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Merge pull request #11 from OpenSourceBrain/development
Improved hybridsmall, valid with netpyne fomat json...
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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: [email protected] | ||
| """ | ||
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| from netpyne import specs | ||
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| netParams = specs.NetParams() # object of class NetParams to store the network parameters | ||
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@@ -26,13 +16,13 @@ | |
| pop_size = 3 | ||
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| # 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 | ||
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| # 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)) | ||
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@@ -42,7 +32,7 @@ | |
| netParams.cellParams['PYR_HH'] = cellRule # add dict to list of cell properties | ||
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| ## 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', | ||
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@@ -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} | ||
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| # 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 | ||
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@@ -75,7 +65,6 @@ | |
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| ############################################################################### | ||
| # SIMULATION PARAMETERS | ||
| ############################################################################### | ||
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@@ -110,8 +99,11 @@ | |
| simConfig.saveDpk = False # save to a .dpk pickled file | ||
| simConfig.saveDat = True | ||
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| simConfig.validateNetParams=True | ||
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| # 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 | ||
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| cfg = simConfig | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| { | ||
| "mod_folder": "../HybridSmall", | ||
| "simConfig": "HybridSmall.py", | ||
| "python_run": "init.py", | ||
| "netParams": "HybridSmall.py" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| """ | ||
| init.py | ||
| Starting script to run NetPyNE-based model. | ||
| """ | ||
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| from netpyne import sim | ||
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| cfg, netParams = sim.loadFromIndexFile('index.npjson') | ||
| sim.createSimulateAnalyze(netParams, cfg) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -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 |
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