15. Applying different channel densities over a cell

Applying different channel densities over a cell. We start with a cell with a long axon, and then apply Hodgkin-Huxley channels over the surface. We look at the effect of changing the density of leak and sodium channels in just the axon of the neuron (not the soma)

This example also shows the use of tags; 300 traces are recorded in this experiment; but we don’t ever need to get involved in managing them directly. We can just specify that all traces recorded on simulation X should be tagged with “SIMY”, and then tell the TagViewer to plot everything with a tag ‘SIMY’

Code

from morphforge.stdimports import *
from morphforgecontrib.data_library.stdmodels import StandardModels


def sim(glk_multiplier, gna_multiplier, tag):
    # Create the environment:
    env = NEURONEnvironment()

    # Create the simulation:
    sim = env.Simulation()

    # Create a cell:
    morph = MorphologyBuilder.get_soma_axon_morph(axon_length=3000.0, axon_radius=0.3, soma_radius=9.0, axon_sections=20)
    cell = sim.create_cell(name="Cell1", morphology=morph)


    lk_chl = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="Lk", env=env)
    na_chl = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="Na", env=env)
    k_chl  = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="K", env=env)

    # Apply the channels uniformly over the cell
    cell.apply_channel(lk_chl)
    cell.apply_channel(na_chl)
    cell.apply_channel(k_chl)

    # Over-ride the parameters in the axon:
    cell.apply_channel(channel=lk_chl, where="axon", parameter_multipliers={'gScale':glk_multiplier})
    cell.apply_channel(channel=na_chl, where="axon", parameter_multipliers={'gScale':gna_multiplier})

    cell.set_passive( PassiveProperty.SpecificCapacitance, qty('1.0:uF/cm2'))


    for cell_location in CellLocator.get_locations_at_distances_away_from_dummy(cell=cell, distances=range(9, 3000, 100)):
        sim.record(cell, what=StandardTags.Voltage, cell_location=cell_location, user_tags=[tag])

    # Create the stimulus and record the injected current:
    cc = sim.create_currentclamp(name="Stim1", amp=qty("250:pA"), dur=qty("5:ms"), delay=qty("100:ms"), cell_location=cell.soma)
    sim.record(cc, what=StandardTags.Current)

    # run the simulation
    return sim.run()


# Display the results:
results_a = [
    sim(glk_multiplier=0.1, gna_multiplier=1.0, tag="SIM1"),
    sim(glk_multiplier=0.5, gna_multiplier=1.0, tag="SIM2"),
    sim(glk_multiplier=1.0, gna_multiplier=1.0, tag="SIM3"),
    sim(glk_multiplier=5.0, gna_multiplier=1.0, tag="SIM4"),
    sim(glk_multiplier=10.0, gna_multiplier=1.0, tag="SIM5"),
]

TagViewer(results_a, timerange=(97.5, 140)*units.ms, show=False,
          plots = [
                    TagPlot("ALL{Voltage,SIM1}", ylabel='gLeak: 0.1\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM2}", ylabel='gLeak: 0.5\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM3}", ylabel='gLeak: 1.0\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM4}", ylabel='gLeak: 5.0\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM5}", ylabel='gLeak: 10.0\nVoltage',yrange=(-80, 50)*units.mV, legend_labeller=None),
                       ])

results_b = [
    sim(gna_multiplier=0.1,  glk_multiplier=1.0, tag="SIM6"),
    sim(gna_multiplier=0.5,  glk_multiplier=1.0, tag="SIM7"),
    sim(gna_multiplier=0.75,  glk_multiplier=1.0, tag="SIM8"),
    sim(gna_multiplier=1.0,  glk_multiplier=1.0, tag="SIM9"),
]

TagViewer(results_b, timerange=(97.5, 140)*units.ms, show=True,
          plots = [
                    TagPlot("ALL{Voltage,SIM6}", ylabel='gNa: 0.10\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM7}", ylabel='gNa: 0.50\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM8}", ylabel='gNa: 0.75\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                    TagPlot("ALL{Voltage,SIM9}", ylabel='gNa: 1.00\nVoltage', yrange=(-80, 50)*units.mV, legend_labeller=None),
                       ])

Figures

../_images/singlecell_simulation080_out2.png

Download Figure

../_images/singlecell_simulation080_out1.png

Download Figure

Output

    No handlers could be found for logger "neurounits"
2013-10-19 15:40:46,704 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:46,704 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-10-19 15:40:48,332 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:48,332 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
Loading Bundle from: /local/scratch/mh735/tmp/morphforge/tmp/simulationresults/75/75b3b2b9bd9b587a14653b96392f3151.bundle (23k) : 0.785 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

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Running Simulation
Time for Extracting Data: (30 records) 0.0145881175995
Running simulation : 0.787 seconds
Post-processing : 0.024 seconds
Entire load-run-save time : 1.596 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:50,867 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:50,867 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
Loading Bundle from: /local/scratch/mh735/tmp/morphforge/tmp/simulationresults/3c/3c25eb16c1ba2f8ae55c84332b3d42d2.bundle (23k) : 0.804 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

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Running Simulation
Time for Extracting Data: (30 records) 0.0151150226593
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Post-processing : 0.022 seconds
Entire load-run-save time : 1.517 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:53,338 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:53,338 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
Loading Bundle from: /local/scratch/mh735/tmp/morphforge/tmp/simulationresults/23/233cfd4eff4b963e94e2c95a824a2ae2.bundle (23k) : 0.780 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

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Running Simulation
Time for Extracting Data: (30 records) 0.0145320892334
Running simulation : 0.676 seconds
Post-processing : 0.019 seconds
Entire load-run-save time : 1.476 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:55,740 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:55,740 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
Loading Bundle from: /local/scratch/mh735/tmp/morphforge/tmp/simulationresults/f9/f99535fae803f8bd6a2aa1ac28fcc754.bundle (23k) : 0.788 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

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Time for Extracting Data: (30 records) 0.0144238471985
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Entire load-run-save time : 1.580 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:58,258 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:58,259 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
Loading Bundle from: /local/scratch/mh735/tmp/morphforge/tmp/simulationresults/f8/f85e809d30b5749eef61273a9aee0212.bundle (23k) : 0.792 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

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Time for Extracting Data: (30 records) 0.015095949173
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No handlers could be found for logger "neurounits"
2013-10-19 15:41:01,070 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:41:01,070 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
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set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

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Running Simulation
Time for Extracting Data: (30 records) 0.014200925827
Running simulation : 0.477 seconds
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Entire load-run-save time : 1.290 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:41:03,264 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:41:03,264 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
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set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

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Running Simulation
Time for Extracting Data: (30 records) 0.0146231651306
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Post-processing : 0.023 seconds
Entire load-run-save time : 1.579 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:41:05,777 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:41:05,778 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
Loading Bundle from: /local/scratch/mh735/tmp/morphforge/tmp/simulationresults/95/9578be9c9b7def3f4320b4ff22c375da.bundle (23k) : 0.787 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_73cae5515813b8c78e05ae21b69025ee.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_e8de507bed64a7a182e7bb3108a43a37.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_e1d9b15c15cf730d6ad5de223a1b3007.so
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Running Simulation
Time for Extracting Data: (30 records) 0.0145888328552
Running simulation : 0.715 seconds
Post-processing : 0.020 seconds
Entire load-run-save time : 1.522 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:41:08,194 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:41:08,194 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
Loading Bundle from: /local/scratch/mh735/tmp/morphforge/tmp/simulationresults/a7/a70c607e497c72a1bae8a43867106a84.bundle (23k) : 0.779 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_c224cc126ae7a2714f42b5c551e02fa6.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_bb9b6fbbfd7217f10a29e5a4c138dd75.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_5163084cbe5b6d3cdf0bea4ed32ff8fc.so
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Running Simulation
Time for Extracting Data: (30 records) 0.0145931243896
Running simulation : 0.666 seconds
Post-processing : 0.020 seconds
Entire load-run-save time : 1.465 seconds
Suceeded
Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
PlotMnager:Saving  _output/figures/singlecell_simulation080/{png,svg}/fig000_Autosave_figure_1.{png,svg}
PlotMnager:Saving  _output/figures/singlecell_simulation080/{png,svg}/fig001_Autosave_figure_2.{png,svg}