Example 23. Action potential propagation and synaptic transmission
Action potential propagation and synaptic transmission. In this simulation, we create 3 neurons; Neuron 1 has an axon, and when the soma is stimulated, we see the action potential propagate along it. Neuron 1 forms synapses onto cell2 and cell3 with different strengths and different positions along the axon.
Code
import matplotlib as mpl
mpl.rcParams['font.size'] = 14
from morphforge.stdimports import *
from morphforgecontrib.stdimports import *
# Create a cell:
def build_cell(name, sim):
my_morph = MorphologyBuilder.get_soma_axon_morph(axon_length=1500.0, axon_radius=0.3, soma_radius=10.0)
my_cell = sim.create_cell(name=name, morphology=my_morph)
na_chls = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="Na", env=sim.environment)
k_chls = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="K", env=sim.environment)
lk_chls = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="Lk", env=sim.environment)
my_cell.apply_channel(lk_chls)
my_cell.apply_channel(k_chls)
my_cell.apply_channel(na_chls)
my_cell.apply_channel(na_chls, where="axon", parameter_multipliers={'gScale':1.0})
return my_cell
# Create a simulation:
env = NEURONEnvironment()
sim = env.Simulation()
# Two cells:
cell1 = build_cell(name="cell1", sim=sim)
cell2 = build_cell(name="cell2", sim=sim)
cell3 = build_cell(name="cell3", sim=sim)
# Connect with a synapse:
simple_ampa_syn = """
define_component syn_simple {
g' = - g/g_tau
i = gmax * (v-erev) * g
gmax = 300pS * scale
erev = 0mV
g_tau = 10ms
<=> INPUT v: mV METADATA {"mf":{"role":"MEMBRANEVOLTAGE"} }
<=> OUTPUT i:(mA) METADATA {"mf":{"role":"TRANSMEMBRANECURRENT"} }
<=> PARAMETER scale:()
on on_event(){
g = g + 1.0
}
}
"""
post_syn_tmpl = env.PostSynapticMechTemplate(
NeuroUnitEqnsetPostSynaptic,
eqnset = simple_ampa_syn,
default_parameters = { 'scale':1.0}
)
syn1 = sim.create_synapse(
trigger = env.SynapticTrigger(
SynapticTriggerByVoltageThreshold,
cell_location = CellLocator.get_location_at_distance_away_from_dummy(cell1, 300),
voltage_threshold = qty("0:mV"), delay=qty("0:ms"),
),
postsynaptic_mech = post_syn_tmpl.instantiate(cell_location = cell2.soma,),
)
syn1 = sim.create_synapse(
trigger = env.SynapticTrigger(
SynapticTriggerByVoltageThreshold,
cell_location = CellLocator.get_location_at_distance_away_from_dummy(cell1, 700),
voltage_threshold = qty("0:mV"), delay = qty("0:ms"),
),
postsynaptic_mech = post_syn_tmpl.instantiate(cell_location = cell3.soma, parameter_overrides={'scale':2.0} )
)
# Record Voltages from axons:
for loc in CellLocator.get_locations_at_distances_away_from_dummy(cell1, range(0, 1000, 50)):
sim.record( what=StandardTags.Voltage, cell_location = loc, user_tags=['cell1'])
sim.record(what=StandardTags.Voltage, cell_location = cell2.get_location("soma"), user_tags=['cell2'])
sim.record(what=StandardTags.Voltage, cell_location = cell3.get_location("soma"), user_tags=['cell3'])
# Create the stimulus and record the injected current:
cc = sim.create_currentclamp(name="CC1", amp=qty("200:pA"), dur=qty("1:ms"), delay=qty("100:ms"), cell_location=cell1.get_location("soma"))
sim.record(cc, what=StandardTags.Current)
results = sim.run()
TagViewer(results, timerange=(98, 120)*units.ms,
fig_kwargs = {'figsize':(12, 10)},
show=True,
plots = [
TagPlot('Current', yunit=units.picoamp),
TagPlot('Voltage,cell1', yrange=(-80*units.mV, 50*units.mV), yunit=units.mV),
TagPlot('Voltage AND ANY{cell2,cell3}', yrange=(-70*units.mV, -55*units.mV), yunit=units.millivolt),
],
)
Figures
Download Figure
Output
No handlers could be found for logger "neurounits"
2013-12-01 17:16:17,706 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:16:17,707 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-12-01 17:16:20,322 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:16:20,322 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/53/53c6998e8827a28214a7ec15f50c6a65.bundle (48k) : 0.987 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 /mnt/scratch/tmp/morphforge/tmp/modout/mod_fe29ca000b1bf9f98f8a5a86da5768f4.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_4a46a0f70872d4114e6b6a454639c210.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_8e3462bc4d8c5799b1edfe26d70b04ec.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_e1d9b15c15cf730d6ad5de223a1b3007.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_8c477b241bf2d2faa9a7d850b7091542.hoc
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Running Simulation
Time for Extracting Data: (23 records) 0.0401768684387
Running simulation : 3.909 seconds
Size of results file: 0.6 (MB)
Post-processing : 0.055 seconds
Entire load-run-save time : 4.952 seconds
Suceeded
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
<Parameter [id:56178448] Symbol: 'scale' >
scale
iii 1.0 dimensionless <class 'quantities.quantity.Quantity'>
iiii 1.0 <type 'float'>
Output <StateVariable [id:56249808] Symbol: 'g' >
None
Output <AssignedVariable [id:56249168] Symbol: 'gmax' >
None
Output <AssignedVariable [id:56248528] Symbol: 'i' >
{u'mf': {u'role': u'TRANSMEMBRANECURRENT'}}
input <SuppliedValue [id:56262864] Symbol: 'v' >
{u'mf': {u'role': u'MEMBRANEVOLTAGE'}}
scale <class 'neurounits.ast.astobjects.Parameter'>
gmax <class 'neurounits.ast.astobjects.AssignedVariable'>
v <class 'neurounits.ast.astobjects.SuppliedValue'>
g <class 'neurounits.ast.astobjects.StateVariable'>
Writing assignment for: <EqnAssignmentByRegime [id:56248400] Symbol: gmax >
scale <class 'neurounits.ast.astobjects.Parameter'>
Writing assignment for: <EqnAssignmentByRegime [id:56250000] Symbol: i >
gmax <class 'neurounits.ast.astobjects.AssignedVariable'>
v <class 'neurounits.ast.astobjects.SuppliedValue'>
g <class 'neurounits.ast.astobjects.StateVariable'>
g <class 'neurounits.ast.astobjects.StateVariable'>
<neurounits.codegen.nmodl.MODLBuildParameters object at 0x3593610>
g <class 'neurounits.ast.astobjects.StateVariable'>
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/53//53c6998e8827a28214a7ec15f50c6a65.neuronsim.results.pickle ]
PlotManger saving: _output/figures/poster2/{png,svg}/fig000_Autosave_figure_1.{png,svg}