Example 13. Using a channel library to reduce duplication
Using a channel library to reduce duplication.
We define functions that produce morphology and channel objects for our simulations. We could stop here, and simply import and use the functions in our simulations, but we go a step further, and register them with “ChannelLibrary” and “MorphologyLibrary”. These are basically glorified dictionaries, that do the lookup for the appropriate functors based on a key from the tuple~(modelsrc, celltype, channeltype). The advantage for doing this is that there is single repository for morphologies and channels.
There is not really anythin clever going on here, and you can run simulations completely ignorantly of these classes, I just included it because it made life much easier for me, when I had to start managing lots of channel definitions.
Code
from morphforge.stdimports import *
from morphforgecontrib.stdimports import StdChlLeak,StdChlAlphaBeta
# This can be put into a file that is loaded on
# you path somewhere:
# ======================================================
def getSimpleMorphology():
mDict = {'root': { 'length': 17.5, 'diam': 17.5, 'id':'soma', 'region':'soma', } }
return MorphologyTree.fromDictionary(mDict)
def get_sample_lk(env):
lk_chl = env.Channel(
StdChlLeak,
name="LkChl",
conductance=qty("0.3:mS/cm2"),
reversalpotential=qty("-54.3:mV"),
)
return lk_chl
def get_sample_na(env):
na_state_vars = { "m": {
"alpha":[-4.00,-0.10,-1.00,40.00,-10.00],
"beta": [4.00, 0.00, 0.00,65.00, 18.00]},
"h": {
"alpha":[0.07,0.00,0.00,65.00,20.00] ,
"beta": [1.00,0.00,1.00,35.00,-10.00]}
}
na_chl = env.Channel(
StdChlAlphaBeta,
name="NaChl", ion="na",
equation="m*m*m*h",
conductance=qty("120:mS/cm2"),
reversalpotential=qty("50:mV"),
statevars=na_state_vars,
)
return na_chl
def get_sample_k(env):
k_state_vars = { "n": { "alpha":[-0.55,-0.01,-1.0,55.0,-10.0],
"beta": [0.125,0,0,65,80]},
}
k_chl = env.Channel(
StdChlAlphaBeta,
name="KChl", ion="k",
equation="n*n*n*n",
conductance=qty("36:mS/cm2"),
reversalpotential=qty("-77:mV"),
statevars=k_state_vars,
)
return k_chl
MorphologyLibrary.register_morphology(modelsrc="Sample", celltype="Cell1", morph_functor=getSimpleMorphology)
ChannelLibrary.register_channel(modelsrc="Sample", celltype="Cell1", channeltype="Na", chl_functor=get_sample_na)
ChannelLibrary.register_channel(modelsrc="Sample", celltype="Cell1", channeltype="K", chl_functor=get_sample_k)
ChannelLibrary.register_channel(modelsrc="Sample", celltype="Cell1", channeltype="Lk", chl_functor=get_sample_lk)
# =============================================================
# Now in our script elsewhere, we can use them as:
modelsrc = "Sample"
celltype="Cell1"
# Create the environment:
env = NEURONEnvironment()
# Create the simulation:
sim = env.Simulation()
# Create a cell:
morphology=MorphologyLibrary.get_morphology(modelsrc=modelsrc, celltype=celltype)
cell = sim.create_cell(morphology=morphology)
# Apply the channels uniformly over the cell
na_chl = ChannelLibrary.get_channel(modelsrc=modelsrc, celltype=celltype, channeltype="Na", env=env)
k_chl = ChannelLibrary.get_channel(modelsrc=modelsrc, celltype=celltype, channeltype="K", env=env)
lk_chl = ChannelLibrary.get_channel(modelsrc=modelsrc, celltype=celltype, channeltype="Lk", env=env)
cell.apply_channel( na_chl)
cell.apply_channel( k_chl )
cell.apply_channel( lk_chl)
cell.set_passive( PassiveProperty.SpecificCapacitance, qty('1.0:uF/cm2'))
# Create the stimulus and record the injected current:
cc = sim.create_currentclamp(name="Stim1", amp=qty("150:pA"), dur=qty("5:ms"), delay=qty("100:ms"), cell_location=cell.soma)
sim.record(cc, what=StandardTags.Current)
sim.record(cell, what=StandardTags.Voltage, cell_location=cell.soma)
# run the simulation
results = sim.run()
# Display the results:
TagViewer([results], timerange=(97.5, 140)*units.ms)
Figures
Download Figure
Output
No handlers could be found for logger "neurounits"
2013-12-01 17:11:37,257 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:11:37,258 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-12-01 17:11:39,470 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:11:39,471 - 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/c1/c1265244a5fb5b4ff9665635277c60da.bundle (11k) : 0.844 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)}
Executing: /home/michael/opt//x86_64/bin/modlunit /mnt/scratch/tmp/morphforge/tmp/tmp_77f4939b62aa0aee20909846754ab5d2.mod
/mnt/scratch/tmp/morphforge/tmp/modbuild_21153
Executing: /home/michael/opt//x86_64/bin/nocmodl tmp_77f4939b62aa0aee20909846754ab5d2.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_77f4939b62aa0aee20909846754ab5d2.lo tmp_77f4939b62aa0aee20909846754ab5d2.c
Executing: /home/michael/opt//share/nrn/libtool --mode=link gcc -module -g -O2 -shared -o tmp_77f4939b62aa0aee20909846754ab5d2.la -rpath /home/michael/opt//x86_64/libs tmp_77f4939b62aa0aee20909846754ab5d2.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_77f4939b62aa0aee20909846754ab5d2.c -fPIC -DPIC -o .libs/tmp_77f4939b62aa0aee20909846754ab5d2.o
OP2: libtool: link: gcc -shared -fPIC -DPIC .libs/tmp_77f4939b62aa0aee20909846754ab5d2.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_77f4939b62aa0aee20909846754ab5d2.so.0 -o .libs/tmp_77f4939b62aa0aee20909846754ab5d2.so.0.0.0
libtool: link: (cd ".libs" && rm -f "tmp_77f4939b62aa0aee20909846754ab5d2.so.0" && ln -s "tmp_77f4939b62aa0aee20909846754ab5d2.so.0.0.0" "tmp_77f4939b62aa0aee20909846754ab5d2.so.0")
libtool: link: (cd ".libs" && rm -f "tmp_77f4939b62aa0aee20909846754ab5d2.so" && ln -s "tmp_77f4939b62aa0aee20909846754ab5d2.so.0.0.0" "tmp_77f4939b62aa0aee20909846754ab5d2.so")
libtool: link: ( cd ".libs" && rm -f "tmp_77f4939b62aa0aee20909846754ab5d2.la" && ln -s "../tmp_77f4939b62aa0aee20909846754ab5d2.la" "tmp_77f4939b62aa0aee20909846754ab5d2.la" )
Executing: /home/michael/opt//x86_64/bin/modlunit /mnt/scratch/tmp/morphforge/tmp/tmp_50636df53ea0c4b8840c60f57dd7bf9a.mod
/mnt/scratch/tmp/morphforge/tmp/modbuild_21153
Executing: /home/michael/opt//x86_64/bin/nocmodl tmp_50636df53ea0c4b8840c60f57dd7bf9a.mod
Executing: /home/michael/opt//share/nrn/libtool --mode=compile gcc -DHAVE_CONFIG_H -I"." -I".." -I"/homeNEURON -- 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
/michael/opt//include/nrn" -I"/home/michael/opt//x86_64/lib" -g -O2 -c -o tmp_50636df53ea0c4b8840c60f57dd7bf9a.lo tmp_50636df53ea0c4b8840c60f57dd7bf9a.c
Executing: /home/michael/opt//share/nrn/libtool --mode=link gcc -module -g -O2 -shared -o tmp_50636df53ea0c4b8840c60f57dd7bf9a.la -rpath /home/michael/opt//x86_64/libs tmp_50636df53ea0c4b8840c60f57dd7bf9a.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_50636df53ea0c4b8840c60f57dd7bf9a.c -fPIC -DPIC -o .libs/tmp_50636df53ea0c4b8840c60f57dd7bf9a.o
OP2: libtool: link: gcc -shared -fPIC -DPIC .libs/tmp_50636df53ea0c4b8840c60f57dd7bf9a.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_50636df53ea0c4b8840c60f57dd7bf9a.so.0 -o .libs/tmp_50636df53ea0c4b8840c60f57dd7bf9a.so.0.0.0
libtool: link: (cd ".libs" && rm -f "tmp_50636df53ea0c4b8840c60f57dd7bf9a.so.0" && ln -s "tmp_50636df53ea0c4b8840c60f57dd7bf9a.so.0.0.0" "tmp_50636df53ea0c4b8840c60f57dd7bf9a.so.0")
libtool: link: (cd ".libs" && rm -f "tmp_50636df53ea0c4b8840c60f57dd7bf9a.so" && ln -s "tmp_50636df53ea0c4b8840c60f57dd7bf9a.so.0.0.0" "tmp_50636df53ea0c4b8840c60f57dd7bf9a.so")
libtool: link: ( cd ".libs" && rm -f "tmp_50636df53ea0c4b8840c60f57dd7bf9a.la" && ln -s "../tmp_50636df53ea0c4b8840c60f57dd7bf9a.la" "tmp_50636df53ea0c4b8840c60f57dd7bf9a.la" )
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_fe29ca000b1bf9f98f8a5a86da5768f4.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_250f079a9019e4d528955aa6190f2826.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_4a46a0f70872d4114e6b6a454639c210.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_126abe6c4d84a6d91e731bb5e7be3f37.hoc
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.00391411781311
Running simulation : 2.607 seconds
Size of results file: 0.0 (MB)
Post-processing : 0.009 seconds
Entire load-run-save time : 3.460 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']
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/c1//c1265244a5fb5b4ff9665635277c60da.neuronsim.results.pickle ]
PlotManger saving: _output/figures/singlecell_simulation065/{png,svg}/fig000_Autosave_figure_1.{png,svg}