Merge pull request #203 from DimitriPlotnikov/master

new neuron model

models/iaf_cond_beta.nestml

@@ -1,56 +1,103 @@
+/* Name: iaf_cond_beta - Simple conductance based leaky integrate-and-fire neuron model.
+
+Description:
+iaf_cond_beta is an implementation of a spiking neuron using IAF dynamics with
+conductance-based synapses. Incoming spike events induce a post-synaptic change
+of conductance modelled by an beta function. The beta function
+is normalised such that an event of weight 1.0 results in a peak current of 1 nS
+at t = tau_syn.
+
+Parameters:
+The following parameters can be set in the status dictionary.
+E_L          double - Leak reversal potential in mV.
+C_m          double - Capacity of the membrane in pF
+t_ref        double - Duration of refractory period in ms.
+V_th         double - Spike threshold in mV.
+V_reset      double - Reset potential of the membrane in mV.
+E_ex         double - Excitatory reversal potential in mV.
+E_in         double - Inhibitory reversal potential in mV.
+g_L          double - Leak conductance in nS;
+tau_ex_rise  double - Rise time of the excitatory synaptic beta function in ms (rise time).
+tau_ex_decay double - Time constant of the excitatory synaptic exponential function in ms (decay time).
+tau_in_rise  double - Rise time of the inhibitory synaptic beta function in ms (rise time).
+tau_in_decay double - Time constant of the excitatory synaptic exponential function in ms (decay time).
+I_e          double - Constant input current in pA.
+F_E          double - Constant External input conductance in nS (excitatory).
+F_I          double - Constant External input conductance in nS (inhibitory).
+
+Sends: SpikeEvent
+
+Receives: SpikeEvent, CurrentEvent, DataLoggingRequest
+
+References:
+Meffin, H., Burkitt, A. N., & Grayden, D. B. (2004). An analytical
+model for the large, fluctuating synaptic conductance state typical of
+neocortical neurons in vivo				. J.  Comput. Neurosci., 16, 159-175.
+Bernander, O ., Douglas, R. J., Martin, K. A. C., & Koch, C. (1991).
+Synaptic background activity influences spatiotemporal integration in
+single pyramidal cells.  Proc. Natl. Acad. Sci. USA, 88(24),
+11569-11573.
+Kuhn, Aertsen, Rotter (2004) Neuronal Integration of Synaptic Input in
+the Fluctuation- Driven Regime. Jneurosci 24(10) 2345-2356
+Author: Schrader, Plesser
+SeeAlso: iaf_cond_exp, iaf_cond_beta_mc, iaf_cond_alpha */
+
 neuron iaf_cond_beta_neuron:
 
 
   state:
     # membrane potential
-    V_m mV
+    V_m mV = E_L
     # inputs from the inh conductance
     GI nS = 0
     # inputs from the exc conductance
     GE nS = 0
+
+    alias I_syn_exc pA = (F_E + GE) * ( V_m - E_ex )
+    alias I_syn_inh pA = (F_I + GI) * ( V_m - E_in )
+    alias I_leak pA = g_L * ( V_m - E_L )
   end
 
   equations:
-    # Implicit
-    GI'' = -GI'/tau_syn_rise_I
-    GI' = GI' - GI/tau_syn_decay_I
+      GI'' = -GI'/tau_syn_rise_I
+      GI' = GI' - GI/tau_syn_decay_I
 
-    GE'' = -GE'/tau_syn_rise_E
-    GE' = GE'  -GE/tau_syn_decay_E
+      GE'' = -GE'/tau_syn_rise_E
+      GE' = GE' -GE/tau_syn_decay_E
 
-    V_m' = -1/Tau * (V_m - E_L)  - 1/C_m * ( GI * (V_m-V_reversalI) + GE * (V_m-V_reversalE) - (I_e + I_stim))
+      V_m' =  (-I_leak - I_syn_exc - I_syn_inh + I_stim + I_e ) / C_m
   end
 
   parameter:
-   V_th mV = -55.0      # Threshold Potential in mV
-   V_reset mV = -60.0   # Reset Potential in mV
-   t_ref ms = 2.0       # Refractory period in ms
-   g_L ms = 16.6667     # Leak Conductance in nS
-   C_m pF = 250.0       # Membrane Capacitance in pF
-   alias Tau ms = (1 / g_L) * C_m
-   V_reversalE mV = 0          # Excitatory reversal Potential in mV
-   V_reversalI mV = -85.0      # Inhibitory reversal Potential in mV
-   E_L mV = -70.0       # Leak reversal Potential (aka resting potential) in mV
-   tau_syn_rise_I ms = 0.2    # Synaptic Time Constant Excitatory Synapse in ms
-   tau_syn_decay_I ms = 2.0    # Synaptic Time Constant for Inhibitory Synapse in ms
-   tau_syn_rise_E ms = 0.2    # Synaptic Time Constant Excitatory Synapse in ms
-   tau_syn_decay_E ms = 2.0    # Synaptic Time Constant for Inhibitory Synapse in ms
-   I_e pA = 0           # Constant Current in pA
-
-   # Input current injected by CurrentEvent.
-   # This variable is used to transport the current applied into the
-   # _dynamics function computing the derivative of the state vector.
-   I_stim pA = 0
+    E_L mV = -85.0mV # Leak reversal Potential (aka resting potential) in mV
+    C_m pF = 250.0pF # Capacity of the membrane
+    t_ref ms = 2.0ms # Refractory period in ms
+    V_th mV = -55.0mV      # Threshold Potential in mV
+    V_reset mV = -60.0mV   # Reset Potential in mV
+    E_ex mV = 0mV          # Excitatory reversal Potential in mV
+    E_in mV = -85.0mV      # Inhibitory reversal Potential in mV
+    g_L nS = 16.6667nS       # Leak Conductance in nS
+    tau_syn_rise_I ms = 0.2ms    # Synaptic Time Constant Excitatory Synapse in ms
+    tau_syn_decay_I ms = 2.0ms   # Synaptic Time Constant for Inhibitory Synapse in ms
+    tau_syn_rise_E ms = 0.2ms    # Synaptic Time Constant Excitatory Synapse in ms
+    tau_syn_decay_E ms = 2.0ms   # Synaptic Time Constant for Inhibitory Synapse in ms
+    I_e pA = 0pA           # Constant Current in pA
+    F_E nS = 0nS            # Constant External input conductance in nS (excitatory).
+    F_I nS = 0nS           # - Constant External input conductance in nS (inhibitory).
+    # Input current injected by CurrentEvent.
+    # This variable is used to transport the current applied into the
+    # _dynamics function computing the derivative of the state vector.
+    I_stim pA = 0pA
   end
 
   internal:
     r integer
 
-    # Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
+    # Impulse to add to GE' on spike arrival to evoke unit-amplitude
     # conductance excursion.
-    PSConInit_E real = 1.0 * e / tau_syn_rise_E # TODO why only one?
+    PSConInit_E real = 1.0 * e / tau_syn_rise_E #
 
-    # Impulse to add to DG_INH on spike arrival to evoke unit-amplitude
+    # Impulse to add to GI' on spike arrival to evoke unit-amplitude
     # conductance excursion.
     PSConInit_I real = 1.0 * e / tau_syn_rise_I
 
@@ -67,13 +114,8 @@ neuron iaf_cond_beta_neuron:
   output: spike
 
   update:
-    if r == 0: # not refractory
-      # TODO intagrate
-
-    else:
-      r = r - 1
-    end
 
+    integrate(V_m)
     if r != 0: # not refractory
       r =  r - 1
       V_m = V_reset # clamp potential
@@ -85,8 +127,8 @@ neuron iaf_cond_beta_neuron:
 
     end
 
-    # TODO DGE = DGE + spikeExc.getSum() * PSConInit_E;
-    # TODO DGI = DGI + spikeInh.getSum() * PSConInit_I;
+    GE' += spikeExc.getSum() * PSConInit_E;
+    GI' += spikeInh.getSum() * PSConInit_I;
     I_stim = currents.getSum()
   end
 

src/test/java/org/nest/integration/NESTCodeGeneratorIntegrationTest.java

@@ -164,7 +164,7 @@ public void testIzhikevich() {
   @Ignore("Don't run this tests on github")
   @Test
   public void testManually() {
-    final List<String> modelName = Lists.newArrayList("models/iaf_cond_exp_implicit.nestml");
+    final List<String> modelName = Lists.newArrayList("models/iaf_cond_beta.nestml");
     modelName.forEach(this::checkCocos);
     modelName.forEach(this::invokeCodeGenerator);
     final List<ASTNESTMLCompilationUnit> roots = modelName.stream()