mean_scaling,
variance_scaling)
# delete all existing synaptic connections and associated information
project.generatedNetworkConnections.reset()
project.morphNetworkConnectionsInfo.deleteAllNetConns()
# generate connections according to graph
utils.nC_generate_gj_network_from_graph(project,
sim_config,
gj_graph,
'Golgi_network_reduced',
'GJGolgi_Reduced',
['GCL', 'ML1', 'ML2', 'ML3'],
'Golgi_gap_2010')
# export generated network structure to graphml for debugging
utils.nC_network_to_graphml(project, '/home/ucbtepi/thesis/data/GoC_net_structures/graph_' + sim_ref + '.graphml')
if simulate:
# generate, compile and run NEURON files
remote_sim_refs = utils.nC_generate_NEURON_and_submit(pm,
project,
sim_config,
sim_ref,
remote_sim_refs,
run_time=14)
if remote_sim_refs:
utils.wait_and_pull_remote(remote_sim_refs, sleep_time=0.5)
print('timestamp ' + timestamp)
System.exit(0)
for cell_type in ['Vervaeke', 'reduced']:
stim = project.elecInputInfo.getStim('network_' + cell_type + '_' +
stim_source + '_AMPAonly')
stim.setRate(NumberGenerator(rate_in_kHz))
project.elecInputInfo.updateStim(stim)
# generate and compile neuron files
print "Generating NEURON scripts..."
project.neuronFileManager.setSuggestedRemoteRunTime(30)
simulator_seed = random.getrandbits(32)
project.neuronFileManager.generateTheNeuronFiles(sim_config, None, NeuronFileManager.RUN_HOC,simulator_seed)
compile_process = ProcessManager(project.neuronFileManager.getMainHocFile())
compile_success = compile_process.compileFileWithNeuron(0,0)
# simulate
if compile_success:
print "Submitting simulation reference " + sim_ref
pm.doRunNeuron(sim_config)
time.sleep(5) # Wait for sim to be kicked off
if not sim_config.getMpiConf().isRemotelyExecuted():
# if running locally, never have more than one sim running
# at the same time
print('Simulating on the local machine.')
timefile_path = sim_path + '/time.dat'
while not os.path.exists(timefile_path):
time.sleep(5)
if sim_config.getMpiConf().isRemotelyExecuted():
wait_and_pull_remote(sim_refs)
print('batch reference net_' + timestamp)
System.exit(0)
project.simulationParameters.setReference(sim_ref)
# create gap junction graph object
gj_graph = utils.random_graph_heterogeneous_synapses(cell_positions)
# delete all existing synaptic connections and associated information
project.generatedNetworkConnections.reset()
project.morphNetworkConnectionsInfo.deleteAllNetConns()
# generate connections according to graph
utils.nC_generate_gj_network_from_graph(project, sim_config, gj_graph,
'Golgi_network_reduced',
'GJGolgi_Reduced',
['GCL', 'ML1', 'ML2', 'ML3'],
'Golgi_gap_2010')
# export generated network structure to graphml for debugging
utils.nC_network_to_graphml(
project, '/home/ucbtepi/thesis/data/GoC_net_structures/graph_' +
sim_ref + '.graphml')
if simulate:
# generate, compile and run NEURON files
remote_sim_refs = utils.nC_generate_NEURON_and_submit(pm,
project,
sim_config,
sim_ref,
remote_sim_refs,
run_time=14)
if remote_sim_refs:
utils.wait_and_pull_remote(remote_sim_refs, sleep_time=0.5)
print('timestamp ' + timestamp)
System.exit(0)
stim_source + '_AMPAonly')
stim.setRate(NumberGenerator(rate_in_kHz))
project.elecInputInfo.updateStim(stim)
# generate and compile neuron files
print "Generating NEURON scripts..."
project.neuronFileManager.setSuggestedRemoteRunTime(30)
simulator_seed = random.getrandbits(32)
project.neuronFileManager.generateTheNeuronFiles(
sim_config, None, NeuronFileManager.RUN_HOC, simulator_seed)
compile_process = ProcessManager(
project.neuronFileManager.getMainHocFile())
compile_success = compile_process.compileFileWithNeuron(0, 0)
# simulate
if compile_success:
print "Submitting simulation reference " + sim_ref
pm.doRunNeuron(sim_config)
time.sleep(5) # Wait for sim to be kicked off
if not sim_config.getMpiConf().isRemotelyExecuted():
# if running locally, never have more than one sim running
# at the same time
print('Simulating on the local machine.')
timefile_path = sim_path + '/time.dat'
while not os.path.exists(timefile_path):
time.sleep(5)
if sim_config.getMpiConf().isRemotelyExecuted():
wait_and_pull_remote(sim_refs)
print('batch reference net_' + timestamp)
System.exit(0)
cell_type)
stim.setAmp(NumberGenerator(amplitude_in_nA))
project.elecInputInfo.updateStim(stim)
# generate and compile neuron files
print "Generating NEURON scripts..."
project.neuronFileManager.setSuggestedRemoteRunTime(10)
simulator_seed = random.getrandbits(32)
project.neuronFileManager.generateTheNeuronFiles(
sim_config, None, NeuronFileManager.RUN_HOC, simulator_seed)
compile_process = ProcessManager(
project.neuronFileManager.getMainHocFile())
compile_success = compile_process.compileFileWithNeuron(0, 0)
# simulate
if compile_success:
print "Submitting simulation reference " + sim_ref
pm.doRunNeuron(sim_config)
time.sleep(2) # Wait for sim to be kicked off
if not sim_config.getMpiConf().isRemotelyExecuted():
# if running locally, never have more than one sim running
# at the same time
print('Simulating on the local machine.')
timefile_path = sim_path + '/time.dat'
while not os.path.exists(timefile_path):
time.sleep(5)
if sim_config.getMpiConf().isRemotelyExecuted():
utils.wait_and_pull_remote(sim_refs, sleep_time=5)
print('batch reference ' + timestamp_prefix + timestamp)
System.exit(0)
amplitude_in_nA = amplitude/1000.
for cell_type in ['Vervaeke', 'reduced']:
stim = project.elecInputInfo.getStim('cclamp_network_' + cell_type)
stim.setAmp(NumberGenerator(amplitude_in_nA))
project.elecInputInfo.updateStim(stim)
# generate and compile neuron files
print "Generating NEURON scripts..."
project.neuronFileManager.setSuggestedRemoteRunTime(10)
simulator_seed = random.getrandbits(32)
project.neuronFileManager.generateTheNeuronFiles(sim_config, None, NeuronFileManager.RUN_HOC,simulator_seed)
compile_process = ProcessManager(project.neuronFileManager.getMainHocFile())
compile_success = compile_process.compileFileWithNeuron(0,0)
# simulate
if compile_success:
print "Submitting simulation reference " + sim_ref
pm.doRunNeuron(sim_config)
time.sleep(2) # Wait for sim to be kicked off
if not sim_config.getMpiConf().isRemotelyExecuted():
# if running locally, never have more than one sim running
# at the same time
print('Simulating on the local machine.')
timefile_path = sim_path + '/time.dat'
while not os.path.exists(timefile_path):
time.sleep(5)
if sim_config.getMpiConf().isRemotelyExecuted():
utils.wait_and_pull_remote(sim_refs, sleep_time=5)
print('batch reference ' + timestamp_prefix + timestamp)
System.exit(0)