diff --git a/NetPyNE/HybridSmall/HybridSmall.py b/NetPyNE/HybridSmall/HybridSmall.py
index ea93f23..25de36c 100644
--- a/NetPyNE/HybridSmall/HybridSmall.py
+++ b/NetPyNE/HybridSmall/HybridSmall.py
@@ -1,13 +1,3 @@
-"""
-params.py
-
-netParams is a dict containing a set of network parameters using a standardized structure
-
-simConfig is a dict containing a set of simulation configurations using a standardized structure
-
-Contributors: salvadordura@gmail.com
-"""
-
from netpyne import specs
netParams = specs.NetParams() # object of class NetParams to store the network parameters
@@ -26,13 +16,13 @@
pop_size = 3
# Population parameters
-netParams.popParams['PYR_HH'] = {'cellModel': 'HH', 'cellType': 'PYR', 'numCells': pop_size} # add dict with params for this pop
-netParams.popParams['PYR_Izhi'] = {'cellModel': 'Izhi', 'cellType': 'PYR', 'numCells': pop_size} # add dict with params for this pop
+netParams.popParams['PYR_HH'] = {'cellType': 'PYR_HH', 'numCells': pop_size} # add dict with params for this pop
+netParams.popParams['PYR_Izhi'] = {'cellType': 'PYR_Izhi', 'numCells': pop_size} # add dict with params for this pop
# Cell parameters list
## PYR cell properties (HH)
-cellRule = {'conds': {'cellType': 'PYR', 'cellModel': 'HH'}, 'secs': {}}
+cellRule = {'secs': {}}
cellRule['secs']['soma'] = {'geom': {}, 'topol': {}, 'mechs': {}} # soma properties
cellRule['secs']['soma']['geom'] = {'diam': 18.8, 'L': 18.8, 'Ra': 123.0, 'pt3d':[]}
cellRule['secs']['soma']['geom']['pt3d'].append((0, 0, 0, 18.8))
@@ -42,7 +32,7 @@
netParams.cellParams['PYR_HH'] = cellRule # add dict to list of cell properties
## PYR cell properties (Izhi)
-cellRule = {'conds': {'cellType': 'PYR', 'cellModel': 'Izhi'}, 'secs': {}}
+cellRule = {'secs': {}}
cellRule['secs']['soma'] = {'geom': {}, 'pointps':{}} # soma properties
cellRule['secs']['soma']['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
cellRule['secs']['soma']['pointps']['Izhi'] = {'mod':'Izhi2007b',
@@ -58,15 +48,15 @@
# Stimulation parameters
netParams.stimSourceParams['bkg1'] = {'type': 'NetStim', 'rate': 20, 'noise': 0}
netParams.stimSourceParams['bkg2'] = {'type': 'NetStim', 'rate': 20, 'noise': 1}
-netParams.stimTargetParams['bg->PYR_Izhi'] = {'source': 'bkg1', 'conds': {'cellType': 'PYR', 'cellModel': 'Izhi'},
- 'connFunc': 'fullConn','weight': 0.01, 'delay': 0, 'synMech': 'syn2'}
-netParams.stimTargetParams['bg->PYR_HH'] = {'source': 'bkg2', 'conds': {'cellType': 'PYR', 'cellModel': 'HH'},
- 'connFunc': 'fullConn','weight': 0.005, 'synMech': 'syn1', 'sec': 'soma', 'loc': 1.0, 'delay': 0}
+netParams.stimTargetParams['bg->PYR_Izhi'] = {'source': 'bkg1', 'conds': {'cellType': 'PYR_Izhi'},
+ 'weight': 0.01, 'delay': 0, 'synMech': 'syn2'}
+netParams.stimTargetParams['bg->PYR_HH'] = {'source': 'bkg2', 'conds': {'cellType': 'PYR_HH'},
+ 'weight': 0.005, 'synMech': 'syn1', 'sec': 'soma', 'loc': 1.0, 'delay': 0}
# Connectivity parameters
netParams.connParams['PYR->PYR'] = {
- 'preConds': {'cellType': 'PYR'}, 'postConds': {'cellType': 'PYR'},
+ 'preConds': {'cellType': ['PYR_HH', 'PYR_Izhi']}, 'postConds': {'cellType': ['PYR_HH', 'PYR_Izhi']},
'weight': 0.0, # weight of each connection
'delay': '0.2+normal(13.0,1.4)', # delay min=0.2, mean=13.0, var = 1.4
'threshold': 10, # threshold
@@ -75,7 +65,6 @@
-
###############################################################################
# SIMULATION PARAMETERS
###############################################################################
@@ -110,8 +99,11 @@
simConfig.saveDpk = False # save to a .dpk pickled file
simConfig.saveDat = True
+simConfig.validateNetParams=True
# Analysis and plotting
simConfig.analysis['plotRaster'] = {'orderInverse': False} #True # Whether or not to plot a raster
simConfig.analysis['plotTraces'] = {'include': [1,51]} # plot recorded traces for this list of cells
#simConfig.analysis['plotRatePSD'] = {'include': ['allCells', 'PYR_HH', 'PYR_Izhi'], 'smooth': 10} # plot recorded traces for this list of cells
+
+cfg = simConfig
\ No newline at end of file
diff --git a/NetPyNE/HybridSmall/index.npjson b/NetPyNE/HybridSmall/index.npjson
new file mode 100644
index 0000000..c3cc48a
--- /dev/null
+++ b/NetPyNE/HybridSmall/index.npjson
@@ -0,0 +1,6 @@
+{
+ "mod_folder": "../HybridSmall",
+ "simConfig": "HybridSmall.py",
+ "python_run": "init.py",
+ "netParams": "HybridSmall.py"
+}
\ No newline at end of file
diff --git a/NetPyNE/HybridSmall/init.py b/NetPyNE/HybridSmall/init.py
new file mode 100644
index 0000000..e9f3c35
--- /dev/null
+++ b/NetPyNE/HybridSmall/init.py
@@ -0,0 +1,10 @@
+"""
+init.py
+
+Starting script to run NetPyNE-based model.
+"""
+
+from netpyne import sim
+
+cfg, netParams = sim.loadFromIndexFile('index.npjson')
+sim.createSimulateAnalyze(netParams, cfg)
diff --git a/NetPyNE/UI/clean.sh b/NetPyNE/UI/clean.sh
index a2c5a9d..8403c75 100755
--- a/NetPyNE/UI/clean.sh
+++ b/NetPyNE/UI/clean.sh
@@ -1,2 +1,2 @@
-rm -rf x86_64 __pycache__
+rm -rf x86_64 arm64 __pycache__ *dat
mv *mod *hoc *nrn_py *netpyne.py *nrn.py *dat *spikes *props *txt NET*nml LEMS*json test*json /tmp
diff --git a/NeuroML2/HybridSmall.net.nml b/NeuroML2/HybridSmall.net.nml
index 562e96e..189e2d0 100644
--- a/NeuroML2/HybridSmall.net.nml
+++ b/NeuroML2/HybridSmall.net.nml
@@ -23,10 +23,10 @@
-
+ |
Cell exported from NetPyNE:
-{'conds': {'cellType': 'PYR', 'cellModel': 'HH'}, 'secs': {'soma': {'geom': {'diam': 18.8, 'L': 18.8, 'Ra': 123.0, 'pt3d': [(0, 0, 0, 18.8), (0, 0, 18.8, 18.8)]}, 'topol': {}, 'mechs': {'hh': {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}}}}}
-
+{secs: {'soma': {'geom': {'diam': 18.8, 'L': 18.8, 'Ra': 123.0, 'pt3d': [(0, 0, 0, 18.8), (0, 0, 18.8, 18.8)]}, 'topol': {}, 'mechs': {'hh': {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}}}}}
+
@@ -38,7 +38,7 @@
-
+
@@ -52,11 +52,11 @@
|
-
+
-
+
@@ -68,7 +68,7 @@
-
+
@@ -84,40 +84,40 @@
-
-
-
-
-
-
+
+
+
+
+
+
-
-
-
-
+
+
+
+
-
-
-
-
-
+
+
+
+
+
-
-
-
+
+
+
-
-
-
+
+
+
-
-
-
+
+
+
diff --git a/NeuroML2/LEMS_HybridSmall.xml b/NeuroML2/LEMS_HybridSmall.xml
index 07993a5..b5691ef 100644
--- a/NeuroML2/LEMS_HybridSmall.xml
+++ b/NeuroML2/LEMS_HybridSmall.xml
@@ -18,27 +18,27 @@
-
-
-
+
+
+
-
-
-
+
+
+
-
-
-
+
+
+
-
-
-
+
+
+
|