Example 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.stdimports import StdChlLeak, 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] ]
results = [simulate(current_inj_level='%d:pA' % i) for i in [50] ]
# Create an output .pdf of the first simulation:
SimulationMRedoc.build( results[0] ).to_pdf(__file__ + '.pdf')
TagViewer(results, timerange=(95, 200)*units.ms, show=True)
Figures
Download Figure
Download Figure
Download Figure
Download Figure
Download Figure
Download Figure
Output
No handlers could be found for logger "neurounits"
2013-12-01 17:10:52,111 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:10:52,111 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-12-01 17:10:54,239 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:10:54,239 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
['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/5b/5b26463f7871798c2f37d8f819bb039a.bundle (12k) : 0.826 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}
Executing: /home/michael/opt//x86_64/bin/modlunit /mnt/scratch/tmp/morphforge/tmp/tmp_35ef696eee624ddddad719ec8975e2b8.mod
/mnt/scratch/tmp/morphforge/tmp/modbuild_20285
Executing: /home/michael/opt//x86_64/bin/nocmodl tmp_35ef696eee624ddddad719ec8975e2b8.mod
Executing: /home/michael/opt//share/nrn/libtool --mode=compile gcc -DHAVE_CONFIG_H -I"." -I".." -I"/home/michael/opt//include/nrn" -I"/home/michael/opt//x86_64/lib" -g -O2 -c -o tmp_35ef696eee624ddddad719ec8975e2b8.lo tmp_35ef696eee624ddddad719ec8975e2b8.c
Executing: /home/michael/opt//share/nrn/libtool --mode=link gcc -module -g -O2 -shared -o tmp_35ef696eee624ddddad719ec8975e2b8.la -rpath /home/michael/opt//x86_64/libs tmp_35ef696eee624ddddad719ec8975e2b8.lo -L/home/michael/opt//x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt//x86_64/lib/libnrniv.la -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -livoc -lneuron_gnu -lmeschach -lsundials -lm -ldl
OP1: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/michael/opt//include/nrn -I/home/michael/opt//x86_64/lib -g -O2 -c tmp_35ef696eee624ddddad719ec8975e2b8.c -fPIC -DPIC -o .libs/tmp_35ef696eee624ddddad719ec8975e2b8.o
OP2: libtool: link: gcc -shared -fPIC -DPIC .libs/tmp_35ef696eee624ddddad719ec8975e2b8.o -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt/x86_64/lib/libnrniv.so /home/michael/opt/x86_64/lib/libnrnoc.so /home/michael/opt/x86_64/lib/liboc.so /home/michael/opt/x86_64/lib/libmemacs.so /home/michael/opt/x86_64/lib/libnrnmpi.so /home/michael/opt/x86_64/lib/libscopmath.so /home/michael/opt/x86_64/lib/libsparse13.so -lreadline -lncurses /home/michael/opt/x86_64/lib/libivoc.so /home/michael/opt/x86_64/lib/libneuron_gnu.so /home/michael/opt/x86_64/lib/libmeschach.so /home/michael/opt/x86_64/lib/libsundials.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,tmp_35ef696eee624ddddad719ec8975e2b8.so.0 -o .libs/tmp_35ef696eee624ddddad719ec8975e2b8.so.0.0.0
libtool: link: (cd ".libs" && rm -f "tmp_35ef696eee624ddddad719ec8975e2b8.so.0" && ln -s "tmp_35ef696eee624ddddad719ec8975e2b8.so.0.0.0" "tmp_35ef696eee624ddddad719ec8975e2b8.so.0")
libtool: link: (cd ".libs" && rm -f "tmp_35ef696eee624ddddad719ec8975e2b8.so" && ln -s "tmp_35ef696eee624ddddad719ec8975e2b8.so.0.0.0" "tmp_35ef696eee624ddddad719ec8975e2b8.so")
libtool: link: ( cd ".libs" && rm -f "tmp_35ef696eee624ddddad719ec8975e2b8.la" && ln -s "../tmp_35ef696eee624ddddad719ec8975e2b8.la" "tmp_35ef696eee624ddddad719ec8975e2b8.la" )
Executing: /home/michael/opt//x86_64/bin/modlunit /mnt/scratch/tmp/morphforge/tmp/tmp_948523052657a5cf46d1539c09528f1c.mod
/mnt/scratch/tmp/morphforge/tmp/modbuild_20285
Executing: /home/michael/opt//x86_64/bin/nocmodl tmp_948523052657a5cf46d1539c09528f1c.mod
Executing: /home/michael/opt//share/nrn/libtool --mode=compile gcc -DHAVE_CONFIG_H -I"." -I".." -I"/home/michael/opt//include/nrn" -I"/home/michael/opt//x86_64/lib" -g -O2 -c -o tmp_948523052657a5cf46d1539c09528f1c.lo tmp_948523052657a5cf46d1539c09528f1c.c
Executing: /home/michael/opt//share/nrn/libtool --mode=link gcc -module -g -O2 -shared -o tmp_948523052657a5cf46d1539c09528f1c.la -rpath /home/michael/opt//x86_64/libs tmp_948523052657a5cf46d1539c09528f1c.lo -L/home/michael/opt//x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt//x86_64/lib/libnrniv.la -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -livoc -lneuron_gnu -lmeschach -lsundials -lm -ldl
OP1: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/michael/opt//include/nrn -I/home/michael/opt//x86_64/lib -g -O2 -c tmp_948523052657a5cf46d1539c09528f1c.c -fPIC -DPIC -o .libs/tmp_948523052657a5cf46d1539c09528f1c.o
OP2: libtool: link: gcc -shared -fPIC -DPIC .libs/tmp_948523052657a5cf46d1539c09528f1c.o -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt/x86_64/lib/libnrniv.so /home/michael/opt/x86_64/lib/libnrnoc.so /home/michael/opt/x86_64/lib/liboc.so /home/michael/opt/x86_64/lib/libmemacs.so /home/michael/opt/x86_64/lib/libnrnmpi.so /home/michael/opt/x86_64/lib/libscopmath.so /home/michael/opt/x86_64/lib/libsparse13.so -lreadline -lncurses /home/michael/opt/x86_64/lib/libivoc.so /home/michael/opt/x86_64/lib/libneuron_gnu.so /home/michael/opt/x86_64/lib/libmeschach.so /home/michael/opt/x86_64/lib/libsundials.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,tmp_948523052657a5cf46d1539c09528f1c.so.0 -o .libs/tmp_948523052657a5cf46d1539c09528f1c.so.0.0.0
libtool: link: (cd ".libs" && rm -f "tmp_948523052657a5cf46d1539c09528f1c.so.0" && ln -s "tmp_948523052657a5cf46d1539c09528f1c.so.0.0.0" "tmp_948523052657a5cf46d1539c09528f1c.so.0")
libtool: link: (cd ".libs" && rm -f "tmp_948523052657a5cf46d1539c09528f1c.so" && ln -s "tmp_948523052657a5cf46d1539c09528f1c.so.0.0.0" "tmp_948523052657a5cf46d1539c09528f1c.so")
libtool: link: ( cd ".libs" && rm -f "tmp_948523052657a5cf46d1539c09528f1c.la" && ln -s "../tmp_948523052657a5cf46d1539c09528f1c.la" "tmp_948523052657a5cf46d1539c09528f1c.la" )
Executing: /home/michael/opt//x86_64/bin/modlunit /mnt/scratch/tmp/morphforge/tmp/tmp_8e3f1017ae86fad13f965c3855e4c53b.mod
/mnt/scratch/tmp/morphforge/tmp/modbuild_20285
Executing: /home/michael/opt//x86_64/bin/nocmodl tmp_8e3f1017ae86fad13f965c3855e4c53b.mod
Executing: /home/michael/opt//share/nrn/libtool --mode=compile gcc -DHAVE_CONFIG_H -I"." -I".." -I"/home/michael/opt//include/nrn" -I"/home/michael/opt//x86_64/lib" -g -O2 -c -o tmp_8e3f1017ae86fad13f965c3855e4c53b.lo tmp_8e3f1017ae86fad13f965c3855e4c53b.c
Executing: /home/michael/opt//share/nrn/libtool --mode=link gcc -module -g -O2 -shared -o tmp_8e3f1017ae86fad13f965c3855e4c53b.la -rpath /home/michael/opt//x86_64/libs tmp_8e3f1017ae86fad13f965c3855e4c53b.lo -L/home/michael/opt//x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt//x86_64/lib/libnrniv.la -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -livoc -lneuron_gnu -lmeschach -lsundials -lm -ldl
OP1: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/michael/opt//include/nrn -I/home/michael/opt//x86_64/lib -g -O2 -c tmp_8e3f1017ae86fad13f965c3855e4c53b.c -fPIC -DPIC -o .libs/tmp_8e3f1017ae86fad13f965c3855e4c53b.o
OP2: libtool: link: gcc -shared -fPIC -DPIC .libs/tmp_8e3f1017ae86fad13f965c3855e4c53b.o -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt/x86_64/lib/libnrniv.so /home/michael/opt/x86_64/lib/libnrnoc.so /home/michael/opt/x86_64/lib/liboc.so /home/michael/opt/x86_64/lib/libmemacs.so /home/michael/opt/x86_64/lib/libnrnmpi.so /home/michael/opt/x86_64/lib/libscopmath.so /home/michael/opt/x86_64/lib/libsparse13.so -lreadline -lncurses /home/michael/opt/x86_64/lib/libivoc.so /home/michael/opt/x86_64/lib/libneuron_gnu.so /home/michael/opt/x86_64/lib/libmeschach.so /home/michael/opt/x86_64/lib/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
libsundials.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,tmp_8e3f1017ae86fad13f965c3855e4c53b.so.0 -o .libs/tmp_8e3f1017ae86fad13f965c3855e4c53b.so.0.0.0
libtool: link: (cd ".libs" && rm -f "tmp_8e3f1017ae86fad13f965c3855e4c53b.so.0" && ln -s "tmp_8e3f1017ae86fad13f965c3855e4c53b.so.0.0.0" "tmp_8e3f1017ae86fad13f965c3855e4c53b.so.0")
libtool: link: (cd ".libs" && rm -f "tmp_8e3f1017ae86fad13f965c3855e4c53b.so" && ln -s "tmp_8e3f1017ae86fad13f965c3855e4c53b.so.0.0.0" "tmp_8e3f1017ae86fad13f965c3855e4c53b.so")
libtool: link: ( cd ".libs" && rm -f "tmp_8e3f1017ae86fad13f965c3855e4c53b.la" && ln -s "../tmp_8e3f1017ae86fad13f965c3855e4c53b.la" "tmp_8e3f1017ae86fad13f965c3855e4c53b.la" )
Executing: /home/michael/opt//x86_64/bin/modlunit /mnt/scratch/tmp/morphforge/tmp/tmp_f81186f7d53550cac65242285b734fe5.mod
/mnt/scratch/tmp/morphforge/tmp/modbuild_20285
Executing: /home/michael/opt//x86_64/bin/nocmodl tmp_f81186f7d53550cac65242285b734fe5.mod
Executing: /home/michael/opt//share/nrn/libtool --mode=compile gcc -DHAVE_CONFIG_H -I"." -I".." -I"/home/michael/opt//include/nrn" -I"/home/michael/opt//x86_64/lib" -g -O2 -c -o tmp_f81186f7d53550cac65242285b734fe5.lo tmp_f81186f7d53550cac65242285b734fe5.c
Executing: /home/michael/opt//share/nrn/libtool --mode=link gcc -module -g -O2 -shared -o tmp_f81186f7d53550cac65242285b734fe5.la -rpath /home/michael/opt//x86_64/libs tmp_f81186f7d53550cac65242285b734fe5.lo -L/home/michael/opt//x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt//x86_64/lib/libnrniv.la -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -livoc -lneuron_gnu -lmeschach -lsundials -lm -ldl
OP1: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/michael/opt//include/nrn -I/home/michael/opt//x86_64/lib -g -O2 -c tmp_f81186f7d53550cac65242285b734fe5.c -fPIC -DPIC -o .libs/tmp_f81186f7d53550cac65242285b734fe5.o
OP2: libtool: link: gcc -shared -fPIC -DPIC .libs/tmp_f81186f7d53550cac65242285b734fe5.o -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -Wl,-rpath -Wl,/home/michael/opt/x86_64/lib -L/home/michael/opt//x86_64/lib /home/michael/opt/x86_64/lib/libnrniv.so /home/michael/opt/x86_64/lib/libnrnoc.so /home/michael/opt/x86_64/lib/liboc.so /home/michael/opt/x86_64/lib/libmemacs.so /home/michael/opt/x86_64/lib/libnrnmpi.so /home/michael/opt/x86_64/lib/libscopmath.so /home/michael/opt/x86_64/lib/libsparse13.so -lreadline -lncurses /home/michael/opt/x86_64/lib/libivoc.so /home/michael/opt/x86_64/lib/libneuron_gnu.so /home/michael/opt/x86_64/lib/libmeschach.so /home/michael/opt/x86_64/lib/libsundials.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,tmp_f81186f7d53550cac65242285b734fe5.so.0 -o .libs/tmp_f81186f7d53550cac65242285b734fe5.so.0.0.0
libtool: link: (cd ".libs" && rm -f "tmp_f81186f7d53550cac65242285b734fe5.so.0" && ln -s "tmp_f81186f7d53550cac65242285b734fe5.so.0.0.0" "tmp_f81186f7d53550cac65242285b734fe5.so.0")
libtool: link: (cd ".libs" && rm -f "tmp_f81186f7d53550cac65242285b734fe5.so" && ln -s "tmp_f81186f7d53550cac65242285b734fe5.so.0.0.0" "tmp_f81186f7d53550cac65242285b734fe5.so")
libtool: link: ( cd ".libs" && rm -f "tmp_f81186f7d53550cac65242285b734fe5.la" && ln -s "../tmp_f81186f7d53550cac65242285b734fe5.la" "tmp_f81186f7d53550cac65242285b734fe5.la" )
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_88205c8a06bba8a0808d415d4b9b191d.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_40e684618b2cbfb23d3322a61c77b689.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_df6b8521f579e1ad2aeec575b6207104.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_7600478d01e0b9510e7cb196c284fe70.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_60f36e17742108a7264754d6c012af7b.hoc
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.0036289691925
Running simulation : 4.696 seconds
Size of results file: 0.0 (MB)
Post-processing : 0.007 seconds
Entire load-run-save time : 5.529 seconds
Suceeded
/usr/bin/pdflatex
['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']
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/5b//5b26463f7871798c2f37d8f819bb039a.neuronsim.results.pickle ]
Warning: node 'Cell1', graph 'graphname' size too small for label
Warning: node 'AnonObj0001', graph 'graphname' size too small for label
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