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Merge pull request #251 from Neurosim-lab/development
PR from development to master - VERSION 0.7.2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,53 +1,103 @@ | ||
| from neuron import h, gui | ||
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| pc = h.ParallelContext() | ||
| pc.set_maxstep(10) | ||
| idhost = int(pc.id()) | ||
| nhost = int(pc.nhost()) | ||
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| # Create presyn cell 1 | ||
| pre1_gid = 0 | ||
| pre1_host = 0 | ||
| if idhost == pre1_host: | ||
| pre1 = h.Section(name='pre1') | ||
| pc.set_gid2node(pre1_gid, pre1_host) | ||
| nc = h.NetCon(pre1(0.5)._ref_v, None, sec = pre1) | ||
| nc.threshold = 20.0 | ||
| pc.cell(pre1_gid, nc) | ||
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| # Create presyn cell 2 | ||
| pre2_gid = 1 | ||
| pre2_host = 1 if nhost>1 else 0 | ||
| if idhost == pre2_host: | ||
| pre2 = h.Section(name='pre2') | ||
| pc.set_gid2node(pre2_gid, pre2_host) | ||
| nc = h.NetCon(pre2(0.5)._ref_v, None, sec = pre2) | ||
| nc.threshold = 20.0 | ||
| pc.cell(pre2_gid, nc) | ||
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| # Create postsyn cell | ||
| post_gid = 2 | ||
| post_host = 0 | ||
| if idhost == post_host: | ||
| post = h.Section(name='post') | ||
| postsyn = h.Exp2Syn(post(0.5)) | ||
| pc.set_gid2node(post_gid, post_host) | ||
| nc = h.NetCon(post(0.5)._ref_v, None, sec = post) | ||
| pc.cell(post_gid, nc) # Associate the cell with this host and gid | ||
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| # Connect pre to post cells | ||
| if pc.gid_exists(post_gid): | ||
| nc1 = pc.gid_connect(pre1_gid, postsyn) | ||
| nc1.threshold = 5.0 | ||
| nc2 = pc.gid_connect(pre2_gid, postsyn) | ||
| nc2.threshold = 5.0 | ||
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| # run sim | ||
| h.stdinit() | ||
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| for i in range(3): | ||
| if pc.gid_exists(i): | ||
| print '\ngid: %d, pc.threshold: %.1f' % (i, pc.threshold(i)) | ||
| """ | ||
| 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, sim | ||
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| netParams = specs.NetParams() # object of class NetParams to store the network parameters | ||
| simConfig = specs.SimConfig() # object of class SimConfig to store the simulation configuration | ||
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| ############################################################################### | ||
| # | ||
| # MPI HH TUTORIAL PARAMS | ||
| # | ||
| ############################################################################### | ||
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| ############################################################################### | ||
| # NETWORK PARAMETERS | ||
| ############################################################################### | ||
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| # Population parameters | ||
| netParams.popParams['PYR'] = {'cellModel': 'HH', 'cellType': 'PYR', 'numCells': 5} # add dict with params for this pop | ||
| netParams.popParams['PYR2'] = {'cellModel': 'HH', 'cellType': 'PYR2', 'numCells': 5} # add dict with params for this pop | ||
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| # Cell parameters | ||
| ## PYR cell properties | ||
| cellRule = {'conds': {'cellModel': 'HH', 'cellType': 'PYR'}, 'secs': {}} # cell rule dict | ||
| cellRule['secs']['soma'] = {'geom': {}, 'mechs': {}} # soma params dict | ||
| cellRule['secs']['soma']['geom'] = {'diam': 18.8, 'L': 18.8, 'Ra': 123.0} # soma geometry | ||
| cellRule['secs']['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70} # soma hh mechanism | ||
| cellRule['secs']['soma']['vinit'] = -71 | ||
| netParams.cellParams['PYR'] = cellRule # add dict to list of cell params | ||
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| cellRule = {'conds': {'cellModel': 'HH', 'cellType': 'PYR2'}, 'secs': {}} # cell rule dict | ||
| cellRule['secs']['soma'] = {'geom': {}, 'mechs': {}} # soma params dict | ||
| cellRule['secs']['soma']['geom'] = {'diam': 18.8, 'L': 18.8, 'Ra': 123.0} # soma geometry | ||
| cellRule['secs']['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70} # soma hh mechanism | ||
| cellRule['secs']['soma']['vinit'] = -71 | ||
| netParams.cellParams['PYR2'] = cellRule # add dict to list of cell params | ||
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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['bkg'] = {'type': 'NetStim', 'rate': 10, 'noise': 0.5, 'start': 1} | ||
| netParams.stimSourceParams['bkg2'] = {'type': 'NetStim', 'rate': 10, 'noise': 0.5, 'start': 1} | ||
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| netParams.stimTargetParams['bkg->PYR1'] = {'source': 'bkg', 'conds': {'pop': 'PYR'}, 'weight': 0.1, 'delay': 'uniform(1,5)'} | ||
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| # Connectivity parameters | ||
| netParams.connParams['PYR->PYR'] = { | ||
| 'preConds': {'pop': 'PYR'}, 'postConds': {'pop': ['PYR','PYR2']}, | ||
| 'weight': 0.002, # 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 | ||
| 'convergence': 'uniform(1,15)'} # convergence (num presyn targeting postsyn) is uniformly distributed between 1 and 15 | ||
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| ############################################################################### | ||
| # SIMULATION PARAMETERS | ||
| ############################################################################### | ||
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| # Simulation parameters | ||
| simConfig.duration = 1*1e3 # Duration of the simulation, in ms | ||
| simConfig.dt = 'a' # Internal integration timestep to use | ||
| simConfig.seeds = {'con': 1, 'stim': 1, 'loc': 1} # Seeds for randomizers (connectivity, input stimulation and cell locations) | ||
| simConfig.createNEURONObj = 1 # create HOC objects when instantiating network | ||
| simConfig.createPyStruct = 1 # create Python structure (simulator-independent) when instantiating network | ||
| simConfig.verbose = False # show detailed messages | ||
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| simConfig.checkErrors = 0 | ||
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| # Recording | ||
| simConfig.recordCells = [] # which cells to record from | ||
| simConfig.recordTraces = {'Vsoma':{'se':'soma','loc':0.5,'var':'v','conds': {'cellType': 'PYR2'}}} | ||
| simConfig.recordStim = True # record spikes of cell stims | ||
| simConfig.recordStep = 0.1 # Step size in ms to save data (eg. V traces, LFP, etc) | ||
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| # Saving | ||
| simConfig.filename = 'HHTut' # Set file output name | ||
| simConfig.saveFileStep = 1000 # step size in ms to save data to disk | ||
| simConfig.savePickle = False # Whether or not to write spikes etc. to a .mat file | ||
| simConfig.saveMat = True | ||
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| # Analysis and plotting | ||
| simConfig.analysis['plotRaster'] = {'bla':1} | ||
| #simConfig.analysis['plotTraces'] = {'include': ['all'], 'oneFigPer':'trace'} | ||
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| sim.createSimulateAnalyze() | ||
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| #data=sim.loadSimData('HHTut.mat') | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
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| __version__ = '0.7.1' | ||
| __version__ = '0.7.2' | ||
| __gui__ = True # global option to enable/disable graphics |
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