/* o
Created by BluePyOpt(1.6.56) at 2019-04-05 10:20:15.351108
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has different value %f != %f", $s1, $2, $3)
execerror(error)
}
}
proc check_simulator() {
check_parameter("celsius", 34, celsius)
check_parameter("v_init", -70, v_init)
}
begintemplate CA1_PC_ljp
public init, morphology, geom_nseg_fixed, geom_nsec, gid
public channel_seed, channel_seed_set
public soma, dend, apic, axon, myelin
create soma[1], dend[1], apic[1], axon[1], myelin[1]
objref this, CellRef, segCounts
public all, somatic, apical, axonal, basal, myelinated, APC
objref all, somatic, apical, axonal, basal, myelinated, APC
proc init(/* args: morphology_dir, morphology_name */) {
all = new SectionList()
apical = new SectionList()
axonal = new SectionList()
basal = new SectionList()
somatic = new SectionList()
myelinated = new SectionList()
//gid in this case is only used for rng seeding
gid = 0
//For compatibility with BBP CCells
CellRef = this
forall delete_section()
if(numarg() >= 2) {
load_morphology($s1, $s2)
} else {
load_morphology("morph", "JPM041619B.swc")
}
geom_nseg()
replace_axon()
insertChannel()
biophys()
// Initialize channel_seed_set to avoid accidents
channel_seed_set = 0
// Initialize random number generators
re_init_rng()
}
proc load_morphology(/* morphology_dir, morphology_name */) {localobj morph, import, sf, extension
strdef morph_path
sprint(morph_path, "%s/%s", $s1, $s2)
sf = new StringFunctions()
extension = new String()
sscanf(morph_path, "%s", extension.s)
sf.right(extension.s, sf.len(extension.s)-4)
if( strcmp(extension.s, ".asc") == 0 ) {
morph = new Import3d_Neurolucida3()
} else if( strcmp(extension.s, ".swc" ) == 0) {
morph = new Import3d_SWC_read()
} else {
printf("Unsupported file format: Morphology file has to end with .asc or .swc" )
quit()
}
morph.quiet = 1
morph.input(morph_path)
import = new Import3d_GUI(morph, 0)
import.instantiate(this)
}
/*
* Assignment of mechanism values based on distance from the soma
* Matches the BluePyOpt method
*/
proc distribute_distance(){local x localobj sl
strdef stmp, distfunc, mech
sl = $o1
mech = $s2
distfunc = $s3
this.soma[0] distance(0, 0.5)
sprint(distfunc, "%%s %s(%%f) = %s", mech, distfunc)
forsec sl for(x, 0) {
sprint(stmp, distfunc, secname(), x, distance(x))
execute(stmp)
}
}
proc geom_nseg() {
this.geom_nsec() //To count all sections
//TODO: geom_nseg_fixed depends on segCounts which is calculated by
// geom_nsec. Can this be collapsed?
this.geom_nseg_fixed(40)
this.geom_nsec() //To count all sections
}
proc insertChannel() {
forsec this.all {
insert pas
insert kdr
insert nax
}
forsec this.apical {
insert kad
insert hd
insert can
insert cal
insert cat
insert kca
insert cagk
insert cacum
}
forsec this.axonal {
insert kmb
insert kap
}
forsec this.basal {
insert kad
insert hd
insert can
insert cal
insert cat
insert kca
insert cagk
insert cacum
}
forsec this.somatic {
insert kmb
insert kap
insert hd
insert can
insert cal
insert cat
insert kca
insert cagk
insert cacum
}
forsec this.myelinated {
}
}
proc biophys() {
forsec CellRef.all {
cm = 1
ena = 50
ek = -90
}
forsec CellRef.apical {
gkdrbar_kdr = 0.0055270993957421688
gcalbar_cal = 3.1575509224141886e-06
gcanbar_can = 8.3243837821670623e-07
gcatbar_cat = 1.6449327082216909e-06
gbar_kca = 3.210675468305099e-05
gbar_cagk = 0.00030669706151496492
gbar_nax = 0.073919051500270616
Ra = 327.27384393007276
g_pas = 8.5556158557126456e-06
}
forsec CellRef.axonal {
gbar_nax = 0.39994130911723047
gkdrbar_kdr = 0.0050266760254191207
gbar_kmb = 0.031801163682107718
gkabar_kap = 0.14579312041061812
Ra = 52.091059973471488
g_pas = 7.3095048653079982e-05
e_pas = -73.404743913496077
}
forsec CellRef.basal {
gkdrbar_kdr = 0.0055270993957421688
gcalbar_cal = 3.1575509224141886e-06
gcanbar_can = 8.3243837821670623e-07
gcatbar_cat = 1.6449327082216909e-06
gbar_kca = 3.210675468305099e-05
gbar_cagk = 0.00030669706151496492
gbar_nax = 0.010561406939749714
Ra = 322.51189157163469
g_pas = 3.6087588075606985e-05
}
forsec CellRef.somatic {
gkabar_kap = 0.097892971983605623
gbar_nax = 0.060826138425220819
gbar_kmb = 0.00054492051103007899
Ra = 296.24675046819135
g_pas = 3.3512379991579063e-05
gkdrbar_kdr = 0.0055270993957421688
gcalbar_cal = 3.1575509224141886e-06
gcanbar_can = 8.3243837821670623e-07
gcatbar_cat = 1.6449327082216909e-06
gbar_kca = 3.210675468305099e-05
gbar_cagk = 0.00030669706151496492
}
forsec CellRef.myelinated {
}
distribute_distance(CellRef.apical, "ghdbar_hd", "(1. + 3./100. * %.17g)*1.2343729426691662e-05")
distribute_distance(CellRef.apical, "e_pas", "(-76.462472592243714-5*%.17g/150)")
distribute_distance(CellRef.apical, "gkabar_kad", "(15./(1. + exp((200-%.17g)/50)))*0.00078221813902690034")
distribute_distance(CellRef.basal, "ghdbar_hd", "(1. + 3./100. * %.17g)*1.2343729426691662e-05")
distribute_distance(CellRef.basal, "e_pas", "(-83.861413584364811-5*%.17g/150)")
distribute_distance(CellRef.basal, "gkabar_kad", "(15./(1. + exp((200-%.17g)/50)))*0.00078221813902690034")
distribute_distance(CellRef.somatic, "e_pas", "(-84.349790366244605-5*%.17g/150)")
distribute_distance(CellRef.somatic, "ghdbar_hd", "(1. + 3./100. * %.17g)*1.2343729426691662e-05")
}
func sec_count(/* SectionList */) { local nSec
nSec = 0
forsec $o1 {
nSec += 1
}
return nSec
}
/*
* Iterate over the section and compute how many segments should be allocate to
* each.
*/
proc geom_nseg_fixed(/* chunkSize */) { local secIndex, chunkSize
chunkSize = $1
soma area(.5) // make sure diam reflects 3d points
secIndex = 0
forsec all {
nseg = 1 + 2*int(L/chunkSize)
segCounts.x[secIndex] = nseg
secIndex += 1
}
}
/*
* Count up the number of sections
*/
proc geom_nsec() { local nSec
nSecAll = sec_count(all)
nSecSoma = sec_count(somatic)
nSecApical = sec_count(apical)
nSecBasal = sec_count(basal)
nSecMyelinated = sec_count(myelinated)
nSecAxonalOrig = nSecAxonal = sec_count(axonal)
segCounts = new Vector()
segCounts.resize(nSecAll)
nSec = 0
forsec all {
segCounts.x[nSec] = nseg
nSec += 1
}
}
/*
* Replace the axon built from the original morphology file with a stub axon
*/
proc replace_axon(){local nSec, L_chunk, dist, i1, i2, count, L_target, chunkSize, L_real localobj diams, lens
L_target = 60 // length of stub axon
nseg0 = 5 // number of segments for each of the two axon sections
nseg_total = nseg0 * 2
chunkSize = L_target/nseg_total
nSec = 0
forsec axonal{nSec = nSec + 1}
// Try to grab info from original axon
if(nSec < 1){ //At least two axon sections have to be present!
execerror("Less than two axon sections are present! Add an axon to the morphology and try again!")
} else {
diams = new Vector()
lens = new Vector()
access axon[0]
i1 = v(0.0001) // used when serializing sections prior to sim start
access axon[1]
i2 = v(0.0001) // used when serializing sections prior to sim start
count = 0
forsec axonal{ // loop through all axon sections
nseg = 1 + int(L/chunkSize/2.)*2 //nseg to get diameter
for (x) {
if (x > 0 && x < 1) {
count = count + 1
diams.resize(count)
diams.x[count-1] = diam(x)
lens.resize(count)
lens.x[count-1] = L/nseg
if( count == nseg_total ){
break
}
}
}
if( count == nseg_total ){
break
}
}
// get rid of the old axon
forsec axonal{delete_section()}
execute1("create axon[2]", CellRef)
L_real = 0
count = 0
// new axon dependant on old diameters
for i=0,1{
access axon[i]
L = L_target/2
nseg = nseg_total/2
for (x) {
if (x > 0 && x < 1) {
diam(x) = diams.x[count]
L_real = L_real+lens.x[count]
count = count + 1
}
}
all.append()
axonal.append()
if (i == 0) {
v(0.0001) = i1
} else {
v(0.0001) = i2
}
}
nSecAxonal = 2
soma[0] connect axon[0](0), 1
axon[0] connect axon[1](0), 1
print "Target stub axon length:", L_target, "um, equivalent length: ", L_real "um"
}
}
func hash_str() {localobj sf strdef right
sf = new StringFunctions()
right = $s1
n_of_c = sf.len(right)
hash = 0
char_int = 0
for i = 0, n_of_c - 1 {
sscanf(right, "%c", & char_int)
hash = (hash * 31 + char_int) % (2 ^ 31 - 1)
sf.right(right, 1)
}
return hash
}
proc re_init_rng() {localobj sf
strdef full_str, name
sf = new StringFunctions()
if(numarg() == 1) {
// We received a third seed
channel_seed = $1
channel_seed_set = 1
} else {
channel_seed_set = 0
}
}
endtemplate CA1_PC_ljp
