sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
9206b43ef8aad1ddfbdb1b290dcc3b7853233a9b967099f6d5eacdc6b56368ee | MATLAB | 48,098 | 1,196 | %% FIXCHANLOCS_TAPPING_MS
%
% Channel order correction for the MS tapping EEG dataset (FieldTrip format).
%
% Background:
% In a subset of participants, a cabling error between the EEG cap and
% the amplifier resulted in an incorrect order of channels at acquisition.
% For these subjects, the data rows (channels)... |
dd1e081480e2af954f84d74e11c62d133181f27fae9fb2dfaa3265a14ecd7fe7 | MATLAB | 48,368 | 1,377 | function [d,si,h]=abfload(fn,varargin)
% ** function [d,si,h]=abfload(fn,varargin)
% loads and returns data in ABF (Axon Binary File) format.
% Data may have been acquired in the following modes:
% (1) event-driven variable-length (currently only abf versions < 2.0)
% (2) event-driven fixed-length or waveform-fixed len... |
0292df90b65ca1b5ef5cde7eb8ce1619dad058ba87be03ec578658f60f560589 | MATLAB | 51,492 | 752 | function [config] = pnh_setparams
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% [config] = pnh_setparams
%
% This function outputs all the settings of a study, to be defined below
%
% Note the consideration of the operating system, because the pointers to
% the file server is dealt with... |
32ab00d66d0e1a760fbfa40eedcadcc2e35ab2c4f4bd06d2585da16b31cbcfc4 | MATLAB | 51,750 | 1,894 | function [R FGA BGA] = ibblender(M,I,modestring,amount,quiet,verbose,rec,FGA,BGA)
% this is the blending section of IMBLEND
% this is not intended to work independently
% i only split this because editing a 3000+ line file is a pita
switch modestring
% CONTRAST MODES
case 'overlay'
% for amount==1, this is a st... |
c2509bb808b9b4cd25ec90cbfa9ebf0e5a44312499d4c3db14441128b86c0867 | MATLAB | 51,898 | 1,224 | %% Analysis script for Spike x Sleep x SUA project
%
% (c) Stephen Whitmarsh, stephen.whitmarsh@gmail.com
%
set(0, 'DefaultFigurePosition', [2500 100 1000 1000]);
set(0, 'DefaultFigurePosition', [200 300 1000 500]);
addpath /network/lustre/iss02/charpier/analyses/stephen.whitmarsh/EpiCode/projects/hspike/
addpath \... |
0d69386858fd6305fced21f5f65be97adcef370094227b94f72fd6b92f8e9f6c | MATLAB | 51,923 | 760 | function [config] = pnh_setparams_new
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% [config] = pnh_setparams
%
% This function outputs all the settings of a study, to be defined below
%
% Note the consideration of the operating system, because the pointers to
% the file server is dealt ... |
11180cab8dcaa5c696c119b598ed33474623a02336ea1dcd71b3889d79e67c12 | MATLAB | 52,317 | 1,574 | function [data, orig_scl_slope, orig_scl_inter, orig_datatype] = load_untouch_nii_gz(file, scl_flag, workdir)
% Wrapper around load_untouch_nii_hdr to work with .gz files. workdir, when specified, is the
% temporary directory to be used for unzipping. When workdir is not specified then a
% random-temporary folder is us... |
9eecba8b503a18368ec38bdae852215839a6f13ce8c1c8e49d77f151aa741bec | MATLAB | 52,580 | 1,148 | classdef activityMap
% activityMap: Class for calculating and storing dF/F activity for 5D movies
% Calculate an activity map for a 5-dimensional ScanImage movie where time is
% the last dimension (order of dimensions x y z c t)
%
% Example usage:
% map = activityMap(params);
% figure, ima... |
a3db13b02ed82d225ff080546e0461fabb7e67137085b3c0836f4228293c57fc | MATLAB | 57,391 | 1,281 | classdef FigMaker
properties
ColorListGem (:,3) double
ColorList13 (:,3) double
end
methods
function obj = FigMaker()
obj.ColorListGem = orderedcolors("gem");
load("colorList13.mat")
obj.ColorList13 = colorList13;
end
end
metho... |
e099a6c7e0abcf98a63d80a9efda07678646548bb9c66767f65369ee9e6a11e2 | MATLAB | 57,736 | 1,271 | %% MOVIESLIDER Embeddable panel for playback, scrolling, and contrast/color map adjustment of 3D movies.
%
% This software depends on the GUI Layout Toolbox:
% http://www.mathworks.com/matlabcentral/fileexchange/47982-gui-layout-toolbox
% Make sure to get the version appropriate for your version of Matlab (R2014b... |
89be65249005faf17d51e9dc16ea3fea1c47585865b2925fd5f0b8b8b5cbb176 | MATLAB | 57,983 | 1,536 | classdef IniConfig < handle
%IniConfig - The class for working with configurations of settings and INI-files.
% This class allows you to create configurations of settings, and to manage them.
% The structure of the storage settings is similar to the structure of
% the storage the settings in the INI-... |
d4ffa9afc3cecb93c451380290fa8d4a249987019cb7cb1bfd6a62cbb6c30d70 | MATLAB | 58,137 | 1,859 | function imcompose(varargin)
% IMCOMPOSE(OPTIONS)
% Opens a simple gui for interactive composition of images from a stack of image layers
% much like common image manipulation applications e.g. GIMP. This was originally
% made to allow use of IMBLEND's features to recompose layer stacks exported fr... |
f0c3a132ba99ef7d3f2bc65cb289c1f22488434526ead3b58815456436e85371 | MATLAB | 58,308 | 1,164 | function Figure_psth
restoredefaultpath
if isunix
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/git/fieldtrip
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/projects/hspike/
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/shared/
... |
bac5d56b7e7bdd65933c273ea07d15e831a90c74a635d160c0384a7e83ea3c3d | MATLAB | 58,708 | 1,530 | %% grating_disc_2Choice_vGitHub.m
function varargout = grating_disc_2Choice_vGitHub(varargin)
% GRATING_DISC_2CHOICE_VGITHUB MATLAB code for grating_disc_2Choice_vGitHub.fig
% GRATING_DISC_2CHOICE_VGITHUB, by itself, creates a new GRATING_DISC_2CHOICE_VGITHUB or raises the existing
% singleton*.
%
% H =... |
d0197c7f75efb0595abb5ad6d0c1c16c4c683f74e5661e25d14087922f512882 | MATLAB | 59,333 | 975 | %% SarginFP_SimBA.m
%
% Fiber Photometry Analysis
%
% It is recommended that users read through the documentation in full
% prior to using this analysis. This applies to each section in the code
%
% All outputs are accessed through the structure element "FP" in the
% MATLAB workspa... |
62fefcb81d245acaaf5541a7b058afe72a8ad190ebe53cb51d9b4d818e123de1 | MATLAB | 60,039 | 998 | function outpict = imblend(FG,BG,opacity,blendmode,varargin)
% IMBLEND(FG, BG, OPACITY, BLENDMODE,{AMOUNT},{COMPMODE},{CAMOUNT},{OPTIONS})
% Blend and composite images or imagesets as one would blend layers in GIMP, Krita,
% or Photoshop. Blending and compositing options are independently configurable.
... |
6e819081bec8d9de517c33aac8ec65a0a23e583da7426dc2bf2dfb476f2f55d7 | MATLAB | 60,105 | 1,322 | %% Analysis script for Valerio Frazzini's study on electrophysiology of pathoanatomy
%
% (c) Stephen Whitmarsh, stephen.whitmarsh@gmail.com
%
% requires bandpassFilter.m from Mario
% requires releaseDec2015 from Neuralynx website
restoredefaultpath
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/scri... |
dbf57fafcef4563de4cd685f42908b6a0f6f20ab62c896130a8e3f962c03ace8 | MATLAB | 60,661 | 1,332 | %% Analysis script for Valerio Frazzini's study on electrophysiology of pathoanatomy
%
% (c) Stephen Whitmarsh, stephen.whitmarsh@gmail.com
%
% requires bandpassFilter.m from Mario
% requires releaseDec2015 from Neuralynx website
%% Add path
restoredefaultpath
if isunix
addpath /network/lustre/iss01/charpier/ana... |
59d8fcf6ddc6bb78f917815b71f9866019ea6c5cc95630a4318c0f5131d15d53 | MATLAB | 61,561 | 926 | function [config] = hspike_setparams(varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% [config] = hspike_setparams(varargin)
%
% This function outputs all the settings of a study, to be defined below
%
% Note the consideration of the operating system, because the pointers to
% the... |
532ba093f68db1a08db9454027da889fa4f7f3f44b4ddaca56e3d4c93dcbbdc9 | MATLAB | 66,638 | 1,163 | %% SarginFP_SimBA.m
%
% Fiber Photometry Analysis
%
% It is recommended that users read through the documentation in full
% prior to using this analysis. This applies to each section in the code
%
% All outputs are accessed through the structure element "FP" in the
% MATLAB workspa... |
5d7b21c3c6dbd3fbd019098ec75fc7af3da491938e5dc8a5bc4eaa0224bb5b81 | MATLAB | 66,641 | 1,163 | %% SarginFP_SimBA.m
%
% Fiber Photometry Analysis
%
% It is recommended that users read through the documentation in full
% prior to using this analysis. This applies to each section in the code
%
% All outputs are accessed through the structure element "FP" in the
% MATLAB workspa... |
9474566472f3227342632036dabf62ee4faf3db5191cb6f838fe78f314d5f1b9 | MATLAB | 67,566 | 1,286 | function plotGrandAverageAll(cfg)
set(groot,'defaultAxesTickLabelInterpreter','none');
hyplabels = ["REM", "AWAKE", "PHASE_1", "PHASE_2", "PHASE_3"];
fname_out = fullfile(cfg{1}.datasavedir, 'GrandAverage.mat');
% organize all dat_unit_windowa in single struct array
iunit = 1;
dat_unit_window ... |
5fdcc32bdc6549803843d65b160a638b7e7afd5f129d4b431ac396459917c07b | MATLAB | 67,803 | 1,198 | function p = pathdef
%PATHDEF Search path defaults.
% PATHDEF returns a string that can be used as input to MATLABPATH
% in order to set the path.
% Copyright 1984-2016 The MathWorks, Inc.
% DO NOT MODIFY THIS FILE. IT IS AN AUTOGENERATED FILE.
% EDITING MAY CAUSE THE FILE TO BECOME UNREADABLE TO
% THE ... |
8f43e7468cbaf9aa6159c324d3fb0b78404cd99385e8eee676c3050f93014f7a | MATLAB | 68,082 | 1,869 | %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright (c) 2026 Medical University of Vienna
% All rights resereved. This program and the accompanying materials are licensed under CC BY 4.0.
% To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/
%
... |
d0bc6a8632e9bfdea678678455786d3900e2016d4c005644c3e47d3e09606bc4 | MATLAB | 68,416 | 1,649 | function data = TDTbin2mat(BLOCK_PATH, varargin)
%TDTBIN2MAT TDT tank data extraction.
% data = TDTbin2mat(BLOCK_PATH), where BLOCK_PATH is a string, retrieves
% all data from specified block directory in struct format. This reads
% the binary tank data and requires no Windows-based software.
%
% data.epocs ... |
711149dec40811956b1a51368859f6df690cb5f3822274ef8d704dc259181c1b | MATLAB | 68,495 | 172 | function parts = hyphenate(word)
% Franklin Liang's word hyphenation algorithm (used by Knuth for TeX/LaTeX).
%
% (c) 2017-2020 Stephen Cobeldick
%
%%% Syntax:
% parts = hyphenate(word)
%
% HYPHENATE provides a function to hyphenate words. HYPHENATE takes the
% word and returns a cell array of parts that can be separat... |
983f02c274cd53248e50e79f1c4851cbf2bf35bc53f2cfd126657924154708e7 | MATLAB | 69,449 | 47 | function thisLUT = fetchLUT(whichlut)
% return a LUT for custom imblend mesh modes
% nothing uses this except imblend
switch whichlut
case 'overlay'
% overlay [0 1 2 3 4]
thisLUT = cat(3,repmat(0:1/19:1,[20 1]), ...
[0,0,0,0,0,0,0,0,0,0,0.0526315789473686,0.157894736842105,0.263157894736842,0.36842105263... |
490b0f2990d853687ad81b8f5cd61ab97d7ec4842aafc7590af227ada2b60c74 | MATLAB | 69,562 | 1,305 | %% this code replicates the results for the main compensatory models in Fig 5
% it calculates the performances scroes, Lifetime sparsity and their
% dimensionality.
% it also does the tuning and calculates the performance
%for the alternative rules in the supplementary materials:
% the alternative models for tuning inp... |
695a561fbe3369663807bab95882925922e8a9f8b558f3faac2e7a339179036a | MATLAB | 72,031 | 1,356 | clear; close all;
%load old data
%load('both_monk_ppc_EM.mat');
%align_where = 'Target_500:1150ms'; align_where2 = '-at2 [500 1150ms]'; freq = 1.5; low_freq = 5:33; high_freq =47:66;
%align_where = 'GoCue_-800:0ms'; align_where2 = 'GoCue [-800 0ms]'; freq = 1.25; low_freq = 4:41; high_freq = 58:81; beta_freq = 18:25;... |
ad742fdefbfa830c95aded4cae251887c5835b294522a087c5f105eaf0dd495d | MATLAB | 72,360 | 1,456 | classdef skeleton
% skeleton: Class for defining and analysing skeletons of 3D objects
% This class allows you to take a mask of an object (eg the mushroom
% body), manually define a skeleton by clicking on a montage of the
% mask, and define a "starting point" (eg where stimulation was locally
% ap... |
ee7f6a79e14301f4611192ba74accb6dbe536e6a3de83bab9cc4856db278b449 | MATLAB | 84,886 | 2,706 | function varargout = immodify(inpict,varargin)
% OUTPICT=IMMODIFY(INPICT, {OPTIONS})
% IMMODIFY(INPICT, {OPTIONS})
% Modify images interactively via a simple graphical interface
%
% Color adjustment (RGB, HSL, LCHab, etc)
% Levels & curves adjustment
% Blur
% Flip
% Tone map... |
74d42a9febcabce0e3bb077eec53f0103f3ad0bf1ca18d98373ec53480e1b075 | MATLAB | 90,827 | 2,144 | %% Based on code created by David J. Barker for Morales Laboratory
% Beta Release 7-6-2018; Contact djamesbarker@gmail.com
% Modified by Carissa A. Bruno for the Barker Lab at Rutgers University
% 09-06-2019.
%Updated By David J. Barker on 08-19-20 for bug fixes, to include external
%import of CSV files, and to finaliz... |
cb6700ffd2082ed3a123b58b13fa9db49e1d4b1c317241ecca861bbbedf120b1 | MATLAB | 98,357 | 3,130 | % DEMOS USED IN WEB DOCUMENTATION
% most of these blocks are the same as what's in the html overview
% some of these may be configured for viewing on an inverted display
% if something looks inverted, just check the call to imshow() or imshow2()
% as i am likely the most common user of these files, i tend to leave the... |
61b8d94ee5f2ad39b91cbb18128ca061a7b6c2dc7cd7aa11644e1c66f5454469 | MATLAB | 101,066 | 1,359 | function [config] = preictal_setparams
disp('setting parameters');
if ismac
error('Platform not supported')
elseif isunix
rootpath_analysis = '/network/lustre/iss02/charpier/analyses/vn_preictal';
rootpath_data = '/network/lustre/iss02/epimicro/patients/raw';
os = 'unix';
else... |
4705c290a2af192a1f4b18e9051bfe5fd2462a8594289dcc95488478bf37086e | MATLAB | 120,742 | 2,877 | function results = kbstat(options)
%% Perform statistical analysis based on a generalized linear mixed model.
% The result is a model fit summary, diagnostic plots, a data bar plot, a descriptive statistics
% table, an ANOVA table, and a posthoc pairwise comparison table for selected variables. For more
% information s... |
0107016b656ea65e11bdded71a21a7f740f064005023d822f44249664e9045a9 | MATLAB | 127,210 | 1,975 | function Online_Corr_Publication
%% Settings.
[A_filt,B_filt]=butter(2,30/500,'low'); % filter
data=1; % main data set - Must be set to 1 unless using lme output exclusively
lme_data=0; % makes the lme data set for individual muscles (subject, muscle, mean EVR, RT, condition parameters); EVR is response v... |
f9a7242dad88471ab154f25d5c8da7620ac916ef4e50cf92819b1ac49f0f6a97 | MATLAB | 151,917 | 1,335 | %-----------------------------------------------------------------------
% Job saved on 05-Apr-2019 23:17:00 by cfg_util (rev $Rev: 6460 $)
% spm SPM - SPM12 (6906)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%%
% please ignore the folder directories and fil... |
6bd01e7a968c3fafc868bb953d3801eb1c81a636292a70e14d8f837159d5fed4 | NEURON | 334 | 13 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
begintemplate O1d
public o
objref o[1]
proc init() {
objref o[$1]
}
en... |
28b352f32de0ec486734a82e3594830f34dfe8f846a668efd92cfcdb3e344292 | NEURON | 377 | 34 | : This is a leak channel for potassium
NEURON {
SUFFIX extrapump
USEION k WRITE ik
RANGE pumpik, pumpina
USEION na WRITE ina
}
UNITS {
(S) = (siemens)
(mV) = (millivolts)
(mA) = (milliamp)
}
PARAMETER {
pumpik =0 (mA/cm2)
pumpina =0 (mA/cm2)
}
ASSIGNED {
ik (mA/cm2)
ina (mA/cm... |
da93f21f13522eef276b9b441040d31bcafffba0fb03b15809e6dc90dc09c52b | NEURON | 588 | 46 | TITLE leak
NEURON {
SUFFIX leak
USEION k READ ek WRITE ik
USEION na READ ena WRITE ina
RANGE gkleak, gnaleak, gk, qna, ik, ina
}
UNITS {
(mV) = (millivolt) (mA) = (milliamp)
(um) = (micron)
PI = (pi) (1)
FARADAY = 96485.309 (coul)
}
PARAMETER {
: gkleak = 1e-5 (mho/cm2)
: gnaleak = 1e-5 (mho/cm2)
gkleak ... |
258d01e7f42b5c47ae80126f24a9436501c817ec1d1f705f2316b27db0d91a23 | NEURON | 702 | 50 | : Sodium-dependent potassium current
: Paramaters according to Wang et al. 2003 (based on Bischoff et al. 1998)
NEURON {
SUFFIX kna
USEION na READ nai
USEION k READ ek WRITE ik
RANGE gbar, ik
}
UNITS {
(molar) = (1/liter) : moles do not appear in units
(mM) = (millimolar)
(mA)... |
7d9e73f8b0edca5d7cd2057a9f75d52327797aa9365c45ae9a94b9e6013bb96a | NEURON | 762 | 28 | : Author: David Catherall
: Created: November 2016
: Extracellular potassium ion accumulation
: Upon further inspection, this doesn't appear in Schild 1994. Saving for furture use if needed.
NEURON {
SUFFIX naext
USEION na READ ina WRITE nao
GLOBAL nabath
RANGE fhspace, txfer
}
UNITS {
(mV) = (millivolt)
... |
7fa9918526144f9e35632c260ca7759e105715f08dc96f6f06614ffcebe4060f | NEURON | 795 | 54 |
COMMENT
Kexternal - Based on Frankenhauser and Hodgkin, 1956; Kushmerick and Podolsky, 1969
ENDCOMMENT
NEURON {
SUFFIX kextern
RANGE wid, txfer, kinitial
USEION k READ ik WRITE ko
USEION na READ ina WRITE nao
}
UNITS {
(mM) = (milli/liter)
(um) = (micron)
FARADAY = (faraday) (coulomb)
(mola... |
adc1cbdb2d110c43937630524a9091dc9f87310b2c4a762e5901d2094c97d7c2 | NEURON | 811 | 29 | : Author: David Catherall
: Created: November 2016
: Extracellular potassium ion accumulation
: Adapted from Hines and Carnevale 2000: Guide to NMODL
: Upon further inspection, this doesn't appear in Schild 1994. Saving for furture use if needed.
NEURON {
SUFFIX kext
USEION k READ ik WRITE ko
GLOBAL kbath
RANGE... |
04c0defe2bd21bde6c16a298f230c5b85127ae002fcebe63dbd994a02769319f | NEURON | 816 | 34 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Nikki Pelot
Date created: February 14, 2016
Description:
- S... |
ec45309a23fd1be5a13b7cbcf67fa4edc401e0c0da6474a8f0332f2d4bd9654d | NEURON | 828 | 55 |
COMMENT
Longitudinal diffusion and integration of sodium (no buffering)
(equivalent modified euler with standard method and
equivalent to diagonalized linear solver with CVODE )
From Canavier et al. 1999
ENDCOMMENT
NEURON {
SUFFIX nadifl
USEION na READ ina WRITE nai
USEION k READ ik WRITE ki
RANGE D
}
U... |
07a0c59af72cfb06e37d56a0e18a9a38b16df4813defc1347c9268cf44db3e5e | NEURON | 830 | 29 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
objref s[1]
create node[1]
objref fiber
proc CreateAxon_CFiber() {
... |
a579563ea9a454441b745c539cff247c410fd7c52f5c50a0b8dfaf3bb484b239 | NEURON | 836 | 34 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Eric Musselman
Date created: June 10, 2016
Description:
- Sa... |
c42ae674b6c656330704bc3c211cede16aff2d09078367b1b7975e8333fb35aa | NEURON | 874 | 34 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Daniel Marshall
Date created: May 26, 2022
Description:
- Sa... |
8f0e5307987fe490eba440788440992a19eef6fc10675b0becb6bed0e606562c | NEURON | 902 | 67 | :sheets 2007
NEURON {
SUFFIX kdrTiger
USEION k READ ek WRITE ik
RANGE gbar, ena, ik,ek, celsiusT
}
UNITS {
(S) = (siemens)
(mV) = (millivolts)
(mA) = (milliamp)
}
PARAMETER {
gbar (S/cm2)
celsiusT
kvot_qt
k1=15.4 (mV)
Vh=35 (mV)
}
ASSIGNED {
v (mV) : NEURON provides this
... |
621d8268050c38cdc1c955674c4fe109bf374666b41dc557f9af6d9c98fe1c93 | NEURON | 912 | 54 | TITLE K ion dynamics with pointer
COMMENT
#-*-#
### k_ion_dynamics - koi
------------------------
Mechanism for controlling K ion concentrations. This mechanism reads Ik and writes to the ki and ko ion pools.
#-*-#
ENDCOMMENT
NEURON {
SUFFIX koi
USEION k READ ik WRITE ki, ko
RANGE kiinf, koinf
}
UNITS {
... |
45e2fb5225f67edf99f4db8cbf42a5a65f0da8d2dffe560e8a20f7d21ac08ee1 | NEURON | 932 | 55 | TITLE na ion dynamics
COMMENT
#-*-#
### na_ion_dynamics - naoi
------------------------------
Mechanism for controlling Na ion concentrations. This mechanism reads Ina and writes to the nao and nai ion pools.
#-*-#
ENDCOMMENT
NEURON {
SUFFIX naoi
USEION na READ ina WRITE nai, nao
RANGE naiinf, naoinf
}
... |
71fae8b57e820be9c967beaa5d91f28b7d22e491bb0f1c2a5019feb45a3b60e1 | NEURON | 943 | 37 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Eric Musselman
Date created: May 3, 2022
Description:
- save... |
0f664d84ddcd9ca8a7ea41335efea344cafc9109ed39bcc09624a52b75db8e95 | NEURON | 995 | 32 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Daniel Marshall
Date created: June 2, 2023
Description:
- sa... |
fca243470b8f36a89b25f1828a4092ae85f88c8bf9d61a1a8d9243f0f8a3bfa7 | NEURON | 1,008 | 38 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Nikki Pelot
Date created: January 29, 2016
Description:
- Sp... |
a65d9d0fa68e0194b4633669f27b48a512bd0e5f217b6024887e4cbf9b22e706 | NEURON | 1,012 | 58 | :Current Clamp
NEURON {
POINT_PROCESS trainIClamp
RANGE del, PW, train, amp, freq, i, conv, pulsecount, onoff
ELECTRODE_CURRENT i
}
UNITS { (na) = (nanoamp) }
PARAMETER{
del (ms)
PW (ms)
train (ms)
amp (na)
freq (1/s)
conv = 1000 (ms/s)
pulsecount (s/s)
onoff (s/s)
}
ASSIG... |
4db5f1fccc4d318df542dc27e6f2201a0215655ed16c9a6ae9fc0c782f60b83f | NEURON | 1,018 | 70 |
TITLE PUMP
: Sodium potassium pump -- Canavier, 1999
:
UNITS {
(molar) = (1/liter)
(pA) = (picoamp)
(mV) = (millivolt)
(uS) = (micromho)
(mA) = (milliamp)
(mM) = (millimolar)
}
INDEPENDENT {v FROM -100 TO 50 WITH 50 (mV)}
NEURON {
SUFFIX pump
USEION na READ nai WRITE ina
USEION k WRITE... |
feda678599b588499c5e776b04672c848a6749928267b736584f082fd133cd64 | NEURON | 1,181 | 73 |
: SK model based on Aradi and Holmes 1999
:
:
NEURON {
SUFFIX SK
USEION ca READ ica
USEION k READ ek WRITE ik
RANGE gskbar, cal, gsk, sstau, cascale
GLOBAL ca0, stau
}
UNITS {
(molar) = (1/liter)
(mM) = (millimolar)
(mV) = (millivolt)
(mA) = (milliamp)
(S) = (siemens)
}
PARAMETER {
gskbar = .01 (S/cm2) ... |
af5259431847b101731abe80fd628b2e4405abdd7e0109919797766f54fef9c8 | NEURON | 1,202 | 51 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Nikki Pelot
Date created: February 4, 2016
Description:
- Ge... |
49222ac1a405389487f7b9aa70f3f57d3a2338671403a1de5f7b1ff313332dc9 | NEURON | 1,237 | 51 | NEURON {
SUFFIX caextscale_nonnode
USEION ca READ cao, ica WRITE cao
GLOBAL cabath
RANGE fhspace, txfer, Vol_peri, L, nseg, SA, Volratio, lseg, A_peri :Allows variables to be modified in hoc and collected in vectors
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
FARADAY = 96485 (coulombs)
:FARADA... |
05610a8c8d9ed0aca044e29f66459ec8751ef59e26fa9f29893c01fbd75a3968 | NEURON | 1,253 | 45 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Nikki Pelot
Date created: January 28, 2016
Description:
- Lo... |
6224fc9fbc7ca66a682a1263a45cb5cf2deea4f0b371f160e95b877c016fcd03 | NEURON | 1,277 | 53 | NEURON {
SUFFIX kld_nonnode
USEION k READ ko, ik WRITE ko
GLOBAL kbath
RANGE fhspace, txfer, Vol_peri, L, nseg, SA, Volratio, lseg, A_peri :Allows variables to be modified in hoc and collected in vectors
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
FARADAY = 96485 (coulombs)
:FARADAY = (faraday... |
72cbb08a7f93e71bf51827540708fbecb6c14958d051719961cc689d0cc6b1f2 | NEURON | 1,287 | 52 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Nikki Pelot
Date created: March 11, 2016
Description:
- Gene... |
d7c3ffc49a34d5ab7f23d05cb3e28647b6193cd50ff5d2f5218bb513636b48fb | NEURON | 1,289 | 52 | NEURON {
SUFFIX nald_nonnode
USEION na READ nao, ina WRITE nao
GLOBAL nabath
RANGE fhspace, txfer, Vol_peri, L, nseg, SA, Volratio, lseg, A_peri :Allows variables to be modified in hoc and collected in vectors
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
FARADAY = 96485 (coulombs)
:FARADAY = (f... |
abe98d52b8e21f77c2649cfccec9316a57ec0f746017d67d23ca0f218f1dbbb0 | NEURON | 1,291 | 52 | NEURON {
SUFFIX caextscale_node
USEION ca READ cao, ica WRITE cao
GLOBAL cabath
RANGE fhspace, txfer, Vol_peri, L, nseg, SA, Volratio, lseg, A_peri :Allows variables to be modified in hoc and collected in vectors
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
FARADAY = 96485 (coulombs)
:FARADAY =... |
cf725b2b3d377b67d1e942459264457f28047bdcdc3ae47180238f5fa1eab9b4 | NEURON | 1,296 | 76 | TITLE slowly activating potassium current (M-current)
COMMENT
*********************************************
reference: Yamada, Koch & Adams (1989)
Methods in Neuronal Modeling, MIT press
found in: bullfrog sympathetic ganglion cells
******************************************... |
ab1e594da171af99ab666910249591f06f32a4a2025e81c6a81cf67dd5266fe7 | NEURON | 1,311 | 87 | TITLE l-calcium channel
: l-type calcium channel - Milgiore et al. 1995
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
F = (faraday) (coulomb)
R = (k-mole) (joule/degC)
TEMP = 25 (degC)
}
PARAMETER {
v (mV)
celsius (degC)
gcalbar=.003 (mho/cm2)
ki=.001 (mM)
ca0 = .00007 (mM) : initial calcium concentratio... |
3d57e9aecade4c4cbb793cb54ab2160d6f3ff43c4a1ae00969bc1cb7cb763f19 | NEURON | 1,340 | 54 | NEURON {
SUFFIX kld_node
USEION k READ ko, ik WRITE ko
GLOBAL kbath
RANGE fhspace, txfer, Vol_peri, L, nseg, SA, Volratio, lseg, A_peri :Allows variables to be modified in hoc and collected in vectors
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
FARADAY = 96485 (coulombs)
:FARADAY = (faraday) (... |
8fc38c02c251a9af91dd2f52f5353df2602a63e86e0b0c10659f9eb83e8ef30f | NEURON | 1,344 | 54 | NEURON {
SUFFIX nald_node
USEION na READ nao, ina WRITE nao
GLOBAL nabath
RANGE fhspace, txfer, Vol_peri, L, nseg, SA, Volratio, lseg, A_peri :Allows variables to be modified in hoc and collected in vectors
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
FARADAY = 96485 (coulombs)
:FARADAY = (fara... |
db44d2d943ffb22606bd8e0656f8d531e7295be5b3801efd868846d89cad48c7 | NEURON | 1,344 | 60 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
#-*-#
# balannce.hoc
----------------
This scipt contains a function that b... |
03d80c345efe8323be7df0261af763c655ef46b8bb7bd5519f265e2bc2489483 | NEURON | 1,418 | 92 | TITLE nahh
: From Traub & Miles "Neuronal networks of the hippocampus" (1991)
: Cummins et al. (2007), Sheets et al. (2007)
NEURON {
SUFFIX nahh
USEION na READ ena WRITE ina
RANGE gnabar, m, h, ishift, mshift, hshift
GLOBAL inf,tau
}
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
}
PARAMETER {
v (mV)
celsius ... |
06f413d2671577449ae4b9bc6e5de8de47c41d842e8d3d712eebc38574b8b84a | NEURON | 1,447 | 81 | : This channels is implemented by Jenny Tigerholm.
:The steady state curves are collected from Winkelman 2005
:The time constat is from Gold 1996 and Safron 1996
: To plot this model run KA_Winkelman.m
NEURON {
SUFFIX kf
USEION k READ ek WRITE ik
RANGE gbar, ek, ik
RANGE tau_m, minf, hinf,tau_h,m,h, celsiusT
}
UN... |
e35033892cfe98c6a0a199f40644f0b35bcf1243501756de4c6dfe8f0b5a12f6 | NEURON | 1,462 | 55 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Eric Musselman
Date created: August 10, 2021
Description:
- ... |
0b6fd4ed06f40755deba5b6a9880a2a2baf221268a59e0372bcc53705b068dff | NEURON | 1,473 | 53 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
/*
Author: Nikki Pelot
Date created: January 28, 2016
Description:
- Lo... |
3415991e92ace03fa23ef8cfc212e637ef6209e87ac3dc40546abd1c106df418 | NEURON | 1,478 | 84 | : Chapman JB, Johnson EA, Kootsey JM. (1983)
: Electrical and Biochemical Properties of an Enzyme Model of the Sodium Pump
: J. Membrane Biol. 74, 139-153
: note default step 5 voltage dependence
: extended by Michael Hines as a component of larger models.
: I.e. modifies nai, ki, contributes to ina, ik, and consumes... |
e16e872a1864ee4f713ae3acc855d26f33aa5a1e7d07330f40068e3c1391197d | NEURON | 1,482 | 83 | TITLE hh.mod squid sodium, potassium, and leak channels
COMMENT
ENDCOMMENT
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(S) = (siemens)
}
? interface
NEURON {
SUFFIX NaV7
USEION na READ ena WRITE ina
RANGE gnabar, gna, ina
RANGE minf, hinf, htau, mtau
THREADSAFE :... |
26edd3bbd95f5b6554e683847b2d1c5780a08466a6b6e0f26d7024595dfbbfd6 | NEURON | 1,487 | 76 | : This is mainly the 7.3 channel.
: It is an inactivation potassium current
: The inactivation long time constant is based on the article Passmore 2003.
: The steady state inactivation and short time constant is from Maingret 2008 (which is based on Passmore 2003)
: To plot the model run kv73_passmore_delmas.m
NEURON ... |
437766a6538c3002844c759d7719d2ba3b83e77e37de318756c69fe0fda97b55 | NEURON | 1,530 | 91 | TITLE Borg-Graham type generic K-DR channel
: Borg-Graham 1987
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
}
PARAMETER {
v (mV)
ek (mV)
celsius (degC)
gkdrbar=.003 (mho/cm2)
vhalfn=-32 (mV)
vhalfl=-61 (mV)
a0l=0.001 (/ms)
a0n=0.03 (/ms)
zetan=-5 ... |
16cc1ff494fb7bfd193cd8ee5833ea549fcd5dd78f6363dfc9a80d6dfd24488d | NEURON | 1,573 | 45 | : Author: David Catherall
: Created: November 2016
: Extracellular calcium ion accumulation
: Neuron Block creates mechanism
NEURON {
SUFFIX caexttest :Sets suffix of mechanism for insertion into models
USEION ca READ ica WRITE cao :Lays out which NEURON variables will be used/modified by file
GLOBAL c... |
78d1d6659dcc451074630e2c24c7093a3a3a73a9d1821823b0e5391af5b9a134 | NEURON | 1,603 | 57 | : Author: David Catherall
: Created: November 2016
: leak is the background Na and Ca current in Schild 1994
: Neuron Block creates mechanism
NEURON {
SUFFIX leakSchild :Sets suffix of mechanism for insertion into models
USEION na READ ena WRITE ina :Lays out which NEURON variables will be used/modified by file... |
1f906735b75d207d70e99ca9898fe0acad0c3d39ebfdf1ce5cceb2f2c1636bac | NEURON | 1,618 | 80 | : This channels is implemented by Jenny Tigerholm.
:The steady state curves are collected from Winkelman 2005
:The time constat is from Gold 1996 and Safron 1996
: To plot this model run KA_Winkelman.m
: Adopted and altered by Nathan Titus
NEURON {
SUFFIX ka34
USEION k READ ek WRITE ik
RANGE gbar, ek, ik
RANGE tau... |
84147c009d2ab2e26e2dff94e35a182be35ab696094705e7e3062cec94754a32 | NEURON | 1,629 | 86 | : This channels is implemented by Jenny Tigerholm.
:The steady state curves are collected from Winkelman 2005
:The time constat is from Gold 1996 and Safron 1996
: To plot this model run KA_Winkelman.m
: Adopted and altered by Nathan Titus
NEURON {
SUFFIX NaV9
USEION na READ ena WRITE ina
RANGE gbar, ena, ina
RANG... |
e620ca2f831e2ff604e4f4c424da785fbeb3143b9142dd75008b33c6cb47bd6e | NEURON | 1,709 | 57 | : Author: David Catherall
: Created: November 2016
:CaPump is the Calcium Pump in Schild 1994
: Adapted from Leo Medina's implementation from Lindblad et al Am J Physiol 1996 275:H1666
: Neuron Block creates mechanism
NEURON {
SUFFIX CaPump :Sets suffix of mechanism for insertion into models
USEION ca READ ... |
10d64d22ad407661f7be906142c5c1840cc2c9c81ef4f3bb715564b9b9aaa393 | NEURON | 1,771 | 84 | : This channels is implemented by Jenny Tigerholm.
:The steady state curves are collected from Winkelman 2005
:The time constat is from Gold 1996 and Safron 1996
: To plot this model run KA_Winkelman.m
: Adopted and altered by Nathan Titus
NEURON {
SUFFIX ka14
USEION k READ ek WRITE ik
RANGE gbar, ek, ik
RANGE tau... |
f0138284ca4fb21716fbe0c263a857bf26bbfe429191ec845793f25a662e5c80 | NEURON | 1,889 | 68 | /*
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent
*/
begintemplate GeometryBuilder
public nodelength, MYSAlength, FLUTlength,... |
a10e442333e8148069c3c0352d485c937a6eb16cd114fff85f9d8530d508bcc0 | NEURON | 1,927 | 107 | : The m and h are form sheets 2007
:s and u are form Delmas
: run NaV18_delmas.m to plot the model
NEURON {
SUFFIX nav1p8
USEION na READ ena WRITE ina
RANGE gbar, ena, ina
}
UNITS {
(S) = (siemens)
(mV) = (millivolts)
(mA) = (milliamp)
}
PARAMETER {
gbar = 0 (S/cm2) : =220e-9/(100e-12*1e8) (S/cm2) : 220(nS)... |
54701284663b00c541d42190ea8bda4dc49edfaa52666a876fa831c3374994a8 | NEURON | 2,014 | 55 | : Author: David Catherall
: Created: November 2016
: Extracellular calcium ion accumulation
: Neuron Block creates mechanism
NEURON {
SUFFIX caext :Sets suffix of mechanism for insertion into models
USEION ca READ ica WRITE cao :Lays out which NEURON variables will be used/modified by file
GLOBAL cabat... |
b4238bb105e00f142b10a02cf178304ac865b774016f2e85237564f10de2e8f2 | NEURON | 2,082 | 93 | : h.mod is the h channel
: from Tom Andersson Sensitivity studies of voltage-dpendent conductance in neurons
: Tom has build his model on Kouranova 2008 Hyoerpolarization -activated cyclic nuleotide-gated channel mRNA and protein expression in large versus mall diameter dorsal root ganglion neurons: correlation with hy... |
0667d99aca96dd430b7b41daa444aa7b713414d06d21f328455403fe96f82a9a | NEURON | 2,138 | 64 | : Author: David Catherall
: Created: November 2016
: Intracellular calcium ion accumulation
: Neuron Block creates mechanism
NEURON {
SUFFIX caint :Sets suffix of mechanism for insertion into models
USEION ca READ ica WRITE cai :Lays out which NEURON variables will be used/modified by file
GLOBAL nb ... |
a5e38978423c290cc0a0941e92800cb314ef250ee51b0b29dfb372b6b77a1b40 | NEURON | 2,181 | 66 | : Author: David Catherall
: Created: November 2016
: NaKpump is the Sodium-Potassium Pump in Schild 1994
: Adapted from Leo Medina's implementation from Lindblad et al Am J Physiol 1996 275:H1666
: Original model has been modified to assume constant nai
: Neuron Block creates mechanism
NEURON {
SUFFIX NaKpumpSchil... |
10089655c9927896431ee59157a67480e0a62cd1094d03b104e4765abf8fe1a9 | NEURON | 2,335 | 81 | : Author: David Catherall
: Created: November 2016
: NaCaPump is the Sodium-Calcium Exchanger in Schild 1994
: Adapted from Leo Medina's implementation from Lindblad et al Am J Physiol 1996 275:H1666
: Original model has been modified to assume constant nai
: Neuron Block creates mechanism
NEURON {
SUFFIX NaCaPum... |
9b53c836116302691e2425149bbf06e1494e0d2f7331be5c48122ee8d1bf4cd0 | NEURON | 2,482 | 79 | : Author: David Catherall
: Created: November 2016
: Extracellular calcium ion accumulation
: Neuron Block creates mechanism
NEURON {
SUFFIX caextscale :Sets suffix of mechanism for insertion into models
USEION ca READ ica WRITE cao :Lays out which NEURON variables will be used/modified by file
GLOBAL ... |
24a930a47d525c0b6f151ca10dfbcc2c7c2be53ecfc2855a88eb646bed79d8b9 | NEURON | 2,500 | 76 | : Author: David Catherall
: Created: November 2016
: Intracellular calcium ion accumulation
: Neuron Block creates mechanism
NEURON {
SUFFIX caintscale :Sets suffix of mechanism for insertion into models
USEION ca READ ica WRITE cai :Lays out which NEURON variables will be used/modified by file
GLOBAL n... |
16885d0e01b5c432e8460119730a9d68ce10937b7a9b58d7df2a5b68225b2d6a | NEURON | 2,507 | 70 | : Author: David Catherall
: Created: November 2016
: Intracellular calcium ion accumulation
: Neuron Block creates mechanism
NEURON {
SUFFIX cainttest :Sets suffix of mechanism for insertion into models
USEION ca READ ica WRITE cai :Lays out which NEURON variables will be used/modified by file
GLOBAL n... |
06e074377fd7c34d4f94e5cab5eb501103898a438805f41772943e71559baba4 | NEURON | 2,662 | 131 | : nattxs.mod is a transient ttx-sensitive Na+ current from
: Sheets et al 2007
NEURON {
SUFFIX nattxs
USEION na READ ena WRITE ina
RANGE gbar, ena, ina, celsiusT, Tshift
}
UNITS {
(S) = (siemens)
(mV) = (millivolts)
(mA) = (milliamp)
}
PARAMETER {
gbar = 0 (S/cm2):0.035135 ... |
1a1649f9af454909618e1a022cae85911761e579c9f8c5cfe5be8cb97910dac8 | NEURON | 2,726 | 118 | TITLE hh.mod squid sodium, potassium, and leak channels
COMMENT
HH model using RattayAberham k=12 for 37degC
Remember to set celsius=37 in your HOC file.
Eric Musselman December 5, 2017
ENDCOMMENT
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(S) = (siemens)
}
? interface
NEURON {
... |
1a5c6f05507d6062696708ea5c0cbdce3a8168be8f728f377a577fbd3aab0a92 | NEURON | 2,908 | 110 | : Author: David Catherall
: Created: November 2016
: KCa is the calcium-activated potassium current in Schild 1994
: Neuron Block creates mechanism
NEURON {
SUFFIX kca :Sets suffix of mechanism for insertion into models
USEION k READ ek WRITE ik :Lays out which NEURON variables will be used/modified by ... |
2da69676eb82cc11bc68c7e1b532f4372c1ab376bed3f417d340ce424b98731f | NEURON | 2,914 | 115 | : Author: David Catherall
: Created: January 2018
: Naf is the fast, TTX-sensitive current in Schild 1994
: Neuron Block creates mechanism
NEURON {
SUFFIX naf97 :Sets suffix of mechanism for insertion into models
USEION na READ ena WRITE ina :Lays out which NEURON variables will be used/modified by fi... |
1ca508ee3b2edc254b69cd25f56582edf128fd1d2bb033e55e6a64a72cd1cbb1 | NEURON | 2,950 | 111 | : Author: David Catherall
: Created: November 2016
: Kds is the slowly inactivating delay current in Schild 1994
: Neuron Block creates mechanism
NEURON {
SUFFIX kds :Sets suffix of mechanism for insertion into models
USEION k READ ek WRITE ik :Lays out which NEURON variables will be used/modified by ... |
61dfef9ef3290f34af7c8d1271ca5c7f72d864230c2bd40e4a17b73294d09a83 | NEURON | 2,989 | 112 | : Author: David Catherall
: Created: January 2018
: Nas is the slower, TTX-insensitive current in Schild 1994
: Neuron Block creates mechanism
NEURON {
SUFFIX nas97 :Sets suffix of mechanism for insertion into models
USEION na READ ena WRITE ina :Lays out which NEURON variables will be used/modified b... |
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