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

 Download zip file   Auto-launch 
Help downloading and running models
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.
1 . G√ľnay 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]
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;
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;
function a_cc = XPP2current_clamp(filename, cip_times, cip_vals, props)

% XPP2current_clamp - Converts XPP model data to current-clamp object.
% Usage: 
% a_cc = XPP2current_clamp(filename, cip_times, cip_vals, props)
% Parameters:
%   filename: DAT filename obtained with the XPPAUTO's Graphics->Export
%   	data option.
%   cip_times: Start and end times of current injection [ms].
%   cip_vals: A vector of current injection (CIP) parameter values in the XPPAUTO
%   	simulation [nA]. At least provide a vector with the correct number of
%   	parameter values so the data file can be parsed. If there is only
%   	one trace, provide its applied current level as a scalar.
%   props: A structure with any optional properties.
%     Ihold: [nA] Specifies holding current if different than first step value.
%     dt: Simulation time step of recorded data [s]. Use dt*nout of XPP (Default=1e-3).
%     paramsVary: Structure with variable name associated with an
%     		array. If only one value is given cip_vals, use the
%     		values for this variable for the multiple trials found in file.
%     (others are passed to current_clamp)
% Returns:
%   a_cc: A current_clamp object.
% Description:
% See also: plotXPPparamRanges, current_clamp
% $Id: XPP2current_clamp.m 1188 2010-04-09 19:56:27Z cengiz $
% Author: Cengiz Gunay <cgunay@emory.edu>, 2011/03/04

% Copyright (c) 2011 Cengiz Gunay <cengique@users.sf.net>.
% This work is licensed under the Academic Free License ("AFL")
% v. 3.0. To view a copy of this license, please look at the COPYING
% file distributed with this software or visit
% http://opensource.org/licenses/afl-3.0.php.

% TODO: make this use trace+trace2cc. see example under
% flymotor/paper_full_model/figures_full_morph.m
% advertise this as XPP file loading cap

props = defaultValue('props', struct);

s = load(filename);

% if not varying CIP, take variable values from struct
if isfield(props, 'paramsVary')
  param_names = fieldnames(props.paramsVary);
  num_vals = 1;
  for param_num = 1:length(param_names)
    param_vals = props.paramsVary.(param_names{param_num});
    num_vals = num_vals * length(param_vals);
  cip_vals = repmat(cip_vals, 1, num_vals);

num_traces = length(cip_vals);
num_allpts = size(s, 1);
num_onepts = num_allpts / num_traces;
data = reshape(s(:, 2), num_onepts, num_traces);

I_hold = getFieldDefault(props, 'Ihold', cip_vals(1));

time = s(1:num_onepts, 1);
dt = getFieldDefault(props, 'dt', diff(time(1:2)) * 1e-3);

current_steps = ...
    get(makeIdealClampV([cip_times num_onepts * dt * 1e3], I_hold, cip_vals, I_hold, dt * 1e3, ...
                        filename), 'data');

a_cc = ...
    current_clamp(current_steps, data, dt, 1e-9, 1e-3, ...
                  filename, ...
                  mergeStructs(props, struct('lowPassFreq', 1000, ...
                                             'filename', filename)));

Loading data, please wait...