Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018)

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" ... In this work, we develop and apply an automated, stepwise method for fitting a neuron model to data with fine spatial resolution, such as that achievable with voltage sensitive dyes (VSDs) and Ca2+ imaging. ... We apply our method to simulated data from layer 5 pyramidal cells (L5PCs) and construct a model with reduced neuronal morphology. We connect the reduced-morphology neurons into a network and validate against simulated data from a high-resolution L5PC network model. ..."
1 . Hay E, Hill S, Schürmann F, Markram H, Segev I (2011) Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PLoS Comput Biol 7:e1002107 [PubMed]
2 . Hay E, Segev I (2015) Dendritic Excitability and Gain Control in Recurrent Cortical Microcircuits. Cereb Cortex 25:3561-71 [PubMed]
3 . Mäki-Marttunen T, Halnes G, Devor A, Metzner C, Dale AM, Andreassen OA, Einevoll GT (2018) A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells. J Neurosci Methods 293:264-283 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions:
Simulation Environment: NEURON; NEURON (web link to model); Python; NeuroML;
Model Concept(s):
Implementer(s): Maki-Marttunen, Tuomo [tuomo.maki-marttunen at]; Metzner, Christoph [c.metzner at];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I M; I h; I K,Ca; I Calcium; I A, slow;
Ca_HVA.mod *
Ca_LVAst.mod *
CaDynamics_E2.mod *
Ih.mod *
Im.mod *
K_Pst.mod *
K_Tst.mod *
Nap_Et2.mod *
NaTa_t.mod *
ProbUDFsyn2.mod *
SK_E2.mod *
SKv3_1.mod *
pars_withmids_combfs_final.sav *
TITLE AMPA and NMDA receptor with presynaptic short-term plasticity 

AMPA and NMDA receptor conductance using a dual-exponential profile
presynaptic short-term plasticity based on Fuhrmann et al. 2002
Implemented by Srikanth Ramaswamy, Blue Brain Project, July 2009
Etay: changed weight to be equal for NMDA and AMPA, gmax accessible in Neuron
Tuomo: Changed the data structure so that each instance of this synapse corresponds
       to a group of synapses. The previous activation time and variables Pv and u
       are saved for each "sub-synapse" in this synapse group. Added function
       setVec() which saves the pointer to these data.



        POINT_PROCESS ProbUDFsyn2group  
        RANGE tau_r, tau_d, Nsyns
        RANGE Use, u, Dep, Fac, u0
        RANGE i, g, e, gmax


        tau_r = 0.2   (ms)  : dual-exponential conductance profile
        tau_d = 1.7    (ms)  : IMPORTANT: tau_r < tau_d
        Use = 1.0   (1)   : Utilization of synaptic efficacy (just initial values! Use, Dep and Fac are overwritten by BlueBuilder assigned values) 
        Dep = 100   (ms)  : relaxation time constant from depression
        Fac = 10   (ms)  :  relaxation time constant from facilitation
        e = 0     (mV)  : AMPA and NMDA reversal potential
    	gmax = .001 (uS) : weight conversion factor (from nS to uS)
    	u0 = 0 :initial value of u, which is the running value of Use
        Nsyns = 10 : How many synapses are there actually

The Verbatim block is needed to generate random nos. from a uniform distribution between 0 and 1 
for comparison with Pr to decide whether to activate the synapse or not


double nrn_random_pick(void* r);
void* nrn_random_arg(int argpos);

extern int ifarg(int iarg);
extern int vector_capacity(void* vv);
extern void* vector_arg(int iarg);



        v (mV)
        i (nA)
	g (uS)
        space       : A pointer to the vector containing the synapse times. Note that the underlying vector should not be touched after initialization by setVec().

        A       : state variable to construct the dual-exponential profile - decays with conductance tau_r_AMPA
        B       : state variable to construct the dual-exponential profile - decays with conductance tau_d_AMPA


  LOCAL tp
	A = 0
  B = 0
	tp = (tau_r*tau_d)/(tau_d-tau_r)*log(tau_d/tau_r) :time to peak of the conductance
	factor = -exp(-tp/tau_r)+exp(-tp/tau_d) : Normalization factor - so that when t = tp, gsyn = gpeak
        factor = 1/factor


        SOLVE state METHOD cnexp
        g = gmax*(B-A) :compute time varying conductance as the difference of state variables B and A
        i = g*(v-e) :compute the driving force based on the time varying conductance, membrane potential, and reversal


        A' = -A/tau_r
        B' = -B/tau_d

NET_RECEIVE (weight, Pv, Pr, u, myInd, tsyn (ms)){

        :Randomize which of the synapses is activated. Note that an additional random number is generated by rand() - this may interfere with the random number order in parallel simulations.
          void** vv = (void**)(&space);
          double *x;
          int nx = vector_instance_px(*vv, &x);
          int myInd = rand()%((int)Nsyns);
          _args[4] = myInd;
          _args[5] = x[myInd];                //tsyn
          _args[1] = x[myInd+(int)Nsyns];     //Pv
          _args[3] = x[myInd+2*((int)Nsyns)]; //u
        ::printf("NET_RECEIVE_beg: Pv = %g, Pr = %g, u = %g, myInd = %g, tsyn = %g, t = %g\n", Pv, Pr, u, myInd, tsyn, t)
        :printf("NET_RECEIVE_beg:  myInd = %g/%g, Pv = %g, u = %g, tsyn = %g, t = %g. ", myInd, Nsyns, Pv, u, tsyn, t)

        : calc u at event-
        if (Fac > 0) {
          u = u*exp(-(t - tsyn)/Fac) :update facilitation variable if Fac>0 Eq. 2 in Fuhrmann et al.
        } else {
          u = Use  
        if(Fac > 0){
          u = u + Use*(1-u) :update facilitation variable if Fac>0 Eq. 2 in Fuhrmann et al.

        Pv  = 1 - (1-Pv) * exp(-(t-tsyn)/Dep) :Probability Pv for a vesicle to be available for release, analogous to the pool of synaptic
                                              :resources available for release in the deterministic model. Eq. 3 in Fuhrmann et al.
        Pr  = u * Pv                          :Pr is calculated as Pv * u (running value of Use)
        Pv  = Pv - u * Pv                     :update Pv as per Eq. 3 in Fuhrmann et al.
        :printf("Pv = %g\n", Pv)
        :printf("Pr = %g\n", Pr)
        tsyn = t
	if (erand() < Pr){
          A = A + weight*factor
          B = B + weight*factor
          ::printf ( "Released! value = %g, Pr = %g\n" , erand(), Pr )
          :printf ( "R! Pr = %g\n" , Pr )
        } else {
          ::printf("Not released! value = %g, Pr = %g\n", erand(), Pr )
          :printf ( "NR! Pr = %g\n" , Pr )
          x[myInd] = t;
          x[myInd+(int)Nsyns] = _args[1];
          x[myInd+2*((int)Nsyns)] = _args[3];

         * This function takes a NEURON Random object declared in hoc and makes it usable by this mod file.
         * Note that this method is taken from Brett paper as used by netstim.hoc and netstim.mod
         * which points out that the Random must be in negexp(1) mode
        void** pv = (void**)(&_p_rng);
        if( ifarg(1)) {
            *pv = nrn_random_arg(1);
        } else {
            *pv = (void*)0;

FUNCTION erand() {
	    //FILE *fi;
        double value;
        if (_p_rng) {
                :Supports separate independent but reproducible streams for
                : each instance. However, the corresponding hoc Random
                : distribution MUST be set to Random.negexp(1)
                value = nrn_random_pick(_p_rng);
		        //fi = fopen("RandomStreamMCellRan4.txt", "w");
                //fprintf(fi,"random stream for this simulation = %lf\n",value);
                //printf("random stream for this simulation = %lf\n",value);
                return value;
                : the old standby. Cannot use if reproducible parallel sim
                : independent of nhost or which host this instance is on
                : is desired, since each instance on this cpu draws from
                : the same stream
                erand = exprand(1)
        :erand = value :This line must have been a mistake in Hay et al.'s code, it would basically set the return value to a non-initialized double value.
                       :The reason it sometimes works could be that the memory allocated for the non-initialized happened to contain the random value
                       :previously generated. However, here we commented this line out.

PROCEDURE setVec() {    : Sets the times of firing of each synapse. This should be done only once for each ProbAMPANMDA2group,
                        : before the running of the simulation, and the underlying vector should be untouched after that.
  void** vv;
  vv = (void**)(&space);
  *vv = (void*)0;
  if (ifarg(1)) {
    *vv = vector_arg(1);
    Nsyns = vector_capacity(*vv)/3;

PROCEDURE printVec() { : Prints the previous times of firing of each synapse.
    void** vv = (void**)(&space);
    double *x;
    int nx = vector_instance_px(*vv, &x);
    int i1;
    for (i1=0;i1<Nsyns;i1++) {
      printf("tsyns[%i] = %g, Pv[%i] = %g, u[%i] = %g\n", i1, x[i1], i1, x[i1+(nx/3)], i1, x[i1+2*(nx/3)]);

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