Four-pathway phenomenological synaptic plasticity model (Ebner et al. 2019)

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Accession:251493

Reference:
1 . Ebner C, Clopath C, Jedlicka P, Cuntz H (2019) Unifying Long-Term Plasticity Rules for Excitatory Synapses by Modeling Dendrites of Cortical Pyramidal Neurons. Cell Rep 29:4295-4307.e6 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s): Neocortex V1 L5B pyramidal pyramidal tract GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Synaptic Plasticity; Long-term Synaptic Plasticity; Detailed Neuronal Models; Active Dendrites; Influence of Dendritic Geometry;
Implementer(s): Ebner, Christian [ebner at fias.uni-frankfurt.de];
Search NeuronDB for information about:  Neocortex V1 L5B pyramidal pyramidal tract GLU cell;
// Author: Etay Hay, 2011
//    Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of
//    Dendritic and Perisomatic Active Properties
//    (Hay et al., PLoS Computational Biology, 2011) 
//
// Template for models of L5 Pyramidal Cell

begintemplate L5PCtemplate
  public init
  public locateSites, getLongestBranch
  public soma, dend, apic, axon, getAbsSecIndex
  public all, somatic, apical, axonal, basal, nSecSoma, nSecApical, nSecBasal, nSecAxonal, nSecAll, nSecAxonalOrig, SecSyn, distribute_channels
  objref SecSyn, this
  objref all, somatic, apical, axonal, basal
  strdef tstr

//$s1 - morphology file name
proc init() {localobj nl,import
	all = new SectionList()
	somatic = new SectionList()
	basal = new SectionList()
	apical = new SectionList()
	axonal = new SectionList()
	forall delete_section()

  nl = new Import3d_Neurolucida3()
  nl.quiet = 1
  nl.input($s1)
  import = new Import3d_GUI(nl, 0)
  import.instantiate(this)
  geom_nseg()
  biophys()
	forsec this.all {
		if(diam == 0){
	    diam =  1
	    printf("Error : Morphology problem with section [%s] 0 diam \n", secname())
		}
  }
}

create soma[1], dend[1], apic[1], axon[1]

proc geom() {
}

proc geom_nseg() {local nSec, L1, L2, D1, D2, nSeg1, nSeg2
  soma area(.5) // make sure diam reflects 3d points
  nSec = 0
  forsec all {
    nseg = 1 + 2*int(L/40)
    nSec = nSec + 1
  }

  nSecAll = nSec
  nSec = 0
  forsec somatic { nSec = nSec + 1}
  nSecSoma	= 	nSec
  nSec = 0
  forsec apical { nSec = nSec + 1}
  nSecApical= 	nSec
  nSec = 0
  forsec basal { nSec = nSec + 1}
  nSecBasal	= 	nSec
  nSec = 0
  forsec axonal { nSec = nSec + 1}
  nSecAxonalOrig = nSecAxonal	= 	nSec
}

proc biophys() {localobj bp
	delete_axon()
	area(0.5)
	distance()
	access soma

  bp = new L5PCbiophys()
  bp.biophys(this)
}

// deleting axon, keeping only first 60 micrometers
proc delete_axon(){
    forsec axonal{delete_section()}
    create axon[2]
    access axon[0]{
      L= 30
      diam = 1
      nseg = 1+2*int(L/40)
      all.append()
      axonal.append()
    }
    access axon[1]{
      L= 30
      diam = 1
      nseg = 1+2*int(L/40)
      all.append()
      axonal.append()
    }

  nSecAxonal = 2
  connect axon(0), soma(0.5)
  connect axon[1](0), axon[0](1) 
  access soma
}

proc distribute_channels()	{local dist,val,base,maxLength
	base = $8
	soma distance()
	maxLength = getLongestBranch($s1)

	forsec $s1		{
		if(0==strcmp($s2,"Ra")){
			Ra = $8
		} else {
			for(x) {
				if ($3==3) {
					dist = distance(x)
				} else {
					dist = distance(x)/maxLength
				}
				val = calculate_distribution($3,dist,$4,$5,$6,$7,$8)
				sprint(tstr,"%s(%-5.10f) = %-5.10f",$s2,x,val)
				execute(tstr)
			}
		}
	}
}

// $1 is the distribution type:
//     0 linear, 1 sigmoid, 2 exponential
//     3 step for absolute distance (in microns)
func calculate_distribution()	{local value
	if ($1==0)	{value = $3 + $2*$4}
	if ($1==1) {value = $3 + ($4/(1+exp(($2-$5)/$6)))}
  	if ($1==2) {value = $3 + $6*exp($4*($2-$5))}
	if ($1==3) {
		if (($2 > $5) && ($2 < $6)) {
			value = $3
		} else {
			value = $4
		}
	}
	value = value*$7
	return value
}

// $s1 section
func getLongestBranch(){local maxL,d localobj distallist,sref
    sprint(tstr,"%s distance()",$s1)
    execute(tstr,this)    
    
  	if(0==strcmp($s1,"axon")){
      sprint(tstr,"%s[0] distance(1)",$s1)
      execute(tstr,this)    
  	}

		maxL = 0
		d = 0
		distallist = new SectionList()
		forsec $s1 {
			sref = new SectionRef()
			if (sref.nchild==0) distallist.append()
		}
		forsec distallist{
			d = distance(1)
			if(maxL<d) maxL = d
		}
		// for the soma case
		if (maxL == 0) {
      $s1 {
        maxL = L
      }
    }
		return maxL
	}

// $s1 section
// $2 distance x in micrometers
// return list of [1,2] vectors  - of the appropriate section and the location in each vector
obfunc locateSites() {local maxL,site,d0,d1,siteX,i localobj vv,ll
	ll = new List()

  sprint(tstr,"%s distance()",$s1)
  execute(tstr,this)    
    
	if(0==strcmp($s1,"axon")){
    sprint(tstr,"%s[0] distance(1)",$s1)
    execute(tstr,this)    
	}

	maxL = getLongestBranch($s1)
	site = $2
	i = 0
	forsec $s1 {
    if (distance(0) < distance(1)) {
  		d0 = distance(0)
  		d1 = distance(1)
  	} else {
  		d1 = distance(0)
  		d0 = distance(1)
  	}

    if (site <= d1 && site >= d0) {
      siteX = (site-d0)/(d1-d0)
      secNum = i
      vv = new Vector()
      ll.append(vv.append(secNum,siteX))
		}
		i = i+1
	}
  return ll
}

func getAbsSecIndex(){ local nAbsInd, index  localobj str,strObj
    strObj  =  new StringFunctions()
    str     =  new String()
    nAbsInd = 0
    index   = 0
    if(strObj.substr($s1, "soma") > 0) {
        strObj.tail($s1, "soma", str.s)
        if(sscanf(str.s, "%*c%d", &index) < 0) {
            index = 0
        }
        nAbsInd = index
    }else if (strObj.substr($s1, "axon") >0) {
        strObj.tail($s1, "axon", str.s)
        if(sscanf(str.s, "%*c%d", &index) < 0) {
            index = 0
        }
        nAbsInd = nSecSoma + index
    }else if (strObj.substr($s1, "dend") >0) {
        strObj.tail($s1, "dend", str.s)
        if(sscanf(str.s, "%*c%d", &index) < 0) {
            index = 0
        }
        nAbsInd = nSecSoma + nSecAxonalOrig + index
    }else if (strObj.substr($s1, "apic") > 0) {
        strObj.tail($s1, "apic", str.s)
        if(sscanf(str.s, "%*c%d", &index) < 0) {
            index = 0
        }
        nAbsInd = nSecSoma + nSecAxonalOrig + nSecBasal + index
    }
    return nAbsInd
}


endtemplate L5PCtemplate

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