Drosophila 3rd instar larval aCC motoneuron (Gunay et al. 2015)

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Accession:152028
Single compartmental, ball-and-stick models implemented in XPP and full morphological model in Neuron. Paper has been submitted and correlates anatomical properties with electrophysiological recordings from these hard-to-access neurons. For instance we make predictions about location of the spike initiation zone, channel distributions, and synaptic input parameters.
Reference:
1 . Günay C, Sieling FH, Dharmar L, Lin WH, Wolfram V, Marley R, Baines RA, Prinz AA (2015) Distal spike initiation zone location estimation by morphological simulation of ionic current filtering demonstrated in a novel model of an identified Drosophila motoneuron. PLoS Comput Biol 11:e1004189 [PubMed]
Citations  Citation Browser
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: Drosophila;
Cell Type(s):
Channel(s): I Na,p; I Na,t; I A; I K;
Gap Junctions:
Receptor(s): Cholinergic Receptors;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; XPP; MATLAB;
Model Concept(s):
Implementer(s): Gunay, Cengiz [cgunay at emory.edu]; Sieling, Fred [fred.sieling at gmail.com]; Prinz, Astrid [astrid.prinz at emory.edu];
Search NeuronDB for information about:  Cholinergic Receptors; I Na,p; I Na,t; I A; I K;
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Gunay_etal_2014
neuron-model
aCC-L3-neuron.hoc
aCC-L3-neuron+electrode.xml
aCC-L3-neuron-swc.hoc
calc-impedance.hoc
chan-DmKA-Marley.hoc
chan-DmKdr-Marley.hoc
chan-DmNaP-DmNav10.hoc
chan-DmNaT-ODowd.hoc
collapse-neuron-tree.hoc
current-inj-50pA-read-mV_dt_0.025ms.bin
data-axon-tail2-axon-50um-vc-noKdr-long-back-85mV-Na_4_lines_dt_0.025000ms.bin
data-axon-tail2-axon-70um-vc-noKdr-long-back-85mV-Na_4_lines_dt_0.025000ms.bin
data-axon-tail2-axon-70um-vc-noKdr-long-back-85mV-Na-5xNaP_4_lines_dt_0.025000ms.bin
data-axon-tail2-axon-70um-vc-noKdr-long-back-85mV-Na-5xNaT_4_lines_dt_0.025000ms.bin
data-axon-tail2-axon-70um-vc-noKdr-long-back-85mV-passive_4_lines_dt_0.025000ms.bin
data-axon-tail2-chans-axon_11_lines_dt_0.025000ms.bin
data-axon-tail2-chans-axon-last_11_lines_dt_0.025000ms.bin
data-axon-tail2-chans-botdend_11_lines_dt_0.025000ms.bin
data-axon-tail2-chans-ext-axon-70um_11_lines_dt_0.025000ms.bin
data-axon-tail2-chans-in-all_11_lines_dt_0.025000ms.bin
data-i-syn-10syns-20-EPSCs-10x-10ms-VC-60mV_6_lines_dt_0.025000ms.bin
data-i-syn-4dends-50-EPSCs-10x-10ms-VC-60mV_5_lines_dt_0.025000ms.bin
data-i-vclamp-syn-dend-513-180-EPSCs-10x-1ms-saturating_2_lines_dt_0.025000ms.bin
data-syn-dend-357_2_lines_dt_0.025000ms.bin
data-syn-dend-513_2_lines_dt_0.025000ms.bin
data-syn-dend-520_2_lines_dt_0.025000ms.bin
data-syn-dend-685_2_lines_dt_0.025000ms.bin
data-v-syn-10dends-20-EPSCs-10x-10ms-noVC_6_lines_dt_0.025000ms.bin
data-v-syn-4dends-50-EPSCs-10x-10ms-noVC_6_lines_dt_0.025000ms.bin
data-v-syn-dend-513-180-EPSCs-10x-1ms-saturating-noVC_5_lines_dt_0.025000ms.bin
data-v-syn-dend-685-AP_3_lines_dt_0.025000ms.bin
exp-axon-tail2.ses
exp-axon-tail2-chans-axon.ses
exp-axon-tail2-chans-axon-last.ses
exp-axon-tail2-chans-botdend.ses
exp-axon-tail2-chans-ext-axon-50um-onlyNa.ses
exp-axon-tail2-chans-ext-axon-70um.ses
exp-axon-tail2-chans-ext-axon-70um-10alphasynapses.ses
exp-axon-tail2-chans-ext-axon-70um-10x-mimic-sustained.ses
exp-axon-tail2-chans-ext-axon-70um-10x-mimic-sustained-random.ses
exp-axon-tail2-chans-ext-axon-70um-mimic-synapses.ses
exp-axon-tail2-chans-ext-axon-70um-mimic-synapses-sustained-currents.ses
exp-axon-tail2-chans-ext-axon-70um-mimic-synapses-v-change.ses
exp-axon-tail2-chans-ext-axon-70um-onlyNa.ses
exp-axon-tail2-chans-ext-axon-70um-tomasz.ses
exp-axon-tail2-chans-in-all.ses
figures.m
fitfuncs.hoc
graph-i-vc-ext-axon.ses
iclamp-50pA.ses
IClamp-steps.ses
inc-first.ses
lincir-vclamp.hoc
lincir-vclamp.ses
NaP_NaT_data.csv
neuron-CB.ses
neuron-CB+electrode.hoc
neuron-CB-act-electrode-embed-IClamp.ses
neuron-CB-ext-axon.ses
neuron-CB-ext-axon-2pieces.ses
neuron-CB-ext-axon-2pieces-chans-axon.ses
neuron-CB-ext-axon-2pieces-chans-axon-last.ses
neuron-CB-ext-axon-2pieces-chans-botdend.ses
neuron-CB-ext-axon-2pieces-chans-ext-axon-50um-onlyNa.ses
neuron-CB-ext-axon-2pieces-chans-ext-axon-70um.ses
neuron-CB-ext-axon-2pieces-chans-ext-axon-70um-10alphasynapses.ses *
neuron-CB-ext-axon-2pieces-chans-ext-axon-70um-10x-mimic-sustained.ses *
neuron-CB-ext-axon-2pieces-chans-ext-axon-70um-mimic-synapses.ses *
neuron-CB-ext-axon-2pieces-chans-ext-axon-70um-mimic-synapses-v-change.ses *
neuron-CB-ext-axon-2pieces-chans-ext-axon-70um-onlyNa.ses
neuron-CB-ext-axon-2pieces-chans-in-all.ses
neuron-CB-pas-electrode-embed.ses
neuron-CB-pas-electrode-embed-fit-pas.ses
neuron-CB-pas-electrode-embed-fit-pas-VClamp.ses
neuron-CB-pas-electrode-embed-IClamp.ses
neuron-CB-pas-electrode-embed-test-axon-hh-chans.ses
neuron-Import3D-CellBuilder.ses
neuron-NL-CellBuilder.ses
neuron-NL-CellBuilder-pas.ses
neuron-NL-CellBuilder-pas-electrode.ses
neuron-NL-CellBuilder-pas-Na.ses
neuron-PointProcessMgr-ext-axon-2pieces-chans-ext-axon-70um-10alphasynapses.ses
nrn-fit-cap-02_dt_0.025000ms_dy_1e-9nA.bin
shape-plot.ses
SkeletonTree_ORR_aCC_48h1_NL.hoc
soma-vclamp-testbed.ses
stats.hoc
vclamp_-85_to_-25mV.ses
vclamp_soma_-60mV.ses
vclamp_soma_-60mV_syn1234.ses
vclamp_soma_-60mV_syni.ses
vclamp-family.ses
v-graph.ses
v-graph-bigger.ses
v-graph-bigger-axon-2pieces.ses
                            
// Experiment with 2-component axon extention tail, and only Na channels in SIZ compartments 

// nrngui stuff and ion chans
load_file("inc-first.ses")

strdef file_name, ses_file
file_name = "ext-axon-70um-onlyNa"

sprint(ses_file, "neuron-CB-ext-axon-2pieces-chans-%s.ses", file_name)

//load CellBuilder
{load_file(ses_file)}


{
xpanel("RunControl", 0)
v_init = -60
xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
xbutton("Init & Run","run()")
xbutton("Stop","stoprun=1")
runStopAt = 5
xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 )
runStopIn = 1
xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 )
xbutton("Single Step","steprun()")
t = 200
xvalue("t","t", 2 )
tstop = 110
xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
dt = 0.025
xvalue("dt","dt", 1,"setdt()", 0, 1 )
steps_per_ms = 40
xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 )
screen_update_invl = 0.1
xvalue("Scrn update invl","screen_update_invl", 1,"", 0, 1 )
realtime = 1.12
xvalue("Real Time","realtime", 0,"", 0, 1 )
xpanel(893,777)
}

// load common funcs
load_file("fitfuncs.hoc")

print_elec_cell()

// calc morph stats
load_file("stats.hoc")

load_file("v-graph-bigger-axon-2pieces.ses")

load_file("vclamp_-85_to_-25mV.ses")

load_file("graph-i-vc-ext-axon.ses")

// save state in this file
sprint(state_file_name, "state-neuron-CB+act+elec+ext-axon-2piece-chans-%s.bin", file_name)

// Save voltage from multiple points in the cell
objref axonv[8]
axonv[0] = new Vector()
axonv[1] = new Vector()
axonv[2] = new Vector()
axonv[3] = new Vector()
axonv[4] = new Vector()
axonv[5] = new Vector()
axonv[6] = new Vector()
axonv[7] = new Vector()

// (1) end towards soma, (0) end distal
// axon[13] attaches to soma, axon[0] distal end

// axon[12].nseg=1
// axon[13].nseg=1
// record axon[12].v(0.5) & record axon[13].v(0.5)
// axon[13].ri=25.045413
// axon[12].ri=6.2445732
axon[13] axonv[6].record(&v(0.5))
axon[12] axonv[7].record(&v(0.5))
axonv[6].label("axon[13](0.5)")
axonv[7].label("axon[12](0.5)")

// axon[6] to axon[7] (both have nseg=1)
// axon[7].ri(0.5) = 1.8150921
axon[7] axonv[0].record(&v(0.5))
axon[6] axonv[1].record(&v(0.5))
axonv[0].label("axon[7](0.5)")
axonv[1].label("axon[6](0.5)")

// here we switch
// (0) end towards soma, (1) end distal
// axon_ext[1].nseg=25
// record axon_ext[1].v(0.02) & .v(0.06)
// .ri(0.06) = 98.22134
access axon_ext[1] 
axonv[2].record(&v(0.02))
axonv[3].record(&v(0.06))
axonv[2].label("axon_ext[1](0.02)")
axonv[3].label("axon_ext[1](0.06)")

// axon_ext[0].nseg=5
// record axon_ext[0].v(0.3) & .v(0.5)
// .ri(0.06) = 52.640496
access axon_ext[0] 
axonv[4].record(&v(0.3))
axonv[5].record(&v(0.5))
axonv[4].label("axon_ext[0](0.3)")
axonv[5].label("axon_ext[0](0.5)")


// saves vector into file, uses vector's label for name
// Usage: saveVec(vector, name_append)
// vector: object to write
// name_append: Name to append to file_name
proc saveVec() { strdef savefilename
  objref savefile
  sprint(savefilename, "data-%s_%s_%s_dt_%fms.bin", file_name, $o1.label(), $s2, dt)
  savefile=new File(savefilename)
  savefile.wopen()
  n = $o1.vwrite(savefile)
  if (n == 1) { print "Wrote '", savefilename, "'.\n"
  }
  savefile.close()
}

// run pas and active and save data
// Usage: runSave(name_append)
// name_append: will be appended after "pas"/"act"
proc runSave() { strdef savename
  // start w pas
  axon_ext[1].gmax_DmNaT = 0
  axon_ext[1].gmax_DmNaP = 0

  // run
  run()

  // after running, save the files
  sprint(savename, "pas%s", $s1)
  print axonv.size()
  for i = 0, 7 {
    saveVec(axonv[i], savename)
  }

  // run active & save data
  sprint(savename, "act%s", $s1)
  axon_ext[1].gmax_DmNaT = 0.24 // orig
  //axon_ext[1].gmax_DmNaT = 0.05   
  axon_ext[1].gmax_DmNaP = 0.00011 // orig
  //axon_ext[1].gmax_DmNaP = 0.0003
  run()
  for i = 0, 7 {
    saveVec(axonv[i], savename)
  }
}