def buildRdesigneur():
path = os.path.abspath(os.path.dirname('currentStep_CA3PC-Narayanan2010_v1.0.py'))
cellProto = [ [ "./cells/" + elecFileNames[0], "elec" ] ]
chanProto = [
[path+'/proto20.make_Ca_conc()', 'Ca_conc'], \
['./chans/CaL.xml'], \
['./chans/CaN.xml'], \
['./chans/CaT.xml'], \
['./chans/hd.xml'], \
['./chans/kad.xml'], \
[path+'/proto20.make_K_AHP()', 'kahp'], \
['./chans/kap.xml'], \
[path+'/proto20.make_K_C()', 'kca'], \
['./chans/kdr.xml'], \
['./chans/km.xml'], \
['./chans/na3.xml'] \
]
spineProto = [\
['makeSpineProto()', 'spine']
]
chemProto = []
passiveDistrib = [
[ ".", "#", "RM", "6", "CM", "0.0075", "RA", "2", \
"Em", "-65e-3", "initVm", "-65e-3" ] \
]
chanDistrib = [ \
["Ca_conc", "#soma#,#dend#", "tau", "0.0133" ], \
["CaL", "#dend#,#soma#", "Gbar", "p < 50e-6 ? 25 : 0" ], \
["CaN", "#soma#,#dend#", "Gbar", "28" ], \
["CaT", "#soma#,#dend#", "Gbar", "2.5" ], \
["hd", "#dend#,#soma#", "Gbar", "0.1*(1+1.75*p/100)" ], \
["kad", "#dend#", "Gbar", "p >= 100e-6 ? 1e-3*(7+(11*p)/100) : 0" ], \
["kad", "#soma#", "Gbar", "70" ], \
["kahp", "#", "Gbar", "3" ], \
["kap", "#dend#", "Gbar", "p < 100e-6 ? 1e-3*(7+(11*p)/100 : 0" ], \
["kap", "#soma#", "Gbar", "70" ], \
["kca", "#soma#,#dend#", "Gbar", "8" ], \
#["kdr", "#soma#,#dend#", "Gbar", "300"], \
["kdr", "#soma#,#dend#", "Gbar", "88"], \
#["M", "#soma#,#dend#", "Gbar", "p < 100e-6 ? 1 : 0" ], \
["M", "#soma#,#dend#", "Gbar", "p < 100e-6 ? 0.1 : 0" ], \
#["na3", "#soma#,#dend#", "Gbar", "250" ], \
["na3", "#soma#,#dend#", "Gbar", "180" ] \
]
spineDistrib = [ \
["spine", '#apical#', "spineSpacing", "20e-6", \
"spineSpacingDistrib", "2e-6", \
"angle", "0", \
"angleDistrib", str( 2*PI ), \
"size", "1", \
"sizeDistrib", "0.5" ] \
]
chemDistrib = []
adaptorList = []
rd.addSpineProto()
rdes = rd.rdesigneur(
useGssa = useGssa, \
combineSegments = combineSegments, \
stealCellFromLibrary = True, \
passiveDistrib = passiveDistrib, \
spineDistrib = spineDistrib, \
chanDistrib = chanDistrib, \
chemDistrib = chemDistrib, \
cellProto = cellProto, \
chanProto = chanProto, \
chemProto = chemProto, \
adaptorList = adaptorList
)
return rdes
def buildRdesigneur():
##################################################################
# Here we define which prototypes are to be loaded in to the system.
# Each specification has the format
# source [localName]
# source can be any of
# filename.extension, # Identify type of file by extension, load it.
# function(), # func( name ) builds object of specified name
# file.py:function() , # load Python file, run function(name) in it.
# moose.Classname # Make obj moose.Classname, assign to name.
# path # Already loaded into library or on path.
# After loading the prototypes, there should be an object called 'name'
# in the library.
##################################################################
#cellProto = [ [ "./cells/" + elecFileName, "elec" ] ]
chanProto = [
['./chans/hd.xml'], \
['./chans/kap.xml'], \
['./chans/kad.xml'], \
['./chans/kdr.xml'], \
['./chans/na3.xml'], \
['./chans/nax.xml'], \
['./chans/CaConc.xml'], \
['./chans/Ca.xml'], \
['./chans/NMDA.xml'], \
['./chans/Glu.xml'] \
]
spineProto = [ \
['makeSpineProto()', 'spine' ]
]
chemProto = [ \
['./chem/' + 'psd53.g', 'ltpModel'] \
]
##################################################################
# Here we define what goes where, and any parameters. Each distribution
# has the format
# protoName, path, field, expr, [field, expr]...
# where
# protoName identifies the prototype to be placed on the cell
# path is a MOOSE wildcard path specifying where to put things
# field is the field to assign.
# expr is a math expression to define field value. This uses the
# muParser. Built-in variables are:
# p, g, L, len, dia, maxP, maxG, maxL.
# where
# p = path distance from soma, threaded along dendrite
# g = geometrical distance from soma (shortest distance)
# L = electrotonic distance from soma: number of length constants
# len = length of dendritic compartment
# dia = diameter of dendritic compartment
# maxP = maximal value of 'p' for the cell
# maxG = maximal value of 'g' for the cell
# maxL = maximal value of 'L' for the cell
#
# The muParser provides most math functions, and the Heaviside
# function H(x) = 1 for x > 0 is also provided.
##################################################################
passiveDistrib = [
[ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", \
"Em", "-58e-3", "initVm", "-65e-3" ], \
[ ".", "#axon#", "RA", "0.5" ] \
]
chanDistrib = [ \
["hd", "#dend#,#apical#", "Gbar", "5e-2*(1+(p*3e4))" ], \
["kdr", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \
["na3", "#soma#,#dend#,#apical#", "Gbar", "250" ], \
["nax", "#soma#,#axon#", "Gbar", "1250" ], \
["kap", "#axon#,#soma#", "Gbar", "300" ], \
["kap", "#dend#,#apical#", "Gbar", \
"300*(H(100-p*1e6)) * (1+(p*1e4))" ], \
["Ca_conc", "#soma#,#dend#,#apical#", "tau", "0.0133" ], \
["kad", "#soma#,#dend#,#apical#", "Gbar", \
"300*H(p - 100e-6)*(1+p*1e4)" ], \
["Ca", "#dend#,#apical#", "Gbar", "p<160e-6? 10+ p*0.25e-6 : 50" ], \
["Ca", "#soma#", "Gbar", "10" ], \
["glu", "#dend#,#apical#", "Gbar", "200*H(p-200e-6)" ], \
["NMDA", "#dend#,#apical#", "Gbar", "2*H(p-200e-6)" ] \
]
spineDistrib = [ \
["spine", '#apical#', "spineSpacing", "20e-6", \
"spineSpacingDistrib", "2e-6", \
"angle", "0", \
"angleDistrib", str( 2*PI ), \
"size", "1", \
"sizeDistrib", "0.5" ] \
]
chemDistrib = [ \
[ "ltpModel", "#apical#", "install", "1"]
]
######################################################################
# Here we define the mappings across scales. Format:
# sourceObj sourceField destObj destField offset scale
# where the coupling expression is anything a muParser can evaluate,
# using the input variable x. For example: 8e-5 + 300*x
# For now, let's use existing adaptors which take an offset and scale.
######################################################################
adaptorList = [
['Ca_conc', 'Ca', 'psd/Ca_input', 'concInit', 8e-5, 1],
['Ca_conc', 'Ca', 'dend/Ca_dend_input', 'concInit', 8e-5, 0.1],
['psd/tot_PSD_R', 'n', 'glu', 'Gbar', 0, 0.01],
]
######################################################################
# Having defined everything, now to create the rdesigneur and proceed
# with creating the model.
######################################################################
rd.addSpineProto() # This adds a version with an LCa channel by default.
rdes = rd.rdesigneur(
useGssa = useGssa, \
combineSegments = combineSegments, \
stealCellFromLibrary = True, \
passiveDistrib = passiveDistrib, \
spineDistrib = spineDistrib, \
chanDistrib = chanDistrib, \
chemDistrib = chemDistrib, \
#cellProto = cellProto, \
chanProto = chanProto, \
chemProto = chemProto, \
adaptorList = adaptorList
)
#spineProto = spineProto, \
return rdes
def buildRdesigneur():
cellProto = [ [ "./cells/" + elecFileNames[0], "elec" ] ]
chanProto = [
['./chans/caL.xml'], \
#['./chans/caN.xml'], \
#['./chans/caT.xml'], \
['./chans/hd.xml'], \
['./chans/kad.xml'], \
#['./chans/kahp.xml'], \
['./chans/kap.xml'], \
#['./chans/kc.xml'], \
# ['./chans/kd.xml'], \ #slow subthreshold potassium current
['./chans/kdr.xml'], \
['./chans/km.xml'], \
['./chans/na3.xml'], \
]
spineProto = [\
['makeSpineProto()', 'spine']
]
chemProto = []
passiveDistrib = [
[ ".", "#", "RM", "3", "CM", "0.02", "RA", "2", \
"Em", "-65e-3", "initVm", "-65e-3" ], \
[ ".", "#soma#", "RM", "6", "CM", "0.01", "RA", "2" ] \
]
chanDistrib = [ \
["L", "#dend#,#soma#", "Gbar", "p < 50 ? 13 : 0" ], \
#["Cav2.2", "#soma#,#dend#", "Gbar", "15" ], \
#["CaT", "#soma#,#dend#", "Gbar", "10" ], \
["hd", "#dend#,#soma#", "Gbar", "1*(1+3/100*p)" ], \
["kad", "#soma#,#dend#", "Gbar", "p > 100e-6 ? 110*(1+(11/(7*100))*p) : 0" ], \
#["kahp", "#apical#", "Gbar", "10" ], \
#["kahp", "#soma#", "Gbar", "0" ], \
#["kahp", "#basal", "Gbar", "5" ], \
["kap", "#soma#,#dend#", "Gbar", "p <= 100e-6 ? 110*(1+(11/(7*100))*p) : 0" ], \
#["KC", "#soma#,#dend#", "Gbar", "p < 150e-6 ? 40*(150-p)/150 : 0" ], \
#["kd", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \
["kdr", "#soma#,#dend#", "Gbar", "20"], \
["M", "#soma#,#dend#", "Gbar", "p <= 100e-6 ? 1 : 0" ], \
["na3", "#soma#,#dend#", "Gbar", "350" ], \
]
spineDistrib = [ \
["spine", '#apical#', "spineSpacing", "20e-6", \
"spineSpacingDistrib", "2e-6", \
"angle", "0", \
"angleDistrib", str( 2*PI ), \
"size", "1", \
"sizeDistrib", "0.5" ] \
]
chemDistrib = []
adaptorList = []
rd.addSpineProto()
rdes = rd.rdesigneur(
useGssa = useGssa, \
combineSegments = combineSegments, \
stealCellFromLibrary = True, \
passiveDistrib = passiveDistrib, \
spineDistrib = spineDistrib, \
chanDistrib = chanDistrib, \
chemDistrib = chemDistrib, \
cellProto = cellProto, \
chanProto = chanProto, \
chemProto = chemProto, \
adaptorList = adaptorList
)
return rdes
def buildRdesigneur():
cellProto = [ [ "./cells/" + elecFileNames[0], "elec" ] ]
#chanProto = [
#['/home/sarathy/Work/templates/neurons/cA3_PC_rat/chans/proto20.make_Ca_conc()', 'Ca_conc'], \
#['./chans/CaL.xml'], \
#['./chans/CaN.xml'], \
#['./chans/CaT.xml'], \
#['./chans/hd.xml'], \
#['./chans/kad.xml'], \
#['/home/sarathy/Work/templates/neurons/cA3_PC_rat/chans/proto20.make_K_AHP()', 'kahp'], \
#['./chans/kap.xml'], \
#['/home/sarathy/Work/templates/neurons/cA3_PC_rat/chans/proto20.make_K_C()', 'kca'], \
## ['./chans/kd.xml'], \ #slow subthreshold potassium current
#['./chans/kdr.xml'], \
#['./chans/km.xml'], \
#['./chans/na3.xml'], \
#]
chanProto = [
['/home/sarathy/Work/templates/neurons/ca3_PC_rat/chans/proto20.make_Ca_conc()', 'Ca_conc'], \
['./chans/CaL.xml'], \
['./chans/CaN.xml'], \
['./chans/CaT.xml'], \
['./chans/hd-90.xml'], \
['./chans/hd-82.xml'], \
['./chans/kad.xml'], \
['/home/sarathy/Work/templates/neurons/ca3_PC_rat/chans/proto20.make_K_AHP()', 'kahp'], \
['./chans/kap.xml'], \
['/home/sarathy/Work/templates/neurons/ca3_PC_rat/chans/proto20.make_K_C()', 'kca'], \
# ['./chans/kd.xml'], \ #slow subthreshold potassium current
['./chans/kdr.xml'], \
['./chans/km.xml'], \
['./chans/na3.xml'], \
]
spineProto = [\
['makeSpineProto()', 'spine']
]
chemProto = []
#------------------------Lazarewicz et al 2002----------------------------------------#
passiveDistrib = [
[ ".", "#", "RM", "3", "CM", "0.02", "RA", "2", \
"Em", "-65e-3", "initVm", "-65e-3" ], \
[ ".", "#soma#", "RM", "6", "CM", "0.01" ] \
]
chanDistrib = [ \
["Ca_conc", "#soma#,#dend#", "tau", "0.0133" ], \
["CaL", "#soma#", "Gbar", "13" ], \
["CaL", "#dend#,#apical#,#basal#", "Gbar", "p < 50e-6 ? 13 : 0" ], \
["CaN", "#soma#,#dend#", "Gbar", "15" ], \
["CaT", "#soma#,#dend#", "Gbar", "10" ], \
["hd-82", "#dend#,#apical#", "Gbar", "p > 100 ? 1*(1+3/100*p) : 0" ], \
["hd-90", "#dend#,#basal#", "Gbar", "p <= 100 ? 1*(1+3/100*p) : 0" ], \
["hd-90", "#soma#", "Gbar", "1" ], \
["kad", "#dend#,#apical#,#basal#", "Gbar", "p > 100e-6 ? 110*(1+(11/(7*100))*p) : 0" ], \
["kad", "#soma#", "Gbar", "110" ], \
["kahp", "#soma#", "Gbar", "0" ], \
["kahp", "#dend#,#apical#", "Gbar", "5" ], \
["kahp", "#dend#,#basal#", "Gbar", "10" ], \
["kap", "#dend#,#apical#,#basal#", "Gbar", "p > 100e-6 ? 110*(1+(11/(7*100))*p) : 0" ], \
["kap", "#soma#", "Gbar", "110" ], \
["kap", "#axon#", "Gbar", "200"], \
["kca", "#dend#,#apical#,#basal#", "Gbar", "p < 150e-6 ? 40*(150-p)/150 : 0" ], \
["kca", "#soma#", "Gbar", "40"], \
##["kd", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \
["kdr", "#soma#,#dend#", "Gbar", "100"], \
["kdr", "#axon#", "Gbar", "100"], \
["M", "#soma#,#dend#,#apical#,#basal#", "Gbar", "p <= 100e-6 ? 1 : 0" ], \
["na3", "#soma#,#dend#", "Gbar", "350" ], \
["na3", "#axon#", "Gbar", "1100" ], \
#["na3", "#axon#", "Gbar", "1100" ], \
]
#------------------------Narayanan et al 2010----------------------------------------#
#passiveDistrib = [
#[ ".", "#", "RM", "6", "CM", "0.0075", "RA", "2", \
#"Em", "-65e-3", "initVm", "-65e-3" ], \
##[ ".", "#soma#", "RM", "6", "CM", "0.01", "RA", "2" ] \
#]
#chanDistrib = [ \
#["Ca_conc", "#soma#,#dend#", "tau", "0.0133" ], \
#["CaL", "#dend#,#soma#", "Gbar", "p < 50e-6 ? 25 : 0" ], \
#["CaN", "#soma#,#dend#", "Gbar", "28" ], \
#["CaT", "#soma#,#dend#", "Gbar", "2.5" ], \
#["hd", "#dend#,#soma#", "Gbar", "0.1*(1+1.75*p/100)" ], \
#["kad", "#dend#", "Gbar", "p >= 100e-6 ? 1e-3*(7+(11*p)/100) : 0" ], \
#["kad", "#soma#", "Gbar", "70" ], \
#["kahp", "#", "Gbar", "3" ], \
#["kap", "#dend#", "Gbar", "p < 100e-6 ? 1e-3*(7+(11*p)/100 : 0" ], \
#["kap", "#soma#", "Gbar", "70" ], \
#["kca", "#soma#,#dend#", "Gbar", "8" ], \
##["kd", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \
#["kdr", "#soma#,#dend#", "Gbar", "300"], \
#["M", "#soma#,#dend#", "Gbar", "p < 100e-6 ? 1 : 0" ], \
#["na3", "#soma#,#dend#", "Gbar", "250" ], \
##["na3", "#axon#", "Gbar", "p < 80e-6 ? 5000 : 0" ], \
#]
spineDistrib = [ \
["spine", '#apical#', "spineSpacing", "20e-6", \
"spineSpacingDistrib", "2e-6", \
"angle", "0", \
"angleDistrib", str( 2*PI ), \
"size", "1", \
"sizeDistrib", "0.5" ] \
]
chemDistrib = []
adaptorList = []
rd.addSpineProto()
rdes = rd.rdesigneur(
useGssa = useGssa, \
combineSegments = combineSegments, \
stealCellFromLibrary = True, \
passiveDistrib = passiveDistrib, \
spineDistrib = spineDistrib, \
chanDistrib = chanDistrib, \
chemDistrib = chemDistrib, \
cellProto = cellProto, \
chanProto = chanProto, \
chemProto = chemProto, \
adaptorList = adaptorList
)
return rdes
def buildRdesigneur():
'''
##################################################################
# Here we define which prototypes are to be loaded in to the system.
# Each specification has the format
# source [localName]
# source can be any of
# filename.extension, # Identify type of file by extension, load it.
# function(), # func( name ) builds object of specified name
# file.py:function() , # load Python file, run function(name) in it.
# moose.Classname # Make obj moose.Classname, assign to name.
# path # Already loaded into library or on path.
# After loading the prototypes, there should be an object called 'name'
# in the library.
##################################################################
'''
cellProto = [ [ "./cells/" + elecFileName, "elec" ] ]
chanProto = [
['./chans/hd.xml'], \
['./chans/kap.xml'], \
['./chans/kad.xml'], \
['./chans/kdr.xml'], \
['./chans/na3.xml'], \
['./chans/nax.xml'], \
['./chans/CaConc.xml'], \
['./chans/Ca.xml'], \
['./chans/NMDA.xml'], \
['./chans/Glu.xml'] \
]
spineProto = [ \
['makeSpineProto()', 'spine' ]
]
chemProto = []
##################################################################
# Here we define what goes where, and any parameters. Each distribution
# has the format
# protoName, path, field, expr, [field, expr]...
# where
# protoName identifies the prototype to be placed on the cell
# path is a MOOSE wildcard path specifying where to put things
# field is the field to assign.
# expr is a math expression to define field value. This uses the
# muParser. Built-in variables are:
# p, g, L, len, dia, maxP, maxG, maxL.
# where
# p = path distance from soma, threaded along dendrite
# g = geometrical distance from soma (shortest distance)
# L = electrotonic distance from soma: number of length constants
# len = length of dendritic compartment
# dia = diameter of dendritic compartment
# maxP = maximal value of 'p' for the cell
# maxG = maximal value of 'g' for the cell
# maxL = maximal value of 'L' for the cell
#
# The muParser provides most math functions, and the Heaviside
# function H(x) = 1 for x > 0 is also provided.
##################################################################
passiveDistrib = [
[ ".", "#", "RM", "2.8", "CM", "0.01", "RA", "1.5", \
"Em", "-58e-3", "initVm", "-65e-3" ], \
[ ".", "#axon#", "RA", "0.5" ] \
]
chanDistrib = [ \
["hd", "#dend#,#apical#", "Gbar", "5e-2*(1+(p*3e4))" ], \
["kdr", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \
["na3", "#soma#,#dend#,#apical#", "Gbar", "250" ], \
["nax", "#soma#,#axon#", "Gbar", "1250" ], \
["kap", "#axon#,#soma#", "Gbar", "300" ], \
["kap", "#dend#,#apical#", "Gbar", \
"300*(H(100-p*1e6)) * (1+(p*1e4))" ], \
["Ca_conc", "#soma#,#dend#,#apical#", "tau", "0.0133" ], \
["kad", "#soma#,#dend#,#apical#", "Gbar", \
"300*H(p - 100e-6)*(1+p*1e4)" ], \
["Ca", "#dend#,#apical#", "Gbar", "p<160e-6? 10+ p*0.25e-6 : 50" ], \
["Ca", "#soma#", "Gbar", "10" ], \
["glu", "#dend#,#apical#", "Gbar", "200*H(p-200e-6)" ], \
["NMDA", "#dend#,#apical#", "Gbar", "2*H(p-200e-6)" ] \
]
spineDistrib = [ \
["spine", '#apical#', "spineSpacing", "20e-6", \
"spineSpacingDistrib", "2e-6", \
"angle", "0", \
"angleDistrib", str( 2*PI ), \
"size", "1", \
"sizeDistrib", "0.5" ] \
]
chemDistrib = []
######################################################################
# Here we define the mappings across scales. Format:
# sourceObj sourceField destObj destField offset scale
# where the coupling expression is anything a muParser can evaluate,
# using the input variable x. For example: 8e-5 + 300*x
# For now, let's use existing adaptors which take an offset and scale.
######################################################################
adaptorList = []
######################################################################
# Having defined everything, now to create the rdesigneur and proceed
# with creating the model.
######################################################################
rd.addSpineProto() # This adds a version with an LCa channel by default.
rdes = rd.rdesigneur(
useGssa = useGssa, \
combineSegments = combineSegments, \
stealCellFromLibrary = True, \
passiveDistrib = passiveDistrib, \
spineDistrib = spineDistrib, \
chanDistrib = chanDistrib, \
chemDistrib = chemDistrib, \
cellProto = cellProto, \
chanProto = chanProto, \
chemProto = chemProto, \
adaptorList = adaptorList
)
#spineProto = spineProto, \
return rdes
def buildRdesigneur():
cellProto = [["./cells/" + elecFileNames[0], "elec"]]
#chanProto = [
#['/home/sarathy/Work/templates/neurons/cA3_PC_rat/chans/proto20.make_Ca_conc()', 'Ca_conc'], \
#['./chans/CaL.xml'], \
#['./chans/CaN.xml'], \
#['./chans/CaT.xml'], \
#['./chans/hd.xml'], \
#['./chans/kad.xml'], \
#['/home/sarathy/Work/templates/neurons/cA3_PC_rat/chans/proto20.make_K_AHP()', 'kahp'], \
#['./chans/kap.xml'], \
#['/home/sarathy/Work/templates/neurons/cA3_PC_rat/chans/proto20.make_K_C()', 'kca'], \
## ['./chans/kd.xml'], \ #slow subthreshold potassium current
#['./chans/kdr.xml'], \
#['./chans/km.xml'], \
#['./chans/na3.xml'], \
#]
chanProto = [
['/home/sarathy/Work/templates/neurons/ca3_PC_rat/chans/proto20.make_Ca_conc()', 'Ca_conc'], \
['./chans/CaL.xml'], \
['./chans/CaN.xml'], \
['./chans/CaT.xml'], \
['./chans/hd-90.xml'], \
['./chans/hd-82.xml'], \
['./chans/kad.xml'], \
['/home/sarathy/Work/templates/neurons/ca3_PC_rat/chans/proto20.make_K_AHP()', 'kahp'], \
['./chans/kap.xml'], \
['/home/sarathy/Work/templates/neurons/ca3_PC_rat/chans/proto20.make_K_C()', 'kca'], \
# ['./chans/kd.xml'], \ #slow subthreshold potassium current
['./chans/kdr.xml'], \
['./chans/km.xml'], \
['./chans/na3.xml'], \
]
spineProto = [\
['makeSpineProto()', 'spine']
]
chemProto = []
#------------------------Lazarewicz et al 2002----------------------------------------#
passiveDistrib = [
[ ".", "#", "RM", "3", "CM", "0.02", "RA", "2", \
"Em", "-65e-3", "initVm", "-65e-3" ], \
[ ".", "#soma#", "RM", "6", "CM", "0.01" ] \
]
chanDistrib = [ \
["Ca_conc", "#soma#,#dend#", "tau", "0.0133" ], \
["CaL", "#soma#", "Gbar", "13" ], \
["CaL", "#dend#,#apical#,#basal#", "Gbar", "p < 50e-6 ? 13 : 0" ], \
["CaN", "#soma#,#dend#", "Gbar", "15" ], \
["CaT", "#soma#,#dend#", "Gbar", "10" ], \
["hd-82", "#dend#,#apical#", "Gbar", "p > 100 ? 1*(1+3/100*p) : 0" ], \
["hd-90", "#dend#,#basal#", "Gbar", "p <= 100 ? 1*(1+3/100*p) : 0" ], \
["hd-90", "#soma#", "Gbar", "1" ], \
["kad", "#dend#,#apical#,#basal#", "Gbar", "p > 100e-6 ? 110*(1+(11/(7*100))*p) : 0" ], \
["kad", "#soma#", "Gbar", "110" ], \
["kahp", "#soma#", "Gbar", "0" ], \
["kahp", "#dend#,#apical#", "Gbar", "5" ], \
["kahp", "#dend#,#basal#", "Gbar", "10" ], \
["kap", "#dend#,#apical#,#basal#", "Gbar", "p > 100e-6 ? 110*(1+(11/(7*100))*p) : 0" ], \
["kap", "#soma#", "Gbar", "110" ], \
["kap", "#axon#", "Gbar", "200"], \
["kca", "#dend#,#apical#,#basal#", "Gbar", "p < 150e-6 ? 40*(150-p)/150 : 0" ], \
["kca", "#soma#", "Gbar", "40"], \
##["kd", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \
["kdr", "#soma#,#dend#", "Gbar", "100"], \
["kdr", "#axon#", "Gbar", "100"], \
["M", "#soma#,#dend#,#apical#,#basal#", "Gbar", "p <= 100e-6 ? 1 : 0" ], \
["na3", "#soma#,#dend#", "Gbar", "350" ], \
["na3", "#axon#", "Gbar", "1100" ], \
#["na3", "#axon#", "Gbar", "1100" ], \
]
#------------------------Narayanan et al 2010----------------------------------------#
#passiveDistrib = [
#[ ".", "#", "RM", "6", "CM", "0.0075", "RA", "2", \
#"Em", "-65e-3", "initVm", "-65e-3" ], \
##[ ".", "#soma#", "RM", "6", "CM", "0.01", "RA", "2" ] \
#]
#chanDistrib = [ \
#["Ca_conc", "#soma#,#dend#", "tau", "0.0133" ], \
#["CaL", "#dend#,#soma#", "Gbar", "p < 50e-6 ? 25 : 0" ], \
#["CaN", "#soma#,#dend#", "Gbar", "28" ], \
#["CaT", "#soma#,#dend#", "Gbar", "2.5" ], \
#["hd", "#dend#,#soma#", "Gbar", "0.1*(1+1.75*p/100)" ], \
#["kad", "#dend#", "Gbar", "p >= 100e-6 ? 1e-3*(7+(11*p)/100) : 0" ], \
#["kad", "#soma#", "Gbar", "70" ], \
#["kahp", "#", "Gbar", "3" ], \
#["kap", "#dend#", "Gbar", "p < 100e-6 ? 1e-3*(7+(11*p)/100 : 0" ], \
#["kap", "#soma#", "Gbar", "70" ], \
#["kca", "#soma#,#dend#", "Gbar", "8" ], \
##["kd", "#", "Gbar", "p < 50e-6 ? 500 : 100" ], \
#["kdr", "#soma#,#dend#", "Gbar", "300"], \
#["M", "#soma#,#dend#", "Gbar", "p < 100e-6 ? 1 : 0" ], \
#["na3", "#soma#,#dend#", "Gbar", "250" ], \
##["na3", "#axon#", "Gbar", "p < 80e-6 ? 5000 : 0" ], \
#]
spineDistrib = [ \
["spine", '#apical#', "spineSpacing", "20e-6", \
"spineSpacingDistrib", "2e-6", \
"angle", "0", \
"angleDistrib", str( 2*PI ), \
"size", "1", \
"sizeDistrib", "0.5" ] \
]
chemDistrib = []
adaptorList = []
rd.addSpineProto()
rdes = rd.rdesigneur(
useGssa = useGssa, \
combineSegments = combineSegments, \
stealCellFromLibrary = True, \
passiveDistrib = passiveDistrib, \
spineDistrib = spineDistrib, \
chanDistrib = chanDistrib, \
chemDistrib = chemDistrib, \
cellProto = cellProto, \
chanProto = chanProto, \
chemProto = chemProto, \
adaptorList = adaptorList
)
return rdes
