Merge pull request #28 from HanjiaJiang/new_tripartite_hj

Changing parameter values for astrocyte_lr_1994

doc/htmldoc/model_details/astrocyte_model_implementation.ipynb

@@ -170,7 +170,7 @@
     "    y[0, 1] = 1.0\n",
     "    y[0, 2] = 1.0\n",
     "    fos = []  # full output dict from odeint()\n",
-    "    delta_ip3 = 5.0  # parameter determining the increase in IP3 induced by synaptic input\n",
+    "    delta_ip3 = p.delta_IP3  # parameter determining the increase in IP3 induced by synaptic input\n",
     "\n",
     "    # update time-step by time-step\n",
     "    for k in range(1, n):\n",
@@ -211,7 +211,7 @@
     "    \"Kd_IP3_2\": 0.9434,\n",
     "    \"Km_SERCA\": 0.1,\n",
     "    \"ratio_ER_cyt\": 0.185,\n",
-    "    \"delta_IP3\": 5.0,\n",
+    "    \"delta_IP3\": 0.0002,\n",
     "    \"k_IP3R\": 0.0002,\n",
     "    \"rate_L\": 0.00011,\n",
     "    \"tau_IP3\": 7142.0,\n",
@@ -318,7 +318,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.12.1"
   }
  },
  "nbformat": 4,

models/astrocyte_lr_1994.cpp

@@ -123,7 +123,7 @@ nest::astrocyte_lr_1994::Parameters_::Parameters_()
   , Km_SERCA_( 0.1 )    // µM
   , SIC_scale_( 1.0 )
   , SIC_th_( 0.19669 )    // µM
-  , delta_IP3_( 5.0 )     // µM
+  , delta_IP3_( 0.0002 )  // µM
   , k_IP3R_( 0.0002 )     // 1/(µM*ms)
   , rate_IP3R_( 0.006 )   // 1/ms
   , rate_L_( 0.00011 )    // 1/ms

pynest/examples/astrocytes/astrocyte_brunel_bernoulli.py

@@ -76,7 +76,6 @@
 
 sim_params = {
     "dt": 0.1,  # simulation resolution in ms
-    "pre_sim_time": 100.0,  # pre-simulation time in ms (data not recorded)
     "sim_time": 1000.0,  # simulation time in ms
     "N_rec_spk": 100,  # number of neurons to record from with spike recorder
     "N_rec_mm": 50,  # number of nodes (neurons, astrocytes) to record from with multimeter
@@ -99,7 +98,7 @@
 }
 
 syn_params = {
-    "w_a2n": 0.01,  # weight of astrocyte-to-neuron connection
+    "w_a2n": 0.05,  # weight of astrocyte-to-neuron connection
     "w_e": 1.0,  # weight of excitatory connection in nS
     "w_i": -4.0,  # weight of inhibitory connection in nS
     "d_e": 2.0,  # delay of excitatory connection in ms
@@ -112,8 +111,6 @@
 astrocyte_model = "astrocyte_lr_1994"
 astrocyte_params = {
     "IP3": 0.4,  # IP3 initial value in µM
-    "delta_IP3": 0.5,  # Parameter determining the increase in astrocytic IP3 concentration induced by synaptic input
-    "tau_IP3": 2.0,  # Time constant of the exponential decay of astrocytic IP3
 }
 
 ###############################################################################
@@ -329,7 +326,6 @@ def run_simulation():
     random.seed(sim_params["seed"])
 
     # simulation settings
-    pre_sim_time = sim_params["pre_sim_time"]
     sim_time = sim_params["sim_time"]
 
     # create and connect nodes
@@ -355,10 +351,6 @@ def run_simulation():
     nest.Connect(mm_neuron, neuron_list_for_mm)
     nest.Connect(mm_astro, astro_list_for_mm)
 
-    # run pre-simulation
-    print("Running pre-simulation ...")
-    nest.Simulate(pre_sim_time)
-
     # run simulation
     print("Running simulation ...")
     nest.Simulate(sim_time)

pynest/examples/astrocytes/astrocyte_brunel_fixed_indegree.py

@@ -76,7 +76,6 @@
 
 sim_params = {
     "dt": 0.1,  # simulation resolution in ms
-    "pre_sim_time": 100.0,  # pre-simulation time in ms (data not recorded)
     "sim_time": 1000.0,  # simulation time in ms
     "N_rec_spk": 100,  # number of neurons to record from with spike recorder
     "N_rec_mm": 50,  # number of nodes (neurons, astrocytes) to record from with multimeter
@@ -100,7 +99,7 @@
 }
 
 syn_params = {
-    "w_a2n": 0.01,  # weight of astrocyte-to-neuron connection
+    "w_a2n": 0.05,  # weight of astrocyte-to-neuron connection
     "w_e": 1.0,  # weight of excitatory connection in nS
     "w_i": -4.0,  # weight of inhibitory connection in nS
     "d_e": 2.0,  # delay of excitatory connection in ms
@@ -113,8 +112,6 @@
 astrocyte_model = "astrocyte_lr_1994"
 astrocyte_params = {
     "IP3": 0.4,  # IP3 initial value in µM
-    "delta_IP3": 0.5,  # Parameter determining the increase in astrocytic IP3 concentration induced by synaptic input
-    "tau_IP3": 2.0,  # Time constant of the exponential decay of astrocytic IP3
 }
 
 ###############################################################################
@@ -326,7 +323,6 @@ def run_simulation():
     random.seed(sim_params["seed"])
 
     # simulation settings
-    pre_sim_time = sim_params["pre_sim_time"]
     sim_time = sim_params["sim_time"]
 
     # create and connect nodes
@@ -352,10 +348,6 @@ def run_simulation():
     nest.Connect(mm_neuron, neuron_list_for_mm)
     nest.Connect(mm_astro, astro_list_for_mm)
 
-    # run pre-simulation
-    print("Running pre-simulation ...")
-    nest.Simulate(pre_sim_time)
-
     # run simulation
     print("Running simulation ...")
     nest.Simulate(sim_time)

pynest/examples/astrocytes/astrocyte_interaction.py

@@ -85,7 +85,7 @@
 # neuron parameters
 params_neuro = {"tau_syn_ex": 2.0}
 # astrocyte parameters
-params_astro = {"IP3_0": 0.16}
+params_astro = {"delta_IP3": 0.2}
 # weights of connections
 w_pre2astro = 1.0
 w_pre2post = 1.0

pynest/examples/astrocytes/astrocyte_single.py

@@ -68,10 +68,10 @@
 # simulation time
 sim_time = 60000
 # astrocyte parameters
-params_astro = {"IP3_0": 0.16}
+params_astro = {"delta_IP3": 0.2}
 # Poisson input for the astrocyte
 poisson_rate = 1.0
-poisson_weight = 0.1
+poisson_weight = 1.0
 
 ###############################################################################
 # Create astrocyte and devices and connect them.

pynest/examples/astrocytes/astrocyte_small_network.py

@@ -165,8 +165,7 @@
 astrocyte_model = "astrocyte_lr_1994"
 astrocyte_params = {
     "IP3": 0.4,  # IP3 initial value in µM
-    "delta_IP3": 2.0,  # parameter determining the increase in astrocytic IP3 concentration induced by synaptic input
-    "tau_IP3": 10.0,  # time constant of the exponential decay of astrocytic IP3
+    "delta_IP3": 0.2,  # parameter determining the increase in astrocytic IP3 concentration induced by synaptic input
 }
 
 ###############################################################################