match nml and netpyne

Author: HengyeZhu

NeuroML2/compare_MC/RE/LEMS_RE_reduced_cell_step_test.xml

@@ -13,7 +13,9 @@
 soma['mechs']['pas'] = {'g': 5e-5, 'e': -77}
 soma['mechs']['cadad'] = {'cainf': 0.00024, 'depth': 1, 'kd': 0.0, 'kt': 0.0, 'taur': 5}
 # soma['mechs']['kl'] = {'gmax': 3e-06}
-soma['mechs']['itre'] = {"gmax": 0.002,"shift": 2.0}
+# soma['mechs']['itre'] = {"gmax": 0.002,"shift": 2.0}
+soma['mechs']['hh2ad'] = {"gkbar": 0.01,"gnabar": 0.09,"vtraub": -50.0}
+
 
 RE_HH_reduced_dict = {'secs': {'soma': soma}}
 netParams.cellParams['RE_HH_reduced'] = RE_HH_reduced_dict  # add rule dict to list of cell property rules
@@ -37,7 +39,7 @@
 simConfig.verbose = False           # Show detailed messages
 simConfig.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'}}  # Dict with traces to record
 simConfig.recordStep = 0.01            # Step size in ms to save data (eg. V traces, LFP, etc)
-simConfig.filename = 'RE_reduced_itre'         # Set file output name
+simConfig.filename = 'RE_reduced_hh2ad'         # Set file output name
 simConfig.savePickle = False        # Save params, network and sim output to pickle file
 simConfig.saveDataInclude = ['simData']  
 simConfig.saveJson = True 

NeuroML2/compare_MC/RE/RE_netpy.py

@@ -29,9 +29,10 @@
     <biophysicalProperties id="biophys">
         <membraneProperties>
 
-            <channelDensityNernst id="itre_soma" ionChannel="itre" condDensity="0.002 S_per_cm2" ion="ca"/>
-            <channelDensity ionChannel="pas" id="pas_soma" ion="non_specific"  erev="-77.0 mV" condDensity="5e-5 S_per_cm2"/>
 
+            <channelDensity ionChannel="pas" id="pas_soma" ion="non_specific"  erev="-77.0 mV" condDensity="5e-5 S_per_cm2"/>
+            <channelDensity ionChannel="hh2_k" id="hh2_k_soma" ion="k"  erev="-95.0 mV" condDensity="0.01 S_per_cm2"/>
+            <channelDensity ionChannel="hh2_na" id="hh2_na_soma" ion="na"  erev="50.0 mV" condDensity="0.09 S_per_cm2"/>
 
 
             <spikeThresh value="5mV"/>