cond_exp_neuron.rst @@ -1,5 +1,5 @@ -wb_cond_exp -########### +wb_cond_exp_neuron +################## wb_cond_exp - Wang-Buzsaki model @@ -91,14 +91,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `wb_cond_exp `_. +The model source code can be found in the NESTML models repository here: `wb_cond_exp_neuron `_. -Characterisation -++++++++++++++++ - -.. include:: wb_cond_exp_characterisation.rst +.. include:: wb_cond_exp_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:54.003927 \ No newline at end of file + Generated at 2024-05-22 14:51:14.463571 \ No newline at end of file diff --git a/doc/models_library/wb_cond_multisyn.rst b/doc/models_library/wb_cond_multisyn_neuron.rst similarity index 93% rename from doc/models_library/wb_cond_multisyn.rst rename to doc/models_library/wb_cond_multisyn_neuron.rst index b146f685a..ae60296c0 100644 --- a/doc/models_library/wb_cond_multisyn.rst +++ b/doc/models_library/wb_cond_multisyn_neuron.rst @@ -1,5 +1,5 @@ -wb_cond_multisyn -################ +wb_cond_multisyn_neuron +####################### wb_cond_multisyn - Wang-Buzsaki model with multiple synapses @@ -113,14 +113,11 @@ Equations Source code +++++++++++ -The model source code can be found in the NESTML models repository here: `wb_cond_multisyn `_. - -Characterisation -++++++++++++++++ +The model source code can be found in the NESTML models repository here: `wb_cond_multisyn_neuron `_. -.. include:: wb_cond_multisyn_characterisation.rst +.. include:: wb_cond_multisyn_neuron_characterisation.rst .. footer:: - Generated at 2023-11-16 11:40:53.965800 \ No newline at end of file + Generated at 2024-05-22 14:51:14.559256 \ No newline at end of file diff --git a/doc/sphinx-apidoc/_static/css/custom.css b/doc/sphinx-apidoc/_static/css/custom.css index b24225f7f..4d55f3b80 100644 --- a/doc/sphinx-apidoc/_static/css/custom.css +++ b/doc/sphinx-apidoc/_static/css/custom.css @@ -1,3 +1,7 @@ +.caption-number { + display: none !important; +} + .wy-breadcrumbs-aside { display: none !important; } @@ -71,6 +75,15 @@ t.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { } } +td figure { + margin-bottom: 0 !important; +} + +.figcaption p { + text-align: center; + padding-left: 1em; +} + video { margin-bottom: 20px; background-color: lightgrey; diff --git a/models/neurons/aeif_cond_alpha_neuron.nestml b/models/neurons/aeif_cond_alpha_neuron.nestml index 14e556017..7d2851b86 100644 --- a/models/neurons/aeif_cond_alpha_neuron.nestml +++ b/models/neurons/aeif_cond_alpha_neuron.nestml @@ -63,13 +63,15 @@ model aeif_cond_alpha_neuron: parameters: # membrane parameters + C_m pF = 281.0 pF # Membrane Capacitance - refr_T ms = 2 ms # Duration of refractory period + refr_T ms = 2 ms # Duration of refractory period V_reset mV = -60.0 mV # Reset Potential g_L nS = 30.0 nS # Leak Conductance E_L mV = -70.6 mV # Leak reversal Potential (aka resting potential) # spike adaptation parameters + a nS = 4 nS # Subthreshold adaptation b pA = 80.5 pA # Spike-triggered adaptation Delta_T mV = 2.0 mV # Slope factor @@ -78,12 +80,13 @@ model aeif_cond_alpha_neuron: V_peak mV = 0 mV # Spike detection threshold # synaptic parameters + E_exc mV = 0 mV # Excitatory reversal Potential tau_syn_exc ms = 0.2 ms # Synaptic Time Constant Excitatory Synapse E_inh mV = -85.0 mV # Inhibitory reversal Potential tau_syn_inh ms = 2.0 ms # Synaptic Time Constant for Inhibitory Synapse - # constant external input current + # Constant external input current I_e pA = 0 pA internals: diff --git a/pynestml/codegeneration/autodoc_builder.py b/pynestml/codegeneration/autodoc_builder.py index 991421b4d..2d6903a5c 100644 --- a/pynestml/codegeneration/autodoc_builder.py +++ b/pynestml/codegeneration/autodoc_builder.py @@ -18,24 +18,344 @@ # # You should have received a copy of the GNU General Public License # along with NEST. If not, see . -import os.path + from typing import Optional, Mapping, Any -from pynestml.codegeneration.autodoc_code_generator_utils import AutoDocCodeGeneratorUtils +import matplotlib.pyplot as plt +import numpy as np +import os +import re + from pynestml.codegeneration.builder import Builder -from pynestml.exceptions.generated_code_build_exception import GeneratedCodeBuildException from pynestml.frontend.frontend_configuration import FrontendConfiguration +def get_model_doc_title(model_fname: str): + with open(model_fname) as f: + model = f.read() + return re.compile(r'\"\"\"[^#]*###').search(model).group()[3:-3].strip() + + class AutodocBuilder(Builder): def __init__(self, options: Optional[Mapping[str, Any]] = None): super().__init__("AUTODOC", options) + self.model_doc_rst = "" def build(self) -> None: - target_path = FrontendConfiguration.get_target_path() + self.target_path = FrontendConfiguration.get_target_path() + + self.generate_all_models() + self.generate_model_docs() + + def generate_all_models(self): + codegen_opts = {} + + from pynestml.frontend.pynestml_frontend import generate_nest_target + + generate_nest_target(input_path=["models/neurons"], + target_path=os.path.join(self.target_path, "nestml-autodoc-target"), + logging_level="DEBUG", + module_name="nestml_autodoc_module", + suffix="_nestml", + codegen_opts=codegen_opts) + + def generate_model_docs(self): + self.model_doc_rst += "Models library\n==============\n\n" + self.model_doc_rst += "Neuron models\n~~~~~~~~~~~~~\n\n" + + self._characterised_models = [] + + self._test("iaf_psc_delta_neuron_nestml") + self._test("iaf_psc_exp_neuron_nestml") + self._test("iaf_psc_alpha_neuron_nestml") + self._test("iaf_cond_exp_neuron_nestml") + self._test("iaf_cond_alpha_neuron_nestml") + self._test("iaf_cond_beta_neuron_nestml") + self._test("izhikevich_neuron_nestml") + self._test("hh_psc_alpha_neuron_nestml") + self._test("aeif_cond_exp_neuron_nestml") + self._test("hh_cond_exp_traub_neuron_nestml") + self._test("iaf_chxk_2008_neuron_nestml") + self._test("iaf_cond_exp_sfa_rr_neuron_nestml") + self._test("mat2_psc_exp_neuron_nestml") + + all_nestml_neuron_models = sorted([s[:-7] for s in list(os.walk("models/neurons"))[0][2] if s[-7:] == ".nestml"]) + self.model_doc_rst += self.generate_neuron_models_documentation(all_nestml_neuron_models) + + self.model_doc_rst += "Synapse models\n~~~~~~~~~~~~~~\n\n" + all_nestml_synapse_models = sorted([s[:-7] for s in list(os.walk("models/synapses"))[0][2] if s[-7:] == ".nestml"]) + self.model_doc_rst += self.generate_synapse_models_documentation(all_nestml_synapse_models) + + with open(os.path.join(self.target_path, "index.rst"), "w") as f: + f.write(self.model_doc_rst) + + def _test(self, model_name): + self._characterised_models.append(model_name.removesuffix(FrontendConfiguration.suffix)) + + self._test_model_psp(model_name) + self._test_model_current_pulse(model_name) + self._test_model_fI_curve(model_name) + + def _test_model_current_pulse(self, model_name, I_min=-100E-12, I_max=500E-12, N=6, + model_opts=None, model_initial_state=None): + r"""Make current pulse curve""" + import nest + + t_stop = 125.1 # [ms] + t_pulse_start = 20. # [ms] + t_pulse_stop = 80. # [ms] + syn_delay = 1. # [ms] + I_stim_vec = np.linspace(I_min, I_max, N) + + for figsize, fname_snip in zip([(8, 5), (4, 3)], ["", "_small"]): + fig, ax = plt.subplots(2, 1, height_ratios=[2, 1], figsize=figsize) + + for i, I_stim in enumerate(I_stim_vec): + nest.ResetKernel() + nest.Install("nestml_autodoc_module") + nest.SetKernelStatus({"resolution": .01}) # aeif_cond_exp model requires resolution <= 0.01 ms + + neuron = nest.Create(model_name, params=model_opts) + if model_initial_state is not None: + nest.SetStatus(neuron, model_initial_state) + + dc = nest.Create("dc_generator", params={"amplitude": 0.}) + nest.Connect(dc, neuron) + + V_m_specifier = "V_m" + multimeter = nest.Create("multimeter") + nest.SetStatus(multimeter, {"record_from": [V_m_specifier], + "interval": nest.resolution}) + nest.Connect(multimeter, neuron) + + sr = nest.Create("spike_recorder") + nest.Connect(neuron, sr) + + nest.Simulate(t_pulse_start) + dc.amplitude = I_stim * 1E12 # 1E12: convert A to pA + + nest.Simulate(t_pulse_stop - t_pulse_start) + dc.amplitude = 0. + + nest.Simulate(t_stop - t_pulse_stop + 10.) # add some extra padding at the end + + dmm = nest.GetStatus(multimeter)[0] + Vms = dmm["events"][V_m_specifier] + ts = np.array(dmm["events"]["times"]) + + ax[0].plot(ts - syn_delay, Vms, label=str(I_stim * 1E12)) + ax[0].set_ylabel(r"$V_m$") + ax[1].plot([0, t_pulse_start, t_pulse_start + 1E-12, t_pulse_stop, t_pulse_stop + 1E-12, t_stop], [0, 0, I_stim * 1E12, I_stim * 1E12, 0, 0], label=str(I_stim * 1E12)) + ax[1].set_ylabel(r"$I_\text{stim}$") + + for _ax in ax: + _ax.set_xlim(0., t_stop) + _ax.grid() + _ax.ticklabel_format(useOffset=False) # Disable offset on current axis + + ax[-1].set_xlabel("Time [ms]") + + plt.tight_layout() + plt.savefig(os.path.join(self.target_path, "nestml_current_pulse_response_[" + model_name + "]" + fname_snip + ".png")) + plt.close(fig) + + def _test_model_fI_curve(self, model_name, model_opts=None, model_initial_state=None): + r"""Make f-I curve""" + import nest + + t_stop = 10000. # [ms] + + I_stim_vec = np.linspace(10E-12, 1E-9, 100) # [A] + rate = float("nan") * np.ones_like(I_stim_vec) + for i, I_stim in enumerate(I_stim_vec): + nest.ResetKernel() + nest.Install("nestml_autodoc_module") + nest.SetKernelStatus({"resolution": .01}) # aeif_cond_exp model requires resolution <= 0.01 ms + + neuron = nest.Create(model_name, params=model_opts) + if model_initial_state is not None: + nest.SetStatus(neuron, model_initial_state) + + dc = nest.Create("dc_generator", params={"amplitude": I_stim * 1E12}) # 1E12: convert A to pA + nest.Connect(dc, neuron) + + V_m_specifier = "V_m" + multimeter = nest.Create("multimeter") + nest.SetStatus(multimeter, {"record_from": [V_m_specifier]}) + nest.Connect(multimeter, neuron) + + sr = nest.Create("spike_recorder") + nest.Connect(neuron, sr) + + nest.Simulate(t_stop) + + dmm = nest.GetStatus(multimeter)[0] + Vms = dmm["events"][V_m_specifier] + ts = dmm["events"]["times"] + + rate[i] = nest.GetStatus(sr)[0]["n_events"] / t_stop * 1000 + + if len(I_stim_vec) < 20: + marker = "o" + else: + marker = None + + for figsize, fname_snip in zip([(8, 5), (4, 3)], ["", "_small"]): + fig, ax = plt.subplots(1, 1, figsize=figsize) + ax = [ax] + ax[0].plot(I_stim_vec * 1E12, rate, marker=marker, label=model_name) + for _ax in ax: + _ax.grid() + _ax.set_ylabel("Firing rate [Hz]") + _ax.ticklabel_format(useOffset=False) # Disable offset on current axis + ax[0].set_xlabel(r"$I_\text{stim}$ [pA]") + plt.tight_layout() + + plt.savefig(os.path.join(self.target_path, "nestml_fI_curve_[" + model_name + "]" + fname_snip + ".png")) + plt.close(fig) + + def _test_model_psp(self, model_name, max_weight: float = 10., model_opts=None, + model_initial_state=None): + import nest + + nest.ResetKernel() + nest.Install("nestml_autodoc_module") + nest.SetKernelStatus({"resolution": .01}) # aeif_cond_exp model requires resolution <= 0.01 ms + + spike_times = [100., 200.] + spike_weights = [1., -1.] + + neuron = nest.Create(model_name, params=model_opts) + + if model_initial_state is not None: + nest.SetStatus(neuron, model_initial_state) + + spikegenerator = nest.Create("spike_generator", + params={"spike_times": spike_times, "spike_weights": spike_weights}) + + nest.Connect(spikegenerator, neuron) + + spike_recorder = nest.Create("spike_recorder") + nest.Connect(neuron, spike_recorder) + + multimeter = nest.Create("multimeter") + + V_m_specifier = "V_m" + nest.SetStatus(multimeter, {"record_from": [V_m_specifier]}) + + nest.Connect(multimeter, neuron) + + nest.Simulate(400.) + + dmm = nest.GetStatus(multimeter)[0] + Vms = dmm["events"][V_m_specifier] + ts = dmm["events"]["times"] + + for figsize, fname_snip in zip([(8, 5), (4, 3)], ["", "_small"]): + fig, ax = plt.subplots(1, 1, figsize=figsize) + ax = [ax] + ax[0].plot(ts, Vms, label=model_name) + for _ax in ax: + _ax.grid() + _ax.ticklabel_format(useOffset=False) # Disable offset on current axis + ax[0].set_xlabel("Time [ms]") + ax[0].set_ylabel("$V_m$ [mV]") + plt.tight_layout() + + plt.savefig(os.path.join(self.target_path, "nestml_psp_[" + model_name + "]" + fname_snip + ".png")) + plt.close(fig) + + def generate_synapse_models_documentation(self, models): + r""" + """ + + s = "" + + for model_name in models: + model_fname = model_name + ".nestml" + + s += "\n" + s += ":doc:`" + model_name + " <" + model_name + ">`" + "\n" + s += "-" * len(":doc:`" + model_name + " <" + model_name + ">`") + "\n" + + model_doc_title = get_model_doc_title(os.path.join("models", "synapses", model_fname)) + if model_doc_title.startswith(model_name): + model_doc_title = model_doc_title.removeprefix(model_name) + model_doc_title = model_doc_title.removeprefix(" - ") + s += "\n" + model_doc_title + "\n" + + s += "\n" + s += "Source file: `" + model_fname + " `_\n" + s += "\n" + + return s + + def generate_neuron_models_documentation(self, model_names): + s = "" + + for model_name in model_names: + model_name.removesuffix("_alt_nestml") + model_name.removesuffix("_nestml") + + model_fname = model_name + ".nestml" + + s += "\n" + s += ":doc:`" + model_name + " <" + model_name + ">`" + "\n" + s += "-" * len(":doc:`" + model_name + " <" + model_name + ">`") + "\n" + + model_doc_title = get_model_doc_title(os.path.join("models", "neurons", model_fname)) + if model_doc_title.startswith(model_name): + model_doc_title = model_doc_title.removeprefix(model_name) + model_doc_title = model_doc_title.removeprefix(" - ") + s += "\n" + model_doc_title + "\n" + + s += "\n" + s += "Source file: `" + model_fname + " `_\n" + s += "\n" + if model_name in self._characterised_models: + s += ".. list-table::\n" + s += "\n" + s += " * - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library" \ + "/nestml_psp_[" + \ + model_name + "_nestml]_small.png\n" + s += " :alt: " + model_name + "\n\n" + s += " Post-synaptic potential\n" + s += "\n" + s += " - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library" \ + "/nestml_current_pulse_response_[" + \ + model_name + "_nestml]_small.png\n" + s += " :alt: " + model_name + "\n\n" + s += " Step current response\n" + s += "\n" + s += " - .. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library" \ + "/nestml_fI_curve_[" + \ + model_name + "_nestml]_small.png\n" + s += " :alt: " + model_name + "\n\n" + s += " Firing rate vs. current\n" + s += "\n" + + with open(os.path.join(self.target_path, model_name + "_characterisation.rst"), "w") as f: + s_ = "Synaptic response\n+++++++++++++++++\n\n" + s_ += ".. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library" \ + "/nestml_psp_[" + \ + model_name + "_nestml].png\n" + s_ += " :alt: " + model_name + " postsynaptic response\n" + s_ += "\n" + s_ += "Response to pulse current injection\n+++++++++++++++++\n\n" + s_ += ".. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library" \ + "/nestml_current_pulse_response_[" + \ + model_name + "_nestml].png\n" + s_ += " :alt: " + model_name + " current pulse response\n" + s_ += "\n" + s_ += "f-I curve\n+++++++++++++++++\n\n" + s_ += ".. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library" \ + "/nestml_fI_curve_[" + \ + model_name + "_nestml].png\n" + s_ += " :alt: " + model_name + " f-I curve\n" + s_ += "\n" + f.write(s_) - try: - AutoDocCodeGeneratorUtils.generate_docs(target_path) - except Exception: - raise GeneratedCodeBuildException("Error occurred while building autodocs") + return s diff --git a/pynestml/codegeneration/autodoc_code_generator.py b/pynestml/codegeneration/autodoc_code_generator.py index 9f1c05fc6..650398619 100644 --- a/pynestml/codegeneration/autodoc_code_generator.py +++ b/pynestml/codegeneration/autodoc_code_generator.py @@ -38,11 +38,14 @@ from pynestml.meta_model.ast_model import ASTModel from pynestml.utils.ast_utils import ASTUtils from pynestml.utils.logger import Logger -from pynestml.utils.string_utils import removesuffix class AutoDocCodeGenerator(CodeGenerator): + r""" + The "autodoc" code generator generates human-readable documentation for each neuron and synapse model. The documentation consists of files in reStructuredText format. + In addition, supported models can be characterised by current injection, measuring the PSP, f-I curve, etc. These characterisations are run using NEST. Figures are saved in PNG format. + """ def __init__(self): # setup the template environment env = Environment(loader=FileSystemLoader(os.path.join(os.path.dirname(__file__), 'resources_autodoc'))) @@ -89,7 +92,7 @@ def generate_neuron_code(self, neuron: ASTModel): :param neuron: a single neuron object. """ nestml_model_doc = self._template_neuron_nestml_model.render(self.setup_neuron_model_generation_helpers(neuron)) - neuron_name = removesuffix(neuron.get_name(), "_neuron") + neuron_name = neuron.get_name() with open(str(os.path.join(FrontendConfiguration.get_target_path(), neuron_name)) + '.rst', 'w+') as f: f.write(str(nestml_model_doc)) @@ -116,7 +119,7 @@ def setup_neuron_model_generation_helpers(self, neuron: ASTModel): namespace['now'] = datetime.datetime.utcnow() namespace['neuron'] = neuron - namespace['neuronName'] = removesuffix(str(neuron.get_name()), "_neuron") + namespace['neuronName'] = neuron.get_name() namespace['printer'] = self._printer namespace['assignments'] = NestAssignmentsHelper() namespace['utils'] = ASTUtils() diff --git a/pynestml/codegeneration/autodoc_code_generator_utils.py b/pynestml/codegeneration/autodoc_code_generator_utils.py deleted file mode 100644 index 137cf3bab..000000000 --- a/pynestml/codegeneration/autodoc_code_generator_utils.py +++ /dev/null @@ -1,393 +0,0 @@ -# -*- coding: utf-8 -*- -# -# autodoc_code_generator_utils.py -# -# This file is part of NEST. -# -# Copyright (C) 2004 The NEST Initiative -# -# NEST is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 2 of the License, or -# (at your option) any later version. -# -# NEST is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with NEST. If not, see . -import copy -import os -import re - -import nest -import numpy as np - -from pynestml.codegeneration.nest_tools import NESTTools -from pynestml.frontend.pynestml_frontend import generate_nest_target -from pynestml.utils.string_utils import removeprefix, removesuffix - -try: - import matplotlib - import matplotlib.pyplot as plt - - TEST_PLOTS = True -except BaseException: - TEST_PLOTS = False - - -def get_model_doc_title(model_fname: str): - with open(model_fname) as f: - model = f.read() - return re.compile(r'\"\"\"[^#]*###').search(model).group()[3:-3].strip() - - -class AutoDocCodeGeneratorUtils: - models_input_path = os.path.realpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "models")) - - @classmethod - def generate_all_models(cls): - codegen_opts = {} - if NESTTools.detect_nest_version().startswith("v3"): - codegen_opts["neuron_parent_class"] = "StructuralPlasticityNode" - codegen_opts["neuron_parent_class_include"] = "structural_plasticity_node.h" - codegen_opts = {} - - generate_nest_target(input_path=os.path.join(cls.models_input_path, "neurons"), - target_path="/tmp/nestml-autodoc", - logging_level="INFO", - module_name="nestml_autodoc_module", - suffix="_nestml", - codegen_opts=codegen_opts) - - @classmethod - def generate_docs(cls, target_path): - nest.ResetKernel() - - try: - nest.Install("nestml_autodoc_module") - except Exception: - cls.generate_all_models() - nest.Install("nestml_autodoc_module") - - s = "Models library\n==============\n\n" - - s += "Neuron models\n~~~~~~~~~~~~~\n\n" - - neuron_models = ["iaf_psc_delta_neuron_nestml", - "iaf_psc_exp_neuron_nestml", - "iaf_psc_alpha_neuron_nestml", - "iaf_cond_exp_neuron_nestml", - "iaf_cond_alpha_neuron_nestml", - "iaf_cond_beta_neuron_nestml", - "izhikevich_neuron_nestml", - "hh_psc_alpha_neuron_nestml", - "hh_cond_exp_traub_neuron_nestml", - "aeif_cond_exp_neuron_nestml", - "aeif_cond_alpha_neuron_nestml"] - - for model in neuron_models: - cls._test_model_curr_inj(model) - cls._test_model_psc(model) - - all_nestml_neuron_models = [s[:-7] for s in list(os.walk(os.path.join(cls.models_input_path, "neurons")))[0][2] if s[-7:] == ".nestml"] - s += cls.generate_neuron_models_documentation(neuron_models, all_nestml_neuron_models, target_path) - - s += "Synapse models\n~~~~~~~~~~~~~~\n\n" - - synapse_models = [("static_synapse", "static_synapse.nestml"), ("noisy_synapse", "noisy_synapse.nestml"), - ("stdp_synapse", "stdp_synapse.nestml"), - ("stdp_nn_pre_centered_synapse", "stdp_nn_pre_centered_synapse.nestml"), - ("stdp_nn_restr_symm_synapse", "stdp_nn_restr_symm_synapse.nestml"), - ("stdp_nn_symm_synapse", "stdp_nn_symm_synapse.nestml"), - ("stdp_triplet_nn_synapse", "stdp_triplet_synapse.nestml"), - ("third_factor_stdp_synapse", "third_factor_stdp_synapse.nestml"), - ("neuromodulated_stdp_synapse", "neuromodulated_stdp_synapse.nestml")] - - all_synapse_models = [s[:-7] for s in list(os.walk(os.path.join(cls.models_input_path, "synapses")))[0][2] if s[-7:] == ".nestml"] - s += cls.generate_synapse_models_documentation(synapse_models, all_synapse_models, target_path) - - with open(os.path.join(target_path, "models_library.rst"), "w") as f: - f.write(s) - - @classmethod - def generate_synapse_models_documentation(cls, models, all_models, target_path): - r""" - allmodels : list of str - List of all model file names (e.g. "iaf_psc_exp") found in the models directory. - models : list of tuples - Tested models and test conditions, in order. - """ - - print("All synapse models = " + str(all_models)) - - untested_models = copy.deepcopy(all_models) - for model in models: - model_fname = removesuffix(model[1], ".nestml") - assert model_fname in all_models - if model_fname in untested_models: - untested_models.remove(model_fname) - print("untested_models = " + str(untested_models)) - - s = "" - - for model in models: - model_name = model[0] - model_fname = model[1] - model_fname_stripped = removesuffix(model_fname, ".nestml") - - if model_fname_stripped in untested_models: - untested_models.remove(model_fname_stripped) - - s += "\n" - s += ":doc:`" + model_name + " <" + model_name + ">`" + "\n" - s += "-" * len(":doc:`" + model_name + " <" + model_name + ">`") + "\n" - - model_doc_title = get_model_doc_title(os.path.join(cls.models_input_path, "synapses", model_fname)) - if model_doc_title.startswith(model_name): - model_doc_title = removeprefix(model_doc_title, model_name) - model_doc_title = removeprefix(model_doc_title, " - ") - s += "\n" + model_doc_title + "\n" - - s += "\n" - s += "Source file: `" + model_name + " `_\n" - s += "\n" - - for model in untested_models: - model_name = removesuffix(model, "_synapse") - model_fname = model_name + ".nestml" - - s += "\n" - s += ":doc:`" + model_name + " <" + model_name + ">`" + "\n" - s += "-" * len(":doc:`" + model_name + " <" + model_name + ">`") + "\n" - - model_doc_title = get_model_doc_title(os.path.join(cls.models_input_path, "synapses", model_name)) - if model_doc_title.startswith(model_name): - model_doc_title = removeprefix(model_doc_title, model_name) - model_doc_title = removeprefix(model_doc_title, " - ") - s += "\n" + model_doc_title + "\n" - - s += "\n" - s += "Source file: `" + model_name + " `_\n" - s += "\n" - - return s - - @classmethod - def generate_neuron_models_documentation(cls, models, all_models, target_path): - """ - models : list of tuples - Tested models and test conditions, in order. - allmodels : list of str - List of all model file names (e.g. "iaf_psc_exp") found in the models directory. - """ - - print("All NESTML neuron models = " + str(all_models)) - - untested_models = copy.deepcopy(all_models) - for model in models: - model_name = removesuffix(model, "_nestml") - assert model_name in all_models - if model_name in untested_models: - untested_models.remove(model_name) - print("Untested NESTML neuron models = " + str(untested_models)) - - s = "" - - for model in models: - testant = removesuffix(model, "_nestml") - model_fname = testant + ".nestml" # strip "_nestml" - model_name = removesuffix(testant, "_neuron") - - s += "\n" - s += ":doc:`" + model_name + " <" + model_name + ">`" + "\n" - s += "-" * len(":doc:`" + model_name + " <" + model_name + ">`") + "\n" - - model_doc_title = get_model_doc_title(os.path.join(cls.models_input_path, "neurons", model_fname)) - if model_doc_title.startswith(model_name): - model_doc_title = removeprefix(model_doc_title, model_name) - model_doc_title = removeprefix(model_doc_title, " - ") - s += "\n" + model_doc_title + "\n" - - s += "\n" - s += "Source file: `" + model_fname + " `_\n" - s += "\n" - s += ".. list-table::\n" - s += "\n" - s += " * - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library" \ - "/nestml_models_library_[" + \ - model_name + "]_synaptic_response_small.png\n" - s += " :alt: " + model_name + "\n" - s += "\n" - s += " - .. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library" \ - "/nestml_models_library_[" + \ - model_name + "]_f-I_curve_small.png\n" - s += " :alt: " + model_name + "\n" - s += "\n" - - with open(os.path.join(target_path, model_name + "_characterisation.rst"), "w") as f: - s_ = "Synaptic response\n-----------------\n\n" - s_ += ".. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library" \ - "/nestml_models_library_[" + \ - model_name + "]_synaptic_response.png\n" - s_ += " :alt: " + testant + "\n" - s_ += "\n" - s_ += "f-I curve\n---------\n\n" - s_ += ".. figure:: https://raw.githubusercontent.com/nest/nestml/master/doc/models_library" \ - "/nestml_models_library_[" + \ - model_name + "]_f-I_curve.png\n" - s_ += " :alt: " + testant + "\n" - s_ += "\n" - f.write(s_) - - for model_name in untested_models: - model_fname = model_name + ".nestml" - model_name = removesuffix(model_name, "_neuron") - - s += "\n" - s += ":doc:`" + model_name + " <" + model_name + ">`" + "\n" - s += "-" * len(":doc:`" + model_name + " <" + model_name + ">`") + "\n" - - model_doc_title = get_model_doc_title(os.path.join(cls.models_input_path, "neurons", model_fname)) - if model_doc_title.startswith(model_name): - model_doc_title = removeprefix(model_doc_title, model_name) - model_doc_title = removeprefix(model_doc_title, " - ") - s += "\n" + model_doc_title + "\n" - - s += "\n" - s += "Source file: `" + model_fname + " `_\n" - s += "\n" - - return s - - @classmethod - def _test_model_curr_inj(cls, testant): - """For different levels of injected current, verify that behaviour is the same between NEST and NESTML""" - model_name = removesuffix(removesuffix(testant, "_nestml"), "_neuron") - t_stop = 1000. # [ms] - - I_stim_vec = np.linspace(10E-12, 1E-9, 100) # [A] - rate_testant = float("nan") * np.ones_like(I_stim_vec) - for i, I_stim in enumerate(I_stim_vec): - - nest.ResetKernel() - nest.SetKernelStatus({"resolution": .01}) # aeif_cond_exp model requires resolution <= 0.01 ms - - # Create the neuron - neuron = nest.Create(testant) - - # Create the dc generator - dc = nest.Create("dc_generator", params={"amplitude": I_stim * 1E12}) # 1E12: convert A to pA - nest.Connect(dc, neuron) - - # Create the multimeter - multimeter = nest.Create("multimeter") - V_m_specifier = "V_m" # "delta_V_m" - nest.SetStatus(multimeter, {"record_from": [V_m_specifier]}) - nest.Connect(multimeter, neuron) - - # Create a spike recorder - if NESTTools.detect_nest_version().startswith("v2"): - sd_testant = nest.Create("spike_detector") - else: - sd_testant = nest.Create("spike_recorder") - - nest.Connect(neuron, sd_testant) - - # Simulate - nest.Simulate(t_stop) - - # Read the membrane potential and spike time values - dmm = nest.GetStatus(multimeter)[0] - Vms = dmm["events"][V_m_specifier] - ts = dmm["events"]["times"] - - rate_testant[i] = nest.GetStatus(sd_testant)[0]["n_events"] / t_stop * 1000 - - if TEST_PLOTS: - # Sub-threshold plot - if len(I_stim_vec) < 20: - marker = "o" - else: - marker = None - fig, ax = plt.subplots(1, 1) - ax = [ax] - ax[0].plot(ts, Vms, label="Testant " + testant) - for _ax in ax: - _ax.legend(loc="upper right") - _ax.grid() - _ax.set_ylabel("Firing rate [Hz]") - ax[0].set_xlabel("$I_{inj}$ [pA]") - plt.savefig( - "/tmp/nestml_nest_integration_test_subthreshold_[" + model_name + "]_[" + testant + "].png") - plt.close(fig) - - # F-I curve - for figsize, fname_snip in zip([(8, 5), (4, 3)], ["", "_small"]): - fig, ax = plt.subplots(1, 1, figsize=figsize) - ax = [ax] - ax[0].plot(I_stim_vec * 1E12, rate_testant, marker=marker, label="Testant " + testant) - for _ax in ax: - _ax.grid() - _ax.set_ylabel("Firing rate [Hz]") - ax[0].set_xlabel("$I_{inj}$ [pA]") - plt.tight_layout() - plt.savefig("/tmp/nestml_models_library_[" + model_name + "]_f-I_curve" + fname_snip + ".png") - plt.close(fig) - - @classmethod - def _test_model_psc(cls, testant): - model_name = removesuffix(removesuffix(testant, "_nestml"), "_neuron") - - nest.ResetKernel() - nest.SetKernelStatus({"resolution": .01}) # aeif_cond_exp model requires resolution <= 0.01 ms - - spike_times = [100.0, 200.0] - spike_weights = [1., -1.] - - # Create a neuron - neuron = nest.Create(testant) - - # Create a spike generator with spike times and spike weights - spikegenerator = nest.Create("spike_generator", - params={"spike_times": spike_times, "spike_weights": spike_weights}) - nest.Connect(spikegenerator, neuron) - - # Create a spike recorder - spike_recorder2 = nest.Create("spike_recorder") - nest.Connect(neuron, spike_recorder2) - - # Create a multimeter - multimeter = nest.Create("multimeter") - V_m_specifier = "V_m" - nest.SetStatus(multimeter, {"record_from": [V_m_specifier]}) - nest.Connect(multimeter, neuron) - - # Simulate - nest.Simulate(400.) - - # Read the membrane potential and spike time values - dmm = nest.GetStatus(multimeter)[0] - Vms = dmm["events"][V_m_specifier] - ts = dmm["events"]["times"] - - # Plot for post-synaptic response - if TEST_PLOTS: - for figsize, fname_snip in zip([(8, 5), (4, 3)], ["", "_small"]): - fig, ax = plt.subplots(1, 1, figsize=figsize) - ax = [ax] - ax[0].plot(ts, Vms, label=testant) - for _ax in ax: - _ax.grid() - ax[0].set_xlabel("Time [ms]") - ax[0].set_ylabel("$V_m$ [mV]") - plt.tight_layout() - plt.savefig( - "/tmp/nestml_models_library_[" + model_name + "]_synaptic_response" + fname_snip + ".png") - plt.close(fig) diff --git a/pynestml/codegeneration/resources_autodoc/nestml_neuron_model.jinja2 b/pynestml/codegeneration/resources_autodoc/nestml_neuron_model.jinja2 index 5617c1104..2d3abf225 100644 --- a/pynestml/codegeneration/resources_autodoc/nestml_neuron_model.jinja2 +++ b/pynestml/codegeneration/resources_autodoc/nestml_neuron_model.jinja2 @@ -48,9 +48,6 @@ Source code The model source code can be found in the NESTML models repository here: `{{neuronName}} `_. -Characterisation -++++++++++++++++ - .. include:: {{neuronName}}_characterisation.rst diff --git a/pynestml/codegeneration/resources_autodoc/nestml_synapse_model.jinja2 b/pynestml/codegeneration/resources_autodoc/nestml_synapse_model.jinja2 index 1215d2b9f..eb40fd47b 100644 --- a/pynestml/codegeneration/resources_autodoc/nestml_synapse_model.jinja2 +++ b/pynestml/codegeneration/resources_autodoc/nestml_synapse_model.jinja2 @@ -28,9 +28,6 @@ Source code The model source code can be found in the NESTML models repository here: `{{synapseName}} `_. -Characterisation -++++++++++++++++ - .. include:: {{synapseName}}_characterisation.rst