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reduced-passive.pDE
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reduced-passive.pDE
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# 06Apr10
# Copied from 1spk-th-072006b-n420-Passive-v7c.pDE
# Modified to have what 1spk-th-10606b-n420+Fix-h+Naf+KDR-3iALpaper-v7.pDE ha
#
#================================================================================
# No sensitivity analysis
Fit-SA 0 0
Tmp-dir MyTemp
#Fit 072006b 311 200 10 3 0.85 1.0 randE Projects/ParSims/Runs_pDE/thin-1stspike/main-n400-Vbtim-simL-v8d-reduced.hoc
#Fit 072006b 199 110 25 3 0.7 1.0 randE Projects/ParSims/Runs_pDE/thin-1stspike/main-n400-Vbtim-simL-v8d-reduced.hoc
#Fit 072006b 713 120 50 3 0.85 1.0 randE Projects/ParSims/Runs_pDE/thin-1stspike/main-n400-Vbtim-simL-v8d-reduced.hoc
Fit 072006b 191 200 10 3 0.85 1.0 randE /home/ximi/Projects/ParSims/reduced-passive.hoc
#================================================================================
# 10oct08 4:40pm
# Set up traces for 072006b
# 10oct08 4pm
# Stage 0; select traces; time v=0 post spike for +1500 800 400 200
# Stich 800 with 3 4 5 spikes; select v of end trace, stitch at same volt after spike
# Determine bl_avg with 13 traces; BL_avg=-74.3052
# Determine BBF; need closer fit first.
# Run Passive fit with 9 traces
# Use lambda_f_d=0.1
Pop-init uniform noset
# Determined BBF=1.6 from run so far. Resume above
#================================================================================
VERBATIM
cell_file_name="n400td-pc2-sp-axn.hoc"
obfunc dfc_set_stims_etc(){
print "check pDE dfc_set_stims++++++++++++++++++++"
/*
if(vdef("aX_hill_nseg"))\
execute( "if(axon_hill.nseg<aX_hill_nseg) axon_hill.nseg=aX_hill_nseg" )
if(vdef("aX_iseg_nseg")) \
execute( "for i=0,aX_iseg_n-1 {if(axon_iseg[i].nseg<aX_iseg_nseg) axon_iseg[i].nseg= aX_iseg_nseg }" )
if(vdef("aX_prox_nseg")) \
execute( "for i=0,aX_prox_n-1 {if(axon_prox[i].nseg<aX_prox_nseg) axon_prox[i].nseg= aX_prox_nseg }" )
if( vdef("aX_mnode_nseg" )) \
execute( "forsec \"mnode\" if(nseg<aX_mnode_nseg) nseg= aX_mnode_nseg" )
*/
// execute( "axon_prox.nseg = aX_prox_nseg" )
// execute( "for i=0,aX_iseg_n-1 {axon_iseg[i].nseg= aX_iseg_nseg }" )
stim.amp=$1
stim.dur=$2
stim.del=$3
print "check stim.del +++++++++++++++++++++++++++"
dfc_options_all( dfc_eD )
return stim
}
obfunc dfc_set_tgt(){
print "dfc_set_tgt()+++++++++++++++++++++++++++"
dfc_tgt.stim_amp=$1
dfc_tgt.stim_dur=$2
dfc_tgt.stim_del=$3
if( numarg()>3 ) dfc_tgt.cut_at2($4,$5)
return dfc_tgt
}
proc dfc_sim_BBF(){
dfc_simL_i.o(0).dc_shift(stim.del+BBFdelay,stim.del+stim.dur+BBFdelay,-BBF*stim.amp)
}
//================================================================================
// New stuff for pkbeg posfix
obfunc dfc_seg_look_options(){ local i localobj dI
dI = new eMatch() if( numarg()>0)dI =$o1
dI.seg_option = 1101
dI.seg_dt = 0.09
dI.seg_slp_dt = 0.09
dI.seg_slp_th = 10
dI.seg_v_th = 0
dI.seg_tiny_last = 0
if( strcmp(dfc_i.id,"072006b-2ms+1500pA-pkbeg") == 0 ){ dI.seg_dt=dI.seg_slp_dt= 0.02 }
return dI
}
obfunc dfc_options_all(){ local i localobj eD
if( numarg()==0 ) eD = dfc_seg_look_options()
if( numarg()> 0 ) eD = dfc_seg_look_options($o1)
eD.match_option = 5.2
eD.alpha = eD.beta = eD.gamma = eD.delta = eD.eta = eD.mF1 = eD.mF2 = eD.pkP = eD.pkPs = 0
eD.ilog = 1
return eD
}
// rough match to train;
// necessary to avoid traces that don't return to baseline
// also check spikes also appear in axon
func dfc_trim(){ local i, t0_tail, f1, f2, r1, r2, res localobj eD
f1=$1 f2=$2
eD = dfc_options_all(dfc_eD)
eD.eta = 1
eD.mF2 = 200
eD.pkP = 1500*5
eD.pkPs = 1
eD.pkPsA = 1
t0_tail = stim.del + stim.dur // end of stimulus
eD.tmin = t0_tail // compare tails after end stimulus: axon vs tgt
r2 = eD.m0( dfc_simL_i.o(1), dfc_tgt_i )
eD.tmin = 0
printf( "\n\t >>dfc_trim: DfpwPkdVa_aXe: " )
r1 = eD.DfpwPkdVa_aXe(dfc_simL_i,dfc_tgt_i,-1,-1) // 800=8.90, 400=15.2, 200=30.82, 1500=6.7
res = r1*f1 + r2*f2
printf( "\n\t dfc_trim t0_tail %g r1,2 %g %g f1,f2 %g %g ri*fi %g %g\n\t res %g<<\n",\
t0_tail, r1,r2, f1,f2, r1*f1, r2*f2, res )
return res
}
//================================================================================
// match first spike (up to tmax)
// gamma and delta to match dV and ddV; largely independent of trace length/stim.amp
// eta scaled by trace length
//================================================================================
func dfc_pkbeg(){ local i, tmax, dV_f, eta_f, r1 localobj eD
tmax = $1
dV_f = 45*2
eta_f = 300 + 100/(tmax-stim.del-1.1) // A + B/(time from stim.del to base of spike) A=for spike; B for before spike
eD = dfc_eD // eD = dfc_options_all(dfc_eD)
// eD.mF2 = 200*10
eD.mF2 = 6000 * stim.amp // peak time error proportional to stimulation amplitude
eD.pkP = 1500*5
eD.pkPs = 1
eD.phi = 600/116/10 // range_dV/range_V old=0.4 * 10
eD.phi_1 = 0.5+0.15
eD.phi_2 = 0.45-0.02
eD.chi = 1000/116/100 // range_ddV/range_V old=0.02 * 8
eD.chi_1 = 0.5+0.15
eD.chi_2 = 0.15
if( numarg()>1) eD.chi_2=$2 // adhoc inserted to override
eD.phi*=dV_f eD.chi*=dV_f
eD.eta = eta_f
// eD.mF2=0 eD.pkP=1000*eta_f // for initial pop for Naf & KDR parms
eD.tmax = tmax
printf( "\n\t >>dfc_pkbeg: DfpwPkdVa: " )
r1 = eD.DfpwPkdVa(dfc_simL_i.o(0),dfc_tgt_i) // 800=8.90, 400=15.2, 200=30.82, 1500=6.7
printf( "\n\t dfc_pkbeg: r1 %g \n\t<<\n", r1 )
return r1
}
ENDVERBATIM
#================================================================================
# Fit-case name template func scale hoc_var hoc_before hoc_after tgt_files tgt_before tgt_after
# Active traces 20kHz
# For Naf & KDR initial parm search
#Fit-case 072006b-2ms+1500pA eMatch dfc_eD.DfpwPkdVa(dfc_simL_i.o(0),dfc_tgt_i) 5 soma dfc_set_stims_etc(1500/1000,2,5);dfc_eD.eta=1;dfc_eD.pkP=1500*5;dfc_eD.pkPs=1 dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF/2ms+1500pA.htf blMax=4 dfc_set_tgt(1500/1000,2,21,136,16)
#Fit-case 072006b-100ms+800pA eMatch dfc_eD.DfpwPkdVa(dfc_simL_i.o(0),dfc_tgt_i) 5 soma dfc_set_stims_etc(800/1000,100,5);dfc_eD.eta=1;dfc_eD.pkP=1500*5;dfc_eD.pkPs=1 dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF/100ms+800pA.htf blMax=4 dfc_set_tgt(800/1000,100,21,200,16)
# End for Naf & KDR initial parm search
# Note dfc_eD.seg_dt=dfc_eD.seg_slp_dt=0.02 cause end_stim almost on peak
# 2:active set ================================================================================
#Fit-case 072006b-2ms+1500pA-pkbeg eMatch dfc_pkbeg(7.36) 1 soma dfc_set_stims_etc(1500/1000,2,5);dfc_eD.seg_dt=dfc_eD.seg_slp_dt=0.02;dfc_eD.pkPs=3 dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_20kHz/2ms+1500pA.htf blMax=4 dfc_set_tgt(1500/1000,2,21,7.36+1+16,16)
# later runs use the following instead
#modified
#Fit-case 2ms+1500pA_chopped.dat eMatch dfc_pkbeg(7.36,0.05) 1 soma dfc_set_stims_etc(1500/1000,2,5);dfc_eD.pkPs=3; dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_20kHz/2ms+1500pA.htf blMax=4 dfc_set_tgt(1500/1000,2,21,7.36+1+16,16)
#Fit-case 072006b-2ms+1500pA-pkbeg eMatch dfc_pkbeg(7.36,0.05) 1 soma dfc_set_stims_etc(1500/1000,2,5);dfc_eD.pkPs=3; dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_20kHz/2ms+1500pA.htf blMax=4 dfc_set_tgt(1500/1000,2,21,7.36+1+16,16)
# Note about TRIMMED file. Each trace was cut at a diffent time from same trace 2 of 072006b-100ms+800pA
# So, all trimmed traces should be compared to trace 2:072006b-100ms+800pA
# Trimmed #1; 26.39
#Fit-case 072006b-100ms+800pA-tr-pkbeg eMatch (dfc_trim(1,1)+dfc_pkbeg(10.03)) 1 soma;axon_inode[4] dfc_set_stims_etc(800/1000,26.39-5,5) dfc_sim_BBF() 1:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_20kHz/100ms+800pA-trimmed.htf blMax=4 dfc_set_tgt(800/1000,26.39-5,5)
# Trimmed #2; 37.49
#Fit-case 072006b-100ms+800pA-tr-pkbeg eMatch (dfc_trim(1,1)+dfc_pkbeg(10.03)) 1 soma;axon_inode[4] dfc_set_stims_etc(800/1000,37.49-5,5) dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_20kHz/100ms+800pA-trimmed.htf blMax=4 dfc_set_tgt(800/1000,37.49-5,5)
#Fit-case 072006b-100ms+400pA-pkbeg eMatch dfc_pkbeg(16.56) 1 soma dfc_set_stims_etc(400/1000,100,5) dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_20kHz/100ms+400pA.htf blMax=4 dfc_set_tgt(400/1000,100,21,16.56+1+16,16)
#Fit-case 072006b-100ms+200pA-pkbeg eMatch dfc_pkbeg(34.01) 1 soma dfc_set_stims_etc(200/1000,100,5) dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_20kHz/100ms+200pA.htf blMax=4 dfc_set_tgt(200/1000,100,21,34.01+1+16,16)
#--------------------------------------------------------------------------------
# Passive traces (all 10kHz)
#+750 has no spike; we could use m0; but we want to penalize unwanted spikes
#Fit-case 072006b-2ms+750pA eMatch dfc_eD.DfpwPkdVa(dfc_simL_i.o(0),dfc_tgt_i) 6.4*dfc_PassWgt*100/tstop soma dfc_set_stims_etc(750/1000,2,5);dfc_eD.eta=1 dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_0kHz/2ms+750pA.htf blMax=4 dfc_set_tgt(750/1000,2,21,136,16)
# m0
Fit-case 072006b-2ms+375pA eMatch dfc_eD.m0(dfc_simL_i.o(0),dfc_tgt_i) 4*dfc_PassWgt*100/tstop soma dfc_set_stims_etc(375/1000,2,5) dfc_sim_BBF() 2:/home/ximi/Projects/ParSims/from_axon_new/htf_files/2ms+375pA.htf blMax=4 dfc_set_tgt(375/1000,2,21,136,16)
# m0
#Fit-case 072006b-100ms+100pA eMatch dfc_eD.m0(dfc_simL_i.o(0),dfc_tgt_i) 7.9*dfc_PassWgt*100/tstop soma dfc_set_stims_etc(100/1000,100,5) dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_20kHz/100ms+100pA.htf blMax=4 dfc_set_tgt(100/1000,100,21,300,16)
#====== 20ms
# m0
Fit-case 072006b-20ms+50pA eMatch dfc_eD.m0(dfc_simL_i.o(0),dfc_tgt_i) 2*dfc_PassWgt*100/tstop soma dfc_set_stims_etc(50/1000,20,5) dfc_sim_BBF() 2:/home/ximi/Projects/ParSims/from_axon_new/htf_files/20ms+50pA.htf blMax=4 dfc_set_tgt(50/1000,20,21,120,16)
# m0
Fit-case 072006b-20ms-50pA eMatch dfc_eD.m0(dfc_simL_i.o(0),dfc_tgt_i) 2*dfc_PassWgt*100/tstop soma dfc_options_all();dfc_set_stims_etc(-50/1000,20,5) dfc_sim_BBF() 2:/home/ximi/Projects/ParSims/from_axon_new/htf_files/20ms-50pA.htf blMax=4 dfc_set_tgt(-50/1000,20,21,120,16)
# m0
Fit-case 072006b-20ms-200pA eMatch dfc_eD.m0(dfc_simL_i.o(0),dfc_tgt_i) 8.3*dfc_PassWgt*100/tstop soma dfc_options_all();dfc_set_stims_etc(-200/1000,20,5) dfc_sim_BBF() 2:/home/ximi/Projects/ParSims/from_axon_new/htf_files/20ms-200pA.htf blMax=4 dfc_set_tgt(-200/1000,20,21,120,16)
#====== 500ms
# m0
#Fit-case 072006b-500ms+50pA eMatch dfc_eD.m0(dfc_simL_i.o(0),dfc_tgt_i) 4.1*dfc_PassWgt*100/tstop soma dfc_set_stims_etc(50/1000,500,21) dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_0kHz/500ms+50pA.htf blMax=19 dfc_set_tgt(50/1000,500,21,800,0)
# m0
#Fit-case 072006b-500ms-50pA eMatch dfc_eD.m0(dfc_simL_i.o(0),dfc_tgt_i) 3.9*dfc_PassWgt*100/tstop soma dfc_set_stims_etc(-50/1000,500,21) dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_0kHz/500ms-50pA.htf blMax=19 dfc_set_tgt(-50/1000,500,21,800,0)
# m0
#Fit-case 072006b-500ms-200pA eMatch dfc_eD.m0(dfc_simL_i.o(0),dfc_tgt_i) 12.7*dfc_PassWgt*100/tstop soma dfc_set_stims_etc(-200/1000,500,21) dfc_sim_BBF() 2:/Volumes/d1/Users/ximing/cNeuro/Data/Grover-2006/072006b/ACSF_0kHz/500ms-200pA.htf blMax=19 dfc_set_tgt(-200/1000,500,21,800,0)
# --------------------------------------------------------------------------------
#
# Fit-parm name set fit-lims
Set-parm dfc_PassWgt 1 0:1
Set-parm RmCm_spine_gbar 0 0:1
Set-parm Spine_number 30000 0:40000
Set-parm BL_avg -74.3052 -80:-60
Set-parm BBF 1.60 0:20
Set-parm BBFdelay 0 0:0.1
Set-parm lambda_f_d 0.1 0.1:2
#Set-parm G_ena 65.4 60:70
#Set-parm G_ek -89.5 -95:-85
Set-parm G_eh -30 -40:-10
Set-parm celsius 35 22:37
#Fit-parm soma_diam_f 1 0.1:3
Fit-parm G_Rm 200 10:400
Fit-parm G_cm 0.9626 0.25:2.5
Fit-parm G_Ra 45 2:150
#Set-parm G_e_pas -77.7604 -100:-65
#---------------------------------------------------------------------------
#Set-parm soma_cm 1.0 0:3
#Set-parm soma_Rm 40 1:100
#Set-parm soma_Ra 100 1:500
#Set-parm soma_l 17 4:30
#Set-parm soma_diam 13.5 2:30
#Set-parm aX_hill_nseg 5 1:100
#Set-parm aX_hill_l 5 1:50
#Set-parm aX_hill_d1 4 0.1:50
#Set-parm aX_hill_d2 1 0.1:50
#Set-parm aX_iseg_nseg 2 1:100
Set-parm aX_iseg_n 2 11:50
#Set-parm aX_iseg_l 58.30 1:100
#Set-parm aX_iseg_d 0.5 0.2:1.0
#Set-parm aX_prox_nseg 11 1:100
#Set-parm aX_prox_n 3 1:50
#Fit-parm aX_prox_l 150 10:500
#Fit-parm aX_prox_d 0.5 0.2:1.0
#Set-parm aX_prox_l 150 10:500
#Set-parm aX_prox_d 0.5 0.2:1.0
#Set-parm aX_inode_n 2 1:50
#Set-parm aX_inode_d 0.4 0.1:2
#Set-parm aX_inode_l 1 0.1:5
#Set-parm aX_mnode_nseg 3 1:100
#Set-parm aX_mnode_n 3 1:100
#Set-parm aX_mnode_d 0.4 1:100
#Set-parm aX_mnode_l 100 1:1000
#Set-parm aX_cm 1.0 0:3
#Set-parm aX_Rm 40 1:100
#Set-parm aX_Ra 100 1:500
#Set-parm aXm_cm 0.04 0:1
#Set-parm aXm_Rm 100 1:500
#--------------------------------------------------------------------------------------
Fit-parm Gbar_Naf 50 10:300
Set-parm s0_Gbar_Naf 500 80:1000
Set-parm aXh_Gbar_Naf 500 100:7000
Set-parm aXi0_Gbar_Naf 2500 100:8500
Set-parm aXi1_Gbar_Naf 3500 100:8000
Set-parm aXr_Gbar_Naf 3000 1000:5000
Set-parm aXm_Gbar_Naf 50 10:100
Set-parm gates_n_Naf_i0 1 1:3
Set-parm vhalf_n_Naf_i0 -30 -45:-25
Set-parm slope_n_Naf_i0 -4.8 -10:-3
Set-parm tauA_n_Naf_i0 0.01 0.0001:0.01
Set-parm tauG_n_Naf_i0 0.8 0.03:0.97
Set-parm vhalf_h_Naf_i0 -64 -68:-48
Set-parm slope_h_Naf_i0 9.06 5:15
Set-parm tauA_h_Naf_i0 8 5:50
Set-parm tauG_h_Naf_i0 0.5 0.2:0.8
Set-parm gates_n_Naf_i1 1 1:3
Set-parm vhalf_n_Naf_i1 -35 -58:-35
Set-parm slope_n_Naf_i1 -5 -10:-3
Set-parm tauA_n_Naf_i1 0.01 0.0001:0.01
Set-parm tauG_n_Naf_i1 0.5 0.03:0.97
Set-parm vhalf_h_Naf_i1 -67 -68:-55
Set-parm slope_h_Naf_i1 9 3:15
Set-parm tauA_h_Naf_i1 8 5:50
Set_parm tauG_h_Naf_i1 0.5 0.2:0.8
#---------------------------------------------------------------------------------
Fit-parm Gbar_KDR 28 10:1000
Set-parm s0_Gbar_KDR 200 80:7000
Set-parm aXh_Gbar_KDR 200 100:7000
Set-parm aXi0_Gbar_KDR 1500 100:7000
Set-parm aXi1_Gbar_KDR 2000 100:7000
Set-parm aXm_Gbar_KDR 5 0.1:100
Set-parm aXr_Gbar_KDR 800 10:1000
Set-parm Gbar_KDR_dslope 0 0:0.008
Set-parm gates_n_KDR_i1 1 1:4
Set-parm vhalf_n_KDR_i1 2 -19:10
Set-parm slope_n_KDR_i1 -13 -15:-6
Set-parm tauA_n_KDR_i1 8 1:50
Set-parm tauG_n_KDR_i1 0.9 0.03:0.97
#---------------------------------------------------------------------------------
Fit-parm Gbar_KA 2 1:100
Set-parm vhalf_n_KA_i1 -30 -35:5
Set-parm slope_n_KA_i1 -10 -40:-5
Set-parm tauA_n_KA_i1 1 0.1:30
Set-parm vhalfD_h_KA_i1 -35 -60:-20
Set-parm slope_h_KA_i1 10 3:20
Set-parm tauA_h_KA_i1 20 31:150
Set-parm Gbar_KA_dslope 0.008 0.0001:0.03
#---------------------------------------------------------------------------------
Fit-parm Gbar_h 0.1058 0.01:4
Set-parm Gbar_h_dslope 0.008 0.0001:0.03
Set-parm gates_n_h_i0 1 1:3
Set-parm vhalf_n_h_i0 -92.07 -110:-70
Set-parm slope_n_h_i0 10 4:12
Set-parm tauA_n_h_i0 100 10:100
Set-parm tau0_n_h_i0 0.001 0.001:0.1
Set-parm tauF_n_h_i0 0 -3.5:2
Set-parm tauG_n_h_i0 0.5 0.05:0.95
Set-parm tauDv_n_h_i0 0 -55:55