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pgleesonpgleeson
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Instance of network in NeuroML
1 parent 883ca07 commit e37f7ab

20 files changed

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lines changed

‎.gitignore‎

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@@ -21,3 +21,5 @@ x86_64
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/pertinh.rate.*.dat
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/rates.png
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/exc2.rate.*.dat
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/NeuroML2/ISN_net.gv
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/NeuroML2/ISN_net.gv.png

‎ISN.py‎

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@@ -1118,6 +1118,55 @@ def run_one(**kwargs):
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run_one()
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elif '-neuroml' in sys.argv:
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fraction_inh_pert_rng = [0.9]
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for fraction_inh_pert in fraction_inh_pert_rng:
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suffix = '';#str(int(fraction_inh_pert*100))
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target_dir = './NeuroML2/';
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run_in_simulator = None
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format = 'hdf5'
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generate(Bee = Bee,
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Bei = Bei,
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Bie = Bie,
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Bii = Bii,
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Be_bkg = Be_bkg,
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Be_stim = Be_stim,
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r_bkg = 0,
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r_stim = r_stim,
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r_bkg_ExtExc=r_bkg_ExtExc,
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r_bkg_ExtInh=r_bkg_ExtInh,
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r_bkg_ExtExc2=r_bkg_ExtExc2,
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Ttrans = Ttrans,
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Tblank= Tblank,
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Tstim = Tstim,
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Tpost = Tpost,
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exc_exc_conn_prob = exc_exc_conn_prob,
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exc_inh_conn_prob = exc_inh_conn_prob,
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inh_exc_conn_prob = inh_exc_conn_prob,
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inh_inh_conn_prob = inh_inh_conn_prob,
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ee2_conn_prob = ee2_conn_prob,
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ie2_conn_prob = ie2_conn_prob,
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connections=connections, connections2=connections2,
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fraction_inh_pert=fraction_inh_pert,
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duration = Ttrans+Tblank+Tstim+Tpost,
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dt = dt,
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scale_populations=scale_populations,
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format=format,
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percentage_exc_detailed=percentage_exc_detailed,
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target_dir=target_dir,
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suffix=suffix,
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run_in_simulator=run_in_simulator,
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num_processors=num_processors,
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exc_target_dendrites=exc_target_dendrites,
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inh_target_dendrites=inh_target_dendrites,
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v_clamp=v_clamp,
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simulation_seed=simulation_seed)
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elif '-perturbation' in sys.argv:
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results = {}
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for fraction_inh_pert in fraction_inh_pert_rng:

‎NeuroML2/ISN_net.net.nml.h5‎

1.74 MB
Binary file not shown.

‎NeuroML2/ISN_net/HH2_476686112.cell.nml‎

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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta5.xsd" id="HH2_476686112">
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<include href="IM.channel.nml"></include>
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<include href="Kd.channel.nml"></include>
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<include href="Leak.channel.nml"></include>
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<include href="Na.channel.nml"></include>
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<include href="IL.channel.nml"></include>
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<cell id="HH2_476686112">
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<notes>Cell model tuned to Allen Institute Cell Types Database, dataset: 476686112
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Tuning procedure metadata:
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{ 'Prototype': 'HH2',
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'analysis_start_time': 0,
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'analysis_var': { 'baseline': 0,
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'dvdt_threshold': 0,
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'peak_delta': 0,
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'peak_threshold': 0},
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'best_cand_analysis': { 'Pop0/0/RS/v:average_1000_1200': -78.72255328033323,
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'Pop0/0/RS/v:average_100_200': -65.77252779422061,
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'Pop0/0/RS/v:value_280': -68.64126,
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'Pop0/1/RS/v:average_1000_1200': -74.92722059696068,
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'Pop0/3/RS/v:max_peak_no': 0,
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'Pop0/5/RS/v:mean_spike_frequency': 18.714016798582136,
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'Pop0/6/RS/v:average_maximum': 33.17997053571429,
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'Pop0/6/RS/v:average_minimum': -56.476617090909095,
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'Pop0/6/RS/v:mean_spike_frequency': 55.981353120197049},
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'best_cand_analysis_full': { 'Pop0/0/RS/v:average_last_1percent': -65.51271753999998,
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'Pop0/0/RS/v:max_peak_no': 0,
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'Pop0/0/RS/v:maximum': -65.50625000000001,
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'Pop0/0/RS/v:min_peak_no': 0,
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'Pop0/0/RS/v:minimum': -80.0,
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'Pop0/1/RS/v:average_last_1percent': -65.52312853333338,
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'Pop0/1/RS/v:max_peak_no': 0,
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'Pop0/1/RS/v:maximum': -65.50625000000001,
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'Pop0/1/RS/v:min_peak_no': 0,
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'Pop0/1/RS/v:minimum': -80.0,
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'Pop0/2/RS/v:average_last_1percent': -65.5411711733338,
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'Pop0/2/RS/v:max_peak_no': 0,
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'Pop0/2/RS/v:maximum': -65.50625000000001,
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'Pop0/2/RS/v:min_peak_no': 0,
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'Pop0/2/RS/v:minimum': -80.0,
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'Pop0/3/RS/v:average_last_1percent': -65.56953700000005,
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'Pop0/3/RS/v:max_peak_no': 0,
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'Pop0/3/RS/v:maximum': -65.50625000000001,
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'Pop0/3/RS/v:min_peak_no': 0,
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'Pop0/3/RS/v:minimum': -80.0,
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'Pop0/4/RS/v:average_last_1percent': -66.03096643333338,
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'Pop0/4/RS/v:average_maximum': 33.325447500000003,
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'Pop0/4/RS/v:average_minimum': -57.043669999999999,
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'Pop0/4/RS/v:first_spike_time': 379.65,
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'Pop0/4/RS/v:interspike_time_covar': 0.1670056648580161,
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'Pop0/4/RS/v:max_interspike_time': 132.25,
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'Pop0/4/RS/v:max_peak_no': 8,
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'Pop0/4/RS/v:maximum': 33.3695,
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'Pop0/4/RS/v:mean_spike_frequency': 8.8301334611600257,
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'Pop0/4/RS/v:min_interspike_time': 78.170000000000016,
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'Pop0/4/RS/v:min_peak_no': 7,
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'Pop0/4/RS/v:minimum': -80.0,
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'Pop0/4/RS/v:peak_decay_exponent': -0.00022030125467418802,
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'Pop0/4/RS/v:peak_linear_gradient': -7.126646060385446e-05,
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'Pop0/4/RS/v:spike_broadening': 1.0010448728115837,
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'Pop0/4/RS/v:spike_frequency_adaptation': -0.025333884347158026,
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'Pop0/4/RS/v:spike_width_adaptation': -0.012600693365119139,
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'Pop0/4/RS/v:trough_decay_exponent': -0.0011866311647981496,
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'Pop0/4/RS/v:trough_phase_adaptation': -0.019680621279523806,
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'Pop0/5/RS/v:average_last_1percent': -66.27569485333333,
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'Pop0/5/RS/v:average_maximum': 33.375539444444449,
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'Pop0/5/RS/v:average_minimum': -56.987409411764709,
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'Pop0/5/RS/v:first_spike_time': 334.90999999999997,
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'Pop0/5/RS/v:interspike_time_covar': 0.12119863770623786,
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'Pop0/5/RS/v:max_interspike_time': 59.399999999999864,
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'Pop0/5/RS/v:max_peak_no': 18,
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'Pop0/5/RS/v:maximum': 33.45196,
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'Pop0/5/RS/v:mean_spike_frequency': 18.714016798582136,
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'Pop0/5/RS/v:min_interspike_time': 38.500000000000057,
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'Pop0/5/RS/v:min_peak_no': 17,
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'Pop0/5/RS/v:minimum': -80.0,
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'Pop0/5/RS/v:peak_decay_exponent': -0.00054370010564261406,
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'Pop0/5/RS/v:peak_linear_gradient': -8.1360928365724255e-05,
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'Pop0/5/RS/v:spike_broadening': 1.0015987533193094,
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'Pop0/5/RS/v:spike_frequency_adaptation': -0.013109979211912471,
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'Pop0/5/RS/v:spike_width_adaptation': -0.0084560923248116135,
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'Pop0/5/RS/v:trough_decay_exponent': -0.0016956229962287789,
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'Pop0/5/RS/v:trough_phase_adaptation': -0.011215164125842465,
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'Pop0/6/RS/v:average_last_1percent': -66.82608678000007,
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'Pop0/6/RS/v:average_maximum': 33.17997053571429,
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'Pop0/6/RS/v:average_minimum': -56.476617090909095,
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'Pop0/6/RS/v:first_spike_time': 294.47,
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'Pop0/6/RS/v:interspike_time_covar': 0.074382566219921301,
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'Pop0/6/RS/v:max_interspike_time': 22.330000000000155,
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'Pop0/6/RS/v:max_peak_no': 56,
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'Pop0/6/RS/v:maximum': 33.81358,
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'Pop0/6/RS/v:mean_spike_frequency': 55.981353120197049,
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'Pop0/6/RS/v:min_interspike_time': 14.67999999999995,
95+
'Pop0/6/RS/v:min_peak_no': 55,
96+
'Pop0/6/RS/v:minimum': -80.0,
97+
'Pop0/6/RS/v:peak_decay_exponent': -0.037356588090453689,
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'Pop0/6/RS/v:peak_linear_gradient': 0.00032391988299466554,
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'Pop0/6/RS/v:spike_broadening': 1.0059878482058517,
100+
'Pop0/6/RS/v:spike_frequency_adaptation': -0.0035034397217121216,
101+
'Pop0/6/RS/v:spike_width_adaptation': -0.0015939130186086541,
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'Pop0/6/RS/v:trough_decay_exponent': 0.0029778843051959029,
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'Pop0/6/RS/v:trough_phase_adaptation': -0.0026612009441887366},
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'comment': 'Ran 3000 evaluations (pop: 300) in 3492.355981 seconds (58.205933 mins total; 1.164119s per eval)\n\n',
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'dataset': 476686112,
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'dt': 0.01,
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'fitness': 0.0012666782135354326,
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'fittest vars': { 'cell:RS/channelDensity:IL_all/mS_per_cm2': 0.19722889609230776,
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'cell:RS/channelDensity:IM_all/mS_per_cm2': 0.06103514392076281,
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'cell:RS/channelDensity:Kd_all/mS_per_cm2': 24.35535649185249,
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'cell:RS/channelDensity:LeakConductance_all/mS_per_cm2': 0.18446807013222372,
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'cell:RS/channelDensity:Na_all/mS_per_cm2': 92.33250718877743,
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'cell:RS/erev_id:IL_all/mV': 71.70782669942088,
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'cell:RS/erev_id:Kd_all/mV+cell:RS/erev_id:IM_all/mV': -87.45598307808358,
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'cell:RS/erev_id:LeakConductance_all/mV': -65.26545903974481,
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'cell:RS/erev_id:Na_all/mV': 52.66359150572609,
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'cell:RS/specificCapacitance:all/uF_per_cm2': 6.927379371444548,
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'cell:RS/vShift_channelDensity:Na_all/mV': -2.771218668715758},
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'max_evaluations': 3000,
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'mutation_rate': 0.9,
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'num_elites': 5,
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'num_offspring': 90,
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'num_selected': 90,
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'parameters': [ 'cell:RS/channelDensity:LeakConductance_all/mS_per_cm2',
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'cell:RS/erev_id:LeakConductance_all/mV',
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'cell:RS/specificCapacitance:all/uF_per_cm2',
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'cell:RS/channelDensity:Na_all/mS_per_cm2',
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'cell:RS/channelDensity:Kd_all/mS_per_cm2',
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'cell:RS/channelDensity:IM_all/mS_per_cm2',
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'cell:RS/channelDensity:IL_all/mS_per_cm2',
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'cell:RS/erev_id:Na_all/mV',
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'cell:RS/erev_id:Kd_all/mV+cell:RS/erev_id:IM_all/mV',
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'cell:RS/erev_id:IL_all/mV',
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'cell:RS/vShift_channelDensity:Na_all/mV'],
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'population_size': 300,
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'reference': 'HH2_2stage_STAGE2',
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'run_directory': 'NT_HH2_2stage_STAGE2_Sun_Mar__4_18.05.41_2018',
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'seed': 1234.0,
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'sim_time': 1500,
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'simulator': 'jNeuroML_NEURON',
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'target_data': { 'Pop0/0/RS/v:average_1000_1200': -80.59196871776581,
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'Pop0/0/RS/v:average_100_200': -64.8002318519633,
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'Pop0/0/RS/v:value_280': -72.0625,
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'Pop0/1/RS/v:average_1000_1200': -76.13684743423462,
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'Pop0/3/RS/v:max_peak_no': 0,
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'Pop0/5/RS/v:mean_spike_frequency': 17.100959791368286,
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'Pop0/6/RS/v:average_maximum': 36.453125,
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'Pop0/6/RS/v:average_minimum': -54.939953,
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'Pop0/6/RS/v:mean_spike_frequency': 52.709364697127846},
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'time': 3492.355980873108,
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'weights': { 'Pop0/0/RS/v:average_1000_1200': 10,
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'Pop0/0/RS/v:average_100_200': 10,
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'Pop0/0/RS/v:value_280': 10,
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'Pop0/1/RS/v:average_1000_1200': 10,
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'Pop0/3/RS/v:max_peak_no': 1,
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'Pop0/5/RS/v:mean_spike_frequency': 1,
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'Pop0/6/RS/v:average_maximum': 1,
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'Pop0/6/RS/v:average_minimum': 1,
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'Pop0/6/RS/v:mean_spike_frequency': 1}}
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</notes>
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<morphology id="morphology_HH2">
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<segment id="0" name="Soma">
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<proximal x="0.000000e+00" y="0.000000e+00" z="0.000000e+00" diameter="30.0"/>
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<distal x="0.000000e+00" y="0.000000e+00" z="0.000000e+00" diameter="30.0"/>
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</segment>
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<segmentGroup neuroLexId="sao864921383" id="Soma">
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<member segment="0"/>
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</segmentGroup>
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<segmentGroup id="all">
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<include segmentGroup="Soma"/>
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</segmentGroup>
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<segmentGroup neuroLexId="GO:0043025" id="soma_group">
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<include segmentGroup="Soma"/>
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</segmentGroup>
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</morphology>
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<biophysicalProperties id="biophys">
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<membraneProperties>
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<channelDensity id="LeakConductance_all" ionChannel="LeakConductance" condDensity="0.184468070132 mS_per_cm2" erev="-65.2654590397 mV" ion="non_specific"/>
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<channelDensity id="Kd_all" ionChannel="Kd" condDensity="24.3553564919 mS_per_cm2" erev="-87.4559830781 mV" ion="k"/>
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<channelDensity id="IM_all" ionChannel="IM" condDensity="0.0610351439208 mS_per_cm2" erev="-87.4559830781 mV" ion="k"/>
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<channelDensity id="IL_all" ionChannel="IL" condDensity="0.197228896092 mS_per_cm2" erev="71.7078266994 mV" ion="ca"/>
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<channelDensityVShift id="Na_all" ionChannel="Na" condDensity="92.3325071888 mS_per_cm2" erev="52.6635915057 mV" ion="na" vShift="-2.77121866872 mV"/>
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<spikeThresh value="0 mV"/>
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<specificCapacitance value="6.92737937144 uF_per_cm2"/>
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<initMembPotential value="-60.0 mV"/>
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</membraneProperties>
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<intracellularProperties>
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<resistivity value="100 ohm_cm"/>
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</intracellularProperties>
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</biophysicalProperties>
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</cell>
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</neuroml>

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