10. Investigating the rheobase of a neuron with a parameter sweep
Investigating the rheobase of a neuron with a parameter sweep
WARNING: The automatic naming and linkage between grpah colors is currently under a refactor; what is done in this script is not representing the best possible solution, or even something that will reliably work in the future!
The aim of this script is just to show that it is possible to run multiple simulations from a single script!
Code
from morphforge.stdimports import *
from morphforgecontrib.simulation.channels.hh_style.core.mmleak import StdChlLeak
from morphforgecontrib.simulation.channels.hh_style.core.mmalphabeta import StdChlAlphaBeta
@cached_functor
def get_Na_Channels(env):
na_state_vars = {"m":
{"alpha": [13.01,0,4,-1.01,-12.56], "beta": [5.73,0,1,9.01,9.69] },
"h":
{"alpha": [0.06,0,0,30.88,26], "beta": [3.06,0,1,-7.09,-10.21]}
}
return env.Channel(
StdChlAlphaBeta,
name="NaChl", ion="na",
equation="m*m*m*h",
conductance=qty("210:nS") / qty("400:um2"),
reversalpotential=qty("50.0:mV"),
statevars=na_state_vars,
)
@cached_functor
def get_Ks_Channels(env):
kf_state_vars = {"ks": {"alpha": [0.2,0,1,-6.96,-7.74 ], "beta": [0.05,0,2,-18.07,6.1 ] } }
return env.Channel(
StdChlAlphaBeta,
name="KsChl", ion="ks",
equation="ks*ks*ks*ks",
conductance=qty("3:nS") / qty("400:um2"),
reversalpotential=qty("-80.0:mV"),
statevars=kf_state_vars,
)
@cached_functor
def get_Kf_Channels(env):
kf_state_vars = {"kf": {"alpha": [ 3.1,0,1,-31.5,-9.3], "beta": [0.44,0,1,4.98,16.19 ] } }
return env.Channel(
StdChlAlphaBeta,
name="KfChl", ion="kf",
equation="kf*kf*kf*kf",
conductance=qty("0.5:nS") / qty("400:um2") ,
reversalpotential=qty("-80.0:mV"),
statevars=kf_state_vars,
)
@cached_functor
def get_Lk_Channels(env):
lk_chl = env.Channel(
StdChlLeak,
name="LkChl",
conductance=qty("3.6765:nS") / qty("400:um2"),
reversalpotential=qty("-51:mV"),
)
return lk_chl
def simulate(current_inj_level):
# Create the environment:
env = NEURONEnvironment()
# Create the simulation:
sim = env.Simulation(name="AA")
# Create a cell:
morphDict1 = {'root': {'length': 20, 'diam': 20, 'id':'soma'} }
morph = MorphologyTree.fromDictionary(morphDict1)
cell = sim.create_cell(name="Cell1", morphology=morph)
lk_chl = get_Lk_Channels(env)
na_chl = get_Na_Channels(env)
potFastChannels = get_Kf_Channels(env)
potSlowChannels = get_Ks_Channels(env)
cell.apply_channel( lk_chl)
cell.apply_channel( na_chl)
cell.apply_channel( potFastChannels)
cell.apply_channel( potSlowChannels)
cell.set_passive( PassiveProperty.SpecificCapacitance, qty('2.0:uF/cm2'))
# Create the stimulus and record the injected current:
cc = sim.create_currentclamp(amp=current_inj_level, dur=qty("100:ms"), delay=qty("100:ms"), cell_location=cell.soma)
sim.record(cc, what=StandardTags.Current)
# Define what to record:
sim.record(cell, what=StandardTags.Voltage, cell_location = cell.soma)
# run the simulation
results = sim.run()
return results
# Display the results:
results = [simulate(current_inj_level='%d:pA' % i) for i in [50,100,150,200, 250, 300] ]
TagViewer(results, timerange=(95, 200)*units.ms, show=True)
Figures
Download Figure
Output
No handlers could be found for logger "neurounits"
2013-10-19 15:40:12,263 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:12,263 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-10-19 15:40:13,866 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:13,866 - 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/a2/a26b9f834d42fb9df2b663d2fd1fdba7.bundle (11k) : 0.794 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-51.0) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(9.19125) * S/m**2}
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_8c985bc4d78348c5e6b5020db7c84b33.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_4a11c42a24cf8094e8128eb36ed4454b.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_d441f583160e57ff5401cbe672e7a2fc.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_f840dc4d53912ca489cb83065e2ac90a.so
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.00105500221252
Running simulation : 0.131 seconds
Post-processing : 0.002 seconds
Entire load-run-save time : 0.927 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:15,614 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:15,615 - 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/a5/a5f2760136d0500d16e585edd8781b53.bundle (11k) : 0.798 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-51.0) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(9.19125) * S/m**2}
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_8c985bc4d78348c5e6b5020db7c84b33.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_4a11c42a24cf8094e8128eb36ed4454b.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_d441f583160e57ff5401cbe672e7a2fc.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_f840dc4d53912ca489cb83065e2ac90a.so
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.0010449886322
Running simulation : 0.119 seconds
Post-processing : 0.003 seconds
Entire load-run-save time : 0.920 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:17,343 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:17,343 - 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/a1/a149219849962767fc3ba050fe64fcb0.bundle (11k) : 0.798 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-51.0) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(9.19125) * S/m**2}
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_3491b26d83ce944c4a48bec588249988.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_10db04e695bde49229cd91f80837e678.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_a7e581760ab76fb7fd4364df6a5cb525.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_cdb90d18701a6ac6f42dafa8f8d2b68b.so
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.00107979774475
Running simulation : 0.118 seconds
Post-processing : 0.002 seconds
Entire load-run-save time : 0.918 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:19,067 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:19,067 - 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/b7/b718a0d40179ae8cd838abaf66951199.bundle (11k) : 0.787 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-51.0) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(9.19125) * S/m**2}
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_bb71ec78e6dab19dcf87e15fc17561eb.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_788287c244f7438044a89398129f898b.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_7408cd406bc1adf0811143f9ef2231f3.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_0b6ff728b56729ca8f05449ed9e44a97.so
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.00105285644531
Running simulation : 0.308 seconds
Post-processing : 0.003 seconds
Entire load-run-save time : 1.098 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:20,988 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:20,989 - 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/da/da53d39cbdc1efb254446b84a99fc168.bundle (11k) : 0.785 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-51.0) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(9.19125) * S/m**2}
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_7610f582ad2abbe48c35a53ca9916058.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_316a63d7a1569a19442d0738a9081666.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_5b95d930087f6bce4c78cdc261821c6a.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_2f3f9ea398f72a5862674d83f114a245.so
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.00104308128357
Running simulation : 0.118 seconds
Post-processing : 0.003 seconds
Entire load-run-save time : 0.906 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-10-19 15:40:22,789 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:22,790 - 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/c6/c6bc427811a04eb29cb45f46c697a32d.bundle (11k) : 0.799 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-51.0) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(9.19125) * S/m**2}
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_762ecdcc92fc56510ed63f453d729fcd.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_c5a5a97cc17f8f6d60395eae5a0c67ed.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_3ccc28a6e495081d0fd8d62d7dc20e60.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_c489958483f5e120000734ea6f939099.so
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.00104308128357
Running simulation : 0.127 seconds
Post-processing : 0.003 seconds
Entire load-run-save time : 0.929 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_simulation040/{png,svg}/fig000_Autosave_figure_1.{png,svg}