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Merge pull request #187 from Neurosim-lab/development
PR from development to master - VERSION 0.6.5
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,3 +1,9 @@ | ||
| # Include the data files | ||
| recursive-include netpyne * | ||
| recursive-include examples * | ||
| recursive-exclude | ||
| recursive-exclude examples * | ||
| global-exclude x86_64 | ||
| global-exclude x86_64/* | ||
| global-exclude .libs* | ||
| global-exclude .libs/* | ||
| global-exclude *.pyc |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,89 @@ | ||
| """ | ||
| tut_artif.py | ||
| Tutorial on artificial cells (no sections) | ||
| """ | ||
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| from netpyne import specs, sim | ||
| from netpyne.specs import Dict | ||
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| netParams = specs.NetParams() # object of class NetParams to store the network parameters | ||
| simConfig = specs.SimConfig() # dictionary to store sets of simulation configurations | ||
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| ############################################################################### | ||
| # NETWORK PARAMETERS | ||
| ############################################################################### | ||
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| # Population parameters | ||
| netParams.popParams['PYR1'] = {'cellModel': 'HH', 'cellType': 'PYR', 'numCells': 100} # pop of HH cells | ||
| netParams.popParams['artif1'] = {'cellModel': 'NetStim', 'numCells': 100, 'rate': 50, 'noise': 0.8, 'start': 1, 'seed': 2} # pop of NetStims | ||
| netParams.popParams['artif2'] = {'cellModel': 'IntFire2', 'numCells': 100, 'ib': 0.0} # pop of IntFire2 | ||
| netParams.popParams['artif3'] = {'cellModel': 'IntFire4', 'numCells': 100, 'taue': 1.0} # pop of IntFire4 | ||
| netParams.popParams['artif4'] = {'cellModel': 'VecStim', 'numCells': 100, 'rate': 5, 'noise': 0.5, 'start': 50, | ||
| 'pulses': [{'start': 200, 'end': 300, 'rate': 60, 'noise':0.2}, {'start': 500, 'end': 800, 'rate': 30, 'noise': 0.5}]} # pop of Vecstims with 2 pulses | ||
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| # Synaptic mechanism parameters | ||
| netParams.synMechParams['AMPA'] = {'mod': 'Exp2Syn', 'tau1': 0.1, 'tau2': 1.0, 'e': 0} | ||
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| # Stimulation parameters | ||
| netParams.stimSourceParams['background'] = {'type': 'NetStim', 'interval': 100, 'number': 1e5, 'start': 500, 'noise': 0.5} # stim using NetStims after 500ms | ||
| netParams.stimTargetParams['bkg->PYR1'] = {'source': 'background', 'conds': {'popLabel': 'PYR1'}, 'sec':'soma', 'loc': 0.5, 'weight': 0.5, 'delay': 1} | ||
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| # Cell parameters | ||
| ## PYR cell properties | ||
| cellParams = Dict() | ||
| cellParams.secs.soma.geom = {'diam': 18.8, 'L': 18.8, 'Ra': 123.0} | ||
| cellParams.secs.soma.mechs.hh = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70} | ||
| cellParams.conds = {'cellType': 'PYR'} | ||
| netParams.cellParams['PYR'] = cellParams | ||
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| # Connections | ||
| netParams.connParams['artif1->PYR1'] = { | ||
| 'preConds': {'popLabel': 'artif1'}, 'postConds': {'popLabel': 'PYR1'}, | ||
| 'convergence': 8, | ||
| 'weight': 0.005, | ||
| 'synMech': 'AMPA', | ||
| 'delay': 'uniform(1,5)'} | ||
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| netParams.connParams['PYR1->artif2'] = { | ||
| 'preConds': {'popLabel': 'PYR1'}, 'postConds': {'popLabel': 'artif2'}, | ||
| 'probability': 0.2, | ||
| 'weight': 0.2, | ||
| 'delay': 'uniform(1,5)'} | ||
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| netParams.addConnParams('artif2->artif3', | ||
| {'preConds': {'popLabel': 'artif2'}, 'postConds': {'popLabel': 'artif3'}, | ||
| 'divergence': 20, | ||
| 'weight': 0.05, | ||
| 'delay': 3}) | ||
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| ############################################################################### | ||
| # SIMULATION PARAMETERS | ||
| ############################################################################### | ||
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| # Simulation parameters | ||
| simConfig.duration = 1*1e3 # Duration of the simulation, in ms | ||
| simConfig.dt = 0.1 # Internal integration timestep to use | ||
| simConfig.createNEURONObj = 1 # create HOC objects when instantiating network | ||
| simConfig.createPyStruct = 1 # create Python structure (simulator-independent) when instantiating network | ||
| simConfig.verbose = 0 #False # show detailed messages | ||
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| # Recording | ||
| simConfig.recordTraces = {'Vsoma':{'sec':'soma','loc':0.5,'var':'v'}} | ||
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| # # Analysis and plotting | ||
| simConfig.analysis['plotRaster'] = True | ||
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| ############################################################################### | ||
| # RUN SIM | ||
| ############################################################################### | ||
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| sim.createSimulateAnalyze() | ||
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