Add documentation on neuron parameters

README.md

@@ -229,7 +229,7 @@ The multi-area model can be run in different modes.
 
    As described in Schmidt et al. (2018) (https://doi.org/10.1371/journal.pcbi.1006359),
    the model can be run in two dynamical regimes - the Ground state and the Metastable state.
-   The state is controlled by the value of the ```cc_weights_factor``` parameter.
+   The state is controlled by the value of the ```cc_weights_factor``` and ```cc_weights_I_factor``` parameters.
 
 ## Test suite
 

multiarea_model/default_params.py

@@ -99,8 +99,10 @@
     'neuron_model': 'iaf_psc_exp',
     # neuron parameters
     'single_neuron_dict': single_neuron_dict,
-    # Mean and standard deviation for the
-    # distribution of initial membrane potentials
+    # The initial membrane potential distribution is chosen 
+    # to be centered on a hyperpolarized state to limit synchronous 
+    # initial firing, which could bring the model into a high-activity 
+    # state when the parameters are set according to the metastable condition.
     'V0_mean': -150.,
     'V0_sd': 50.}
 
@@ -182,8 +184,9 @@
     # activity described in Schmidt et al. (2018). 
     # A weight factor of 1.0 produces Ground state activity.
     'cc_weights_factor': 1.9,
-    # factor to scale cortico-cortical inh. weights in relation
-    # to exc. weights (chi_I)
+    # Factor to scale cortico-cortical inh. weights in relation
+    # to exc. weights (chi_I). Default is 2.0 to reproduce metastable state
+    # activity. For ground state activity, set to 1.0.
     'cc_weights_I_factor': 2.,
 
     # 'switch whether to distribute weights lognormally

run_example_downscaled.py

@@ -14,7 +14,8 @@
 """
 d = {}
 conn_params = {'replace_non_simulated_areas': 'het_poisson_stat',
-               'cc_weights_factor': 1.0} # run model in Ground State
+               'cc_weights_factor': 1.0, # run model in Ground State
+               'cc_weights_I_factor': 1.0}
 network_params = {'N_scaling': 0.01,
                   'K_scaling': 0.01,
                   'fullscale_rates': os.path.join(base_path, 'tests/fullscale_rates.json')}