Ca1 pyramidal neuron: reduction model (Marasco et al. 2012)

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Accession:146376
"... Here we introduce a new, automatic and fast method to map realistic neurons into equivalent reduced models running up to >40 times faster while maintaining a very high accuracy of the membrane potential dynamics during synaptic inputs, and a direct link with experimental observables. The mapping of arbitrary sets of synaptic inputs, without additional fine tuning, would also allow the convenient and efficient implementation of a new generation of large-scale simulations of brain regions reproducing the biological variability observed in real neurons, with unprecedented advances to understand higher brain functions."
Reference:
1 . Marasco A, Limongiello A, Migliore M (2012) Fast and accurate low-dimensional reduction of biophysically detailed neuron models. Sci Rep 2:928 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Dendrite;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell;
Channel(s): I Na,t; I A; I K; I h;
Gap Junctions:
Receptor(s): AMPA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Simplified Models; Detailed Neuronal Models;
Implementer(s): Limongiello, Alessandro [alessandro.limongiello at unina.it];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; AMPA; I Na,t; I A; I K; I h;
/
reduction1.0
MaxStim_Output
morphologies
Readme.html
distr.mod *
h.mod *
kadist.mod *
kaprox.mod *
kdrca1.mod *
na3n.mod *
naxn.mod *
clusterisingMethods.hoc
fixnseg.hoc *
MaxStimPROCEDURE1.0.hoc
mergingMethods.hoc
mosinit.hoc
ranstream.hoc *
REDUCTION1.0.hoc
screenshot.png
SoftReduction1.0.doc
stimulation1.hoc
useful&InitProc.hoc
                            
/*---------------------------------------------------------------------

   Written by Alessandro Limongiello
   University "Federico II" of Naples, 2012

-----------------------------------------------------------------------*/



load_file("nrngui.hoc")

/*---------------------------------------------
                   USEFUL DATA
  ---------------------------------------------*/
  
create soma[1]  
create eqSection[1]  
                                                       	
xopen("fixnseg.hoc")            

Vrest = -65
Ra0 = 150                       //Ohm*cm
RaAx = 50
g_pas0 = 1/28000                //Siemens/cm^2   1/30000
cm0 = 1
freq=50
freqEq=3
factRm = 1
factCm = 1
factRa = 1
celsius = 34
maxStim = 160
maxStimOnOff = 1

xopen("useful&InitProc.hoc") 
xopen("stimulation1.hoc") 


//////   Spike counter//////////

objref apcOr,apcEq

proc insert_APCor() {
    apcOr = new APCount(0.5)
    apcOr.thresh = -10
}
proc insert_APCeq() {
    apcEq = new APCount(0.5)
    apcEq.thresh = -10
}

/*---------------------------------------------
                      MAIN
  ---------------------------------------------*/


synNum = 160
synType = 0
noise0 = 1    
positionSeed = 7638401// 7638401 for geoc70863; 2762668  for geocd1152
poissonSeed = 5273491//5273491 for geoc70863; 1907324  for geocd1152


optFactGmaxSyn = 0
iMorph = 2
optPrint = 0
optPrint1 = 0
optPrint2 = 0
tgraph = 180


objref vbox3

vbox3 = new VBox()    
vbox3.intercept(1)
xpanel("Input Data:")
xbutton("Cell Morphologies","readingFile()")
xvalue("Randomize synapses position","positionSeed",0,"if(firstInit == -1) firstInit = 0")
xvalue("Randomize synapses activation","intervalSynSeed",0,"if(firstInit == -1) firstInit = 0")
xvalue("Randomize synapses weight","gmaxSynSeed",0,"if(firstInit == -1) firstInit = 0")
xvalue("Poisson ON/OFF","noise0",0,"if(firstInit == -1) firstInit = 0")
xvalue("Poisson Seed","poissonSeed",0,"if(firstInit == -1) firstInit = 0")
xvalue("Number of Active Synapses","synNum",0,"if(firstInit == -1) firstInit = 0")
xvalue("MaxStim Value","maxStim",0,"if(firstInit == -1) firstInit = 0")
xvalue("Scaling Procedure ON/OFF","maxStimOnOff",0,"if(firstInit == -1) firstInit = 0")
//xvalue("Full & Reduced Models ON/OFF","optPrint1",0,"if(firstInit == -1) firstInit = 0")
//xvalue("Signal Propagation ON/OFF","optPrint2",0,"if(firstInit == -1) firstInit = 0")
xpanel()
vbox3.intercept(0)
vbox3.map("Input Data", 0, 120, 250, 210)


time0=0
    
objref vbox4

vbox4 = new VBox()    
vbox4.intercept(1)
xpanel("Run Control:")
xbutton("Run the Full & Reduced Models","{init() integrate()}")
xbutton("Run the Full Model","goMorph()")
xbutton("Run the Reduced Model","goEq()")
xbutton("Stop","{stoprun = 1}")
xvalue("tstop","tgraph",0)
xvalue("Simulation Time (sec): ","time0",0)
xvalue("Accuracy: ","accu",0)

xpanel()
vbox4.intercept(0)
vbox4.map("Run Control", 370, 0, 200, 170)    
    
    
firstInit = 1    // 0=file already read but any change in the parameters
                 // 1=first init
                 // -1=file already read and no change in the parameters
                 // 2=file not yet read but any change in the parameters


objref graphCum,graphEq,graphMorph
objref vbox7
        
        
objref pc
pc = new ParallelContext()        
        
proc init(){
    
    t=0
    tstop = tgraph   
    
    while (firstInit==1) {readingFile()} 
    time00 = pc.time()
    AleFunctionalSetting()
    if (optPrint==1) print "FunctionalSetting Time: ", pc.time() - time00


    if (firstInit==0){
        time00 = pc.time()
        cellAnalysis()
        clusteriseAleFunz1()
        reduction()   
    
        {create eqSection[clusterList.count]}
        createEqCell(clusterList,RaMERGINGMETHOD)
        
        if (optPrint==1) print "cellAnalysis+clusteriseAleFunz1+reduction+createEqCell Time: ", pc.time() - time00
        
        printClusterList(clusterList)
        

        objref injCurr, injCurrEq
        time00 = pc.time()
        insertSyn1(synNum,positionSeed,synType,clusterList)
        if (optPrint==1) print "insertSyn1 Time: ", pc.time() - time00
        
        time00 = pc.time()
        changeSurf(clusterList,synNum)
        if (optPrint==1) print "changeSurf Time: ", pc.time() - time00

        firstInit = -1   
    }
    
    time00 = pc.time()
    findSyn(clusterList,optFactGmaxSyn,synNum,synType,iMorph)   
    if (optPrint==1) print "findSyn Time: ", pc.time() - time00
    
    for (i = 0; i < clusterList.count; i = i + 1){print "surfFact",i,": ",surfFact.x(i)}

    time00 = pc.time()
    ind = 1
    forsec "eqSection.*" if (!issection("eqSection[0]")) {g_pas=factRm*surfFactRmCm.x(ind)*g_pas0 cm=factCm*cm0*surfFactRmCm.x(ind) ind=ind+1}
    totEq=0
    forsec "eqSection.*" {
           nseg = int((L/(d_lambda*lambda_f(freqEq))+0.9)/2)*2 + 1 
           totEq=totEq+nseg
    }   
    if (optPrint==1) print "Nseg Time: ", pc.time() - time00

    printf("totSegIni: %d\n", totOr)
    printf("totSegEq: %d\n", totEq)
    printf("_____________________________\n\n")
    
    onfile(clusterList)

    time00 = pc.time()
    canalAllMigliore05()
    initMigliore05() 
    if (optPrint==1) print "canalAllMigliore05+initMigliore05 Time: ", pc.time() - time00 

    vbox7 = new VBox()    
    vbox7.intercept(1)
    graphCum = new Graph()
    graphCum.addvar("soma[0].v(0.5)",2,1)
    graphCum.addvar("eqSection[0].v(0.5)",4,1) 
    graphCum.size(0,tgraph,-70,50)   
    graphEq = new Graph()
    graphEq.addvar("eqSection[0].v(0.5)",4,1) 
    graphEq.size(0,tgraph,-70,50)     
    graphMorph = new Graph()
    graphMorph.addvar("soma[0].v(0.5)",2,1)
    graphMorph.size(0,tgraph,-70,50) 
    vbox7.intercept(0)
    vbox7.map("graphCum", 680, 0,410, 550)     
    
    cumEqMorph = 0
}


objref vecNSpikeOr,vecNSpikeEq,vecISISpikeOr,vecISISpikeEq,vecTTSpikeOr,vecTTSpikeEq


proc integrate() {
    time00 = pc.time()
    //advance()
    
    if (cumEqMorph==0){
                       
        vecNSpikeOr= new Vector()
        vecISISpikeOr= new Vector()
        vecTTSpikeOr= new Vector()
        vecNSpikeEq= new Vector()
        vecISISpikeEq= new Vector()
        vecTTSpikeEq= new Vector()                       
                               
        objref apcOr
        access soma[0]
        insert_APCor() 
        tprecOr=0
        ttOr=0 
        firstSpikeOr = 1  
        
        objref apcEq
        access eqSection[0]
        insert_APCeq() 
        tprecEq=0   
        ttEq=0
        firstSpikeEq = 1        
        
    }  
    
    continuerun(tstop)

    time0 = pc.time()-time00
    print "Time: ",time0
    
    if (cumEqMorph==0){
       accu = accuracy(vecTTSpikeOr,vecTTSpikeEq)
       print "Accuracy: ",accu
    }
}



cumEqMorph = 0  // 0,1,2

proc advance() {

    if(optPrint2) shPlot.flush()
    //if(t==0 && optPrint1) {coloringClusterList(clusterList)}
    
    if (cumEqMorph==0){
        graphCum.plot(t)
        graphCum.flush()
        graphEq.plot(t)
        graphEq.flush()
        graphMorph.plot(t)
        graphMorph.flush()
        
        
        if (apcOr.n==1){tprecOr=apcOr.time if(firstSpikeOr){vecTTSpikeOr.append(tprecOr) firstSpikeOr=0 print "TSpikesOr: ",tprecOr }}                   
        if (apcOr.time>tprecOr && tprecOr!=0){
           //if (apcOr.n==2){vecTTSpikeOr.append(tprecOr)}
           vecTTSpikeOr.append(apcOr.time)
           ttOr = apcOr.time - tprecOr
           vecISISpikeOr.append(ttOr)
           print "TSpikesOr: ",apcOr.time 
           tprecOr=apcOr.time
        }
        
        if (apcEq.n==1){tprecEq=apcEq.time if(firstSpikeEq){vecTTSpikeEq.append(tprecEq) firstSpikeEq=0 print "TSpikesEq: ",tprecEq }}                        
        if (apcEq.time>tprecEq && tprecEq!=0){
           //if (apcEq.n==2){vecTTSpikeEq.append(tprecEq)}
           vecTTSpikeEq.append(apcEq.time)
           ttEq = apcEq.time - tprecEq
           vecISISpikeEq.append(ttEq)
           print "TSpikesEq: ",apcEq.time 
           tprecEq=apcEq.time
        }
               
    } else if (cumEqMorph==1){
        graphEq.plot(t)
        graphEq.flush()
    } else if (cumEqMorph==2){
        graphMorph.plot(t)
        graphMorph.flush()
    }
    
    
    	
    fadvance()  
}


objectvar StimEqListAppp,Exp2SynEqListAppp,NetConEqListAppp

proc go(){
     
     init()          

     objectvar Exp2SynList,NetConList,StimList//,StimEqList,Exp2SynEqList,NetConEqList
     objref synApp,netConApp//stimApp,stimEqApp,synEqApp,netConEqApp

     forall if (!issection("eqSection.*")){
         uninsert pas uninsert na3 uninsert kdr uninsert nax uninsert kap uninsert hd uninsert kad uninsert ds
         delete_section()
     }
     
    vbox7 = new VBox()    
    vbox7.intercept(1)
    graphEq = new Graph()
    graphEq.addvar("eqSection[0].v(0.5)",4,1) 
    graphEq.size(0,tgraph,-70,50)      
    vbox7.intercept(0)
    vbox7.map("graphEq",680,340,410,170)  
  
    cumEqMorph = 1
    //finitialize(Vrest)
    integrate()
    
         
     init()          

     objectvar StimEqList,Exp2SynEqList,NetConEqList
     objref stimEqApp,synEqApp,netConEqApp

     forall if (issection("eqSection.*")){
         uninsert pas uninsert na3 uninsert kdr uninsert nax uninsert kap uninsert hd uninsert kad uninsert ds
         delete_section()
     }
    
    vbox7 = new VBox()    
    vbox7.intercept(1)
    graphMorph = new Graph()
    graphMorph.addvar("soma[0].v(0.5)",2,1)
    graphMorph.size(0,tgraph,-70,50)    
    vbox7.intercept(0)
    vbox7.map("graphMorph",680,510,410,170)      
    
    cumEqMorph = 2   
    integrate()

}

proc goMorph(){
     
     init()          

     objectvar StimEqList,Exp2SynEqList,NetConEqList
     objref stimEqApp,synEqApp,netConEqApp

     forall if (issection("eqSection.*")){
         uninsert pas uninsert na3 uninsert kdr uninsert nax uninsert kap uninsert hd uninsert kad uninsert ds
         delete_section()
     }
    
    vbox7 = new VBox()    
    vbox7.intercept(1)
    graphMorph = new Graph()
    graphMorph.addvar("soma[0].v(0.5)",2,1)
    graphMorph.size(0,tgraph,-70,50)    
    vbox7.intercept(0)
    vbox7.map("graphMorph",680,510,410,170)      
    
    cumEqMorph = 2   
    integrate()

}

proc goEq(){
     
     init()          

     objectvar Exp2SynList,NetConList,StimList//,StimEqList,Exp2SynEqList,NetConEqList
     objref synApp,netConApp//stimApp,stimEqApp,synEqApp,netConEqApp

     forall if (!issection("eqSection.*")){
         uninsert pas uninsert na3 uninsert kdr uninsert nax uninsert kap uninsert hd uninsert kad uninsert ds
         delete_section()
     }
     
    vbox7 = new VBox()    
    vbox7.intercept(1)
    graphEq = new Graph()
    graphEq.addvar("eqSection[0].v(0.5)",4,1) 
    graphEq.size(0,tgraph,-70,50)      
    vbox7.intercept(0)
    vbox7.map("graphEq",680,340,410,170)  
  
    cumEqMorph = 1
    integrate()



}


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