diff --git a/doc/models_library/iaf_psc_exp_dend_neuron.rst b/doc/models_library/iaf_psc_exp_dend_neuron.rst deleted file mode 100644 index ce4c6f49e..000000000 --- a/doc/models_library/iaf_psc_exp_dend_neuron.rst +++ /dev/null @@ -1,97 +0,0 @@ -iaf_psc_exp_dend_neuron -####################### - - -iaf_psc_exp_dend - Leaky integrate-and-fire neuron model with exponential PSCs - -Description -+++++++++++ - -iaf_psc_exp is an implementation of a leaky integrate-and-fire model -with exponential-kernel postsynaptic currents (PSCs) according to [1]_. -Thus, postsynaptic currents have an infinitely short rise time. - -The threshold crossing is followed by an absolute refractory period (t_ref) -during which the membrane potential is clamped to the resting potential -and spiking is prohibited. - -.. note:: - If tau_m is very close to tau_syn_ex or tau_syn_in, numerical problems - may arise due to singularities in the propagator matrics. If this is - the case, replace equal-valued parameters by a single parameter. - - For details, please see ``IAF_neurons_singularity.ipynb`` in - the NEST source code (``docs/model_details``). - - -References -++++++++++ - -.. [1] Tsodyks M, Uziel A, Markram H (2000). Synchrony generation in recurrent - networks with frequency-dependent synapses. The Journal of Neuroscience, - 20,RC50:1-5. URL: https://infoscience.epfl.ch/record/183402 - - -See also -++++++++ - -iaf_cond_exp - - - -Parameters -++++++++++ -.. csv-table:: - :header: "Name", "Physical unit", "Default value", "Description" - :widths: auto - - - "C_m", "pF", "250pF", "Capacity of the membrane" - "tau_m", "ms", "10ms", "Membrane time constant" - "tau_syn_inh", "ms", "2ms", "Time constant of inhibitory synaptic current" - "tau_syn_exc", "ms", "2ms", "Time constant of excitatory synaptic current" - "refr_T", "ms", "2ms", "Duration of refractory period" - "E_L", "mV", "-70mV", "Resting potential" - "V_reset", "mV", "-70mV", "Reset potential of the membrane" - "V_th", "mV", "-55mV", "Spike threshold potential" - "I_e", "pA", "0pA", "constant external input current" - - - -State variables -+++++++++++++++ - -.. csv-table:: - :header: "Name", "Physical unit", "Default value", "Description" - :widths: auto - - - "V_m", "mV", "E_L", "Membrane potential" - "I_dend", "pA", "0pA", "Third factor, to be read out by synapse during weight update" - "refr_t", "ms", "0ms", "Refractory period timer" - "is_refractory", "boolean", "false", "" - - - - -Equations -+++++++++ - - - -.. math:: - \frac{ dV_{m} } { dt }= \frac{ -(V_{m} - E_{L}) } { \tau_{m} } + \frac 1 { C_{m} } \left( { (I_{syn} + I_{e} + I_{stim}) } \right) - - - -Source code -+++++++++++ - -The model source code can be found in the NESTML models repository here: `iaf_psc_exp_dend_neuron `_. - -.. include:: iaf_psc_exp_dend_neuron_characterisation.rst - - -.. footer:: - - Generated at 2024-05-22 14:51:14.593810 \ No newline at end of file diff --git a/doc/models_library/index.rst b/doc/models_library/index.rst index af5b70afe..cbb35b596 100644 --- a/doc/models_library/index.rst +++ b/doc/models_library/index.rst @@ -287,14 +287,6 @@ Source file: `iaf_psc_delta_neuron.nestml ` --------------------------------------------------------- - -iaf_psc_exp_dend - Leaky integrate-and-fire neuron model with exponential PSCs - -Source file: `iaf_psc_exp_dend_neuron.nestml `_ - - :doc:`iaf_psc_exp_htum_neuron ` -------------------------------------------------------- diff --git a/doc/models_library/output.html b/doc/models_library/output.html index 3dd64683d..d2a5c1588 100644 --- a/doc/models_library/output.html +++ b/doc/models_library/output.html @@ -246,13 +246,6 @@

-

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>

diff --git a/models/neurons/iaf_psc_exp_dend_neuron.nestml b/models/neurons/iaf_psc_exp_dend_neuron.nestml deleted file mode 100644 index 38a3e8e73..000000000 --- a/models/neurons/iaf_psc_exp_dend_neuron.nestml +++ /dev/null @@ -1,87 +0,0 @@ -""" -iaf_psc_exp_dend - Leaky integrate-and-fire neuron model with exponential PSCs -######################################################################### - -Description -+++++++++++ - -iaf_psc_exp is an implementation of a leaky integrate-and-fire model -with exponential-kernel postsynaptic currents (PSCs) according to [1]_. -Thus, postsynaptic currents have an infinitely short rise time. - -The threshold crossing is followed by an absolute refractory period (t_ref) -during which the membrane potential is clamped to the resting potential -and spiking is prohibited. - -.. note:: - If tau_m is very close to tau_syn_ex or tau_syn_in, numerical problems - may arise due to singularities in the propagator matrics. If this is - the case, replace equal-valued parameters by a single parameter. - - For details, please see ``IAF_neurons_singularity.ipynb`` in - the NEST source code (``docs/model_details``). - - -References -++++++++++ - -.. [1] Tsodyks M, Uziel A, Markram H (2000). Synchrony generation in recurrent - networks with frequency-dependent synapses. The Journal of Neuroscience, - 20,RC50:1-5. URL: https://infoscience.epfl.ch/record/183402 - - -See also -++++++++ - -iaf_cond_exp -""" -model iaf_psc_exp_dend_neuron: - - state: - V_m mV = E_L # Membrane potential - I_dend pA = 0 pA # Third factor, to be read out by synapse during weight update - refr_t ms = 0 ms # Refractory period timer - - equations: - kernel I_kernel_inh = exp(-t/tau_syn_inh) - kernel I_kernel_exc = exp(-t/tau_syn_exc) - inline I_syn pA = convolve(I_kernel_exc, exc_spikes) * pA - convolve(I_kernel_inh, inh_spikes) * pA - V_m' = -(V_m - E_L) / tau_m + (I_syn + I_e + I_stim) / C_m - refr_t' = -1e3 * ms/s # refractoriness is implemented as an ODE, representing a timer counting back down to zero. XXX: TODO: This should simply read ``refr_t' = -1 / s`` (see https://github.com/nest/nestml/issues/984) - - parameters: - C_m pF = 250 pF # Capacity of the membrane - tau_m ms = 10 ms # Membrane time constant - tau_syn_inh ms = 2 ms # Time constant of inhibitory synaptic current - tau_syn_exc ms = 2 ms # Time constant of excitatory synaptic current - refr_T ms = 2 ms # Duration of refractory period - E_L mV = -70 mV # Resting potential - V_reset mV = -70 mV # Reset potential of the membrane - V_th mV = -55 mV # Spike threshold potential - - # constant external input current - I_e pA = 0 pA - - input: - exc_spikes <- excitatory spike - inh_spikes <- inhibitory spike - I_stim pA <- continuous - - output: - spike - - update: - I_dend *= .95 # I_dend is always evolved, even when refractory - - if refr_t > 0 ms: - # neuron is absolute refractory, do not evolve V_m - integrate_odes(refr_t) - else: - # neuron not refractory - integrate_odes(V_m) - - onCondition(refr_t <= 0 ms and V_m >= V_th): # threshold crossing - # threshold crossing - refr_t = refr_T # start of the refractory period - V_m = V_reset - emit_spike()