sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c69094514d09ae31dcee1ba99e15c5dda249a859b5d7959d365b7d291595f57f | NEURON | 4,713 | 205 | // 0 - Electric mechanisms, 1 - Glutamate mechanisms
currentMechanismSetup = 0
cadifusInElectricalLeaves = 0
cadifusInAllGlu = 0
// Insert-uninsert FRAP and set its params.
// $1 - Boolean. 1 - insert. 0 - uninsert.
proc SectionInsertFRAP() {
if ($1 > 0) {
insert FRAP
DFree_FRAP=0.15 // um2/... |
a52c7613355b85b5074a9d1f18b7d9f275be966de72de9db91299af87dc16d2f | NEURON | 4,742 | 248 | COMMENT
Updated Exp2Syn synapse with Mg-blocked nmda channel.
Defaul values of parameters (time constants etc) set to match synaptic channels in
striatal medium spiny neurons (Du et al., 2017; Chapman et al., 2003; Ding et al., 2008).
Robert . Lindroos @ ki . se
original comment:
________________
Two state kinetic ... |
015fe387309b42f37434d0d12f44b177aab09b070f5b68dc8640a4549980d8df | NEURON | 4,870 | 141 | // This file is original file from Neuron Data base
// https://senselab.med.yale.edu
// Accession:97985
//A 3-d reconstructed neuron model can be simulated in parallel on a dozen or so processors and experience almost linear speedup. Network models can be simulated when there are more processors than cells.
//Referenc... |
4bda19cd0cbff1dc19d16a5e43086acc92eacbd370360a448bb91febbf344d1b | NEURON | 4,876 | 250 | : Eight state kinetic sodium channel gating scheme
: Modified from k3st.mod, chapter 9.9 (example 9.7)
: of the NEURON book
: 12 August 2008, Christoph Schmidt-Hieber
:
: accompanies the publication:
: Schmidt-Hieber C, Bischofberger J. (2010)
: Fast sodium channel gating supports localized and efficient
: axon... |
756275f0366a2b1e03e90bfa66ff7c7c883c84a8b6beed94a25d542362307255 | NEURON | 4,895 | 187 | TITLE simple AMPA receptors
COMMENT
-----------------------------------------------------------------------------
Simple model for glutamate AMPA receptors
=========================================
- FIRST-ORDER KINETICS, FIT TO WHOLE-CELL RECORDINGS
Whole-cell recorded postsynaptic currents mediated by AMP... |
35969be1e971fc02acdf4772e439002749583a07149f0adc68c4931bfd1564d8 | NEURON | 4,901 | 197 | TITLE simple NMDA receptors
NEURON {
POINT_PROCESS adaptive_zahra_NMDA
RANGE g, Alpha, Beta, Erev, gmax, Cdur, iNMDA, mg, Cmax, eta, alpha, w0, weight
RANGE treshf, synon, conc0, mltypeMin, mltype, rate_ltd, rate_ltp, rate_ltd_thrsh, rate_ltp_tresh, tremin
NONSPECIFIC_CURRENT iNMDA
POINTER dopamine
USEION... |
1cf50a0a02c577e7067304078c8767626d6080ab0fa7b0c639ad97f38bbe6aee | NEURON | 4,982 | 255 | COMMENT
Updated Exp2Syn synapse with Mg-blocked nmda channel.
Defaul values of parameters (time constants etc) set to match synaptic channels in
striatal medium spiny neurons (Du et al., 2017; Chapman et al., 2003; Ding et al., 2008).
Robert . Lindroos @ ki . se
original comment:
________________
Two state kinetic ... |
79adfeb2a9c3fe6a0ff74eaea08dcea6f63ad4e854dd8d6b8d5b5d409195f684 | NEURON | 5,048 | 154 | // UI
objref hBoxGeometricalParams
// Data vectors
objref vecVolSphereRatio, vecSurfVolRatio, vecDistance, vecVolume, vecSurface, vectDiam, vecDendrDist
objref f1
f1 = new File()
// Returns graph with default parameters for all plots.
// $o1 - X data
// $o2 - Y data
// $s3 - Label
// $s4 - Units
// $5 - Boolean. Con... |
324f83cb4237e864c37fd196a82d5b52492bfdec5e30d109ad4ed94784d03d49 | NEURON | 5,331 | 177 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
c35414feb3509eec8e228c4eb883f1a19e64345b66161a46095642346a1ae965 | NEURON | 5,340 | 172 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
38fd97a4ef50895e38d31c3da0f830711864156e1361814f71f4e82b9bad2258 | NEURON | 5,555 | 265 | COMMENT
Updated Exp2Syn synapse with Mg-blocked nmda channel.
Defaul values of parameters (time constants etc) set to match synaptic channels in
striatal medium spiny neurons (Du et al., 2017; Chapman et al., 2003; Ding et al., 2008).
Robert . Lindroos @ ki . se
original comment:
________________
Two state kinetic ... |
68c8270a2f3b9d76cece28d015b9390553b76ffd27341d34144456fab77664d2 | NEURON | 5,689 | 137 | // UI
objref hBoxFrapLine, vBoxFrapLineControls, frapioniPlot, graphFrapLine
// Concentration file
objref fileFrapLineConcentration
// Sections affected by FRAP
objref frapLineSections[SizeTotal*2]
// Finds sections within a line and sets initial FRAP concentration on them.
// $1 - AlphaX - line equation parameter
// ... |
9c8c2048421b6f2e8f18e121c6252124e1ddc623d03027ee6f5f032c7131daff | NEURON | 5,708 | 196 | COMMENT
-----------------------------------------------------------------------------
Simple synaptic mechanism derived for first order kinetics of
binding of transmitter to postsynaptic receptors.
A. Destexhe & Z. Mainen, The Salk Institute, March 12, 1993.
Last modif. Sept 8, 1993.
Reference:
Destexhe, A., Mainen,... |
3b049544bf01d7ad3a6f0f0e6ce00755eb06098f96a029fd4f7f11be2d39ce87 | NEURON | 5,770 | 217 | TITLE simple AMPA receptors
COMMENT
-----------------------------------------------------------------------------
Simple model for glutamate AMPA receptors
=========================================
- FIRST-ORDER KINETICS, FIT TO WHOLE-CELL RECORDINGS
Whole-cell recorded postsynaptic currents mediated by AMP... |
bb52b9f20e351629fe83094ca33fedcf648689171d2129b29a7d47ecb2873ce5 | NEURON | 5,788 | 188 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
fde1c084efbbb3cb0a2cd4ee0f99e8ea5b6bbc361608ffbf2842edfc24c80faf | NEURON | 5,842 | 262 | COMMENT
Updated Exp2Syn synapse with Mg-blocked nmda channel.
Defaul values of parameters (time constants etc) set to match synaptic channels in
striatal medium spiny neurons (Du et al., 2017; Chapman et al., 2003; Ding et al., 2008).
Robert . Lindroos @ ki . se
original comment:
________________
Two state kinetic ... |
25cdb110b132e3d035523945e32838a68708bd4446851ce51c1c4ee00154ff6b | NEURON | 5,937 | 148 | // UI
objref vBoxFrapCircleControls, hBoxFrapCircle, plotShapeFrapioniCircle
// Sections affected by FRAP
objref frapCircleSections[SizeTotal*2]
// Random
objref randomFrapCircle
randomFrapCircle = new Random()
// Finds sections within a circle and sets initial FRAP concentration on them.
// $1 - X coordinate circle ... |
8f3a4ead6c8f90fbc74e550d1277076055189a9425b936cde4bcc47fbaea08ad | NEURON | 6,145 | 240 | TITLE simple NMDA receptors
NEURON {
POINT_PROCESS adaptive_shom_NMDA
RANGE g, Alpha, Beta, Erev, gmax, Cdur, iNMDA,mg, Cmax, eta, alpha, nmda_ca_fraction
RANGE w0, threshf, synon, flagx, conc0, mltypeMin, mltype, kernel, kernel_LTD, lthresh_LTP, hthresh_LTP, lthresh_LTD
RANGE ca_nmdai_max, cali_max, cati_max,... |
67a8ed2f79ff3da87797c0f21905358e4a29e68828208d8e7c732c856917b484 | NEURON | 6,168 | 268 | COMMENT
Updated Exp2Syn synapse with Mg-blocked nmda channel.
Defaul values of parameters (time constants etc) set to match synaptic channels in
striatal medium spiny neurons (Du et al., 2017; Chapman et al., 2003; Ding et al., 2008).
Robert . Lindroos @ ki . se
original comment:
________________
Two state kinetic ... |
129c140b4d860294c390007c613377c31cdf184aeb5d3c992844fe42e5ca3904 | NEURON | 6,170 | 168 | // UI
objref vBoxGluMain, graphSEClamp, graphGluout, plotShapeVoltage, plotShapeGluOut, plotShapeitrans
// SEClamp on the soma
objref seClamp
// Sets SEClamp params on the soma.
// $1 - Amplitude
// $2 - Duration
proc stimulGlu() {
soma {
seClamp = new SEClamp(0.5)
seClamp.amp1 = $1 // nA
... |
20eaefd1bc57d030b7121db7e3a54a4d3b381993b35222d617fbfd77cd9e07ce | NEURON | 6,327 | 216 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
5b479de1638b15cb3e840f7b35895ddde1dea532a661c9b590418e643e44a0f5 | NEURON | 6,704 | 234 | TITLE simple AMPA receptors
COMMENT
-----------------------------------------------------------------------------
Simple model for glutamate AMPA receptors
=========================================
- FIRST-ORDER KINETICS, FIT TO WHOLE-CELL RECORDINGS
Whole-cell recorded postsynaptic currents mediated by AMP... |
7e17565780f35877a13a3fd869bfe7da9674c403b00cad0aceeeae89009796a7 | NEURON | 7,016 | 250 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
f27ea2dd5eb67cf792e5574190d704beb9ac9ba99e2477f3acb84af4ed56062f | NEURON | 7,031 | 222 | TITLE Model of AMPA receptors
COMMENT
-----------------------------------------------------------------------------
Kinetic model of AMPA receptors
===============================
6-state gating model:
(scheme 1 from Raman and Trussell, Neuron 9:173-186, 1992)
2 open states provide dual exponenti... |
ed2ed3e60b2ae201965dcc596d101786a32e3f6e14ace6dfc7d5c9b381ebf79a | NEURON | 7,111 | 250 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
df99f1e30cba6b31ce25d4032c1d0d0e0e18167826b4d72716b7a1d6f855672c | NEURON | 7,248 | 250 | TITLE simple AMPA receptors
COMMENT
-----------------------------------------------------------------------------
Simple model for glutamate AMPA receptors
=========================================
- FIRST-ORDER KINETICS, FIT TO WHOLE-CELL RECORDINGS
Whole-cell recorded postsynaptic currents mediated by AMP... |
58eb91ddb8367522e6b4a9b02e378e31d490046eaeae82aabd2d0a67d68cbeff | NEURON | 7,295 | 259 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
2c657cc046c2ed57757b5406cca778cf214b37cf221478b2abee22ec2a2d9745 | NEURON | 7,581 | 189 | /*
The software is for a computer design of the astrocyte models.
The modelling scripts to compute astrocyte physiology were designed from
2D cable compartments implemented in NEURON simulation environment.
Astrocyte models work reliably based on a biophysically detailed multi-compartmental
3D structure with ion ... |
64d011553127d00756baef47df315261b694fddbc65f12ad884b631923f33d42 | NEURON | 7,605 | 295 | COMMENT
Updated Exp2Syn synapse with Mg-blocked nmda channel.
Defaul values of parameters (time constants etc) set to match synaptic channels in
striatal medium spiny neurons (Du et al., 2017; Chapman et al., 2003; Ding et al., 2008).
Robert . Lindroos @ ki . se
original comment:
________________
Two state kinetic ... |
0169e942ea4d31487a9c04bbe811c07dd93cd11e4a649a8f3396c8a420018e80 | NEURON | 7,982 | 266 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
2cac633b2ee4cb686ab1deac55bb36c9aba70df4797d57f3fdb68f239f3b98bd | NEURON | 8,061 | 277 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
e5b166eb54f04289d8cf1b0374863c28f6c57e1e2e03fc7d3129c145c9337fb1 | NEURON | 8,111 | 211 | // UI
objref vBoxPotassiumMain, graphPotassiumSEClamp, graphPotasasiumIn, plotShapeVoltagePotasasium, plotShapePotasasiumIn
// SEClamp on the soma
objref seClamp
// Sets SEClamp params on the soma.
// $1 - Amplitude
// $2 - Duration
proc stimulPotasasium() {
soma {
seClamp = new SEClamp(0.5)
seClam... |
41482114d09aa8b958af80632a7c262d4cf5adbc2b9285ea80756ef79e9d6cab | NEURON | 8,191 | 214 | TITLE kinetic NMDA receptor model
COMMENT
-----------------------------------------------------------------------------
Kinetic model of NMDA receptors
===============================
10-state gating model:
Kampa et al. (2004) J Physiol
U -- Cl -- O
\ | \ \
\ |... |
ed1e4c6ec792e623b34fd4940a5f9e3e226e8486b527c11b4109327c89922b95 | NEURON | 8,252 | 281 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesium block.
... |
ca2c5d35555c7ed5cc3e2d1f7313804dbb87c40c7e771870b666b325c59280f9 | NEURON | 8,545 | 311 | COMMENT
Calcium ion accumulation with radial and longitudinal diffusion, pump,
and SERCA.
Diffusion geometry based on Ca accumulation models from chapter 9
of The NEURON Book.
Mechanistic details of calcium pump and SERCA as described by Fink et al. 2000.
alpha = relative abundance of SERCA.
Current implementatio... |
50356b85f07a75918631a6b4ec0d1284a106a847019abc07d741cd5cea96be9f | NEURON | 8,633 | 386 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: P12-DEV176.CNG.swc
// Generated Tue May 30 13:23:24 BST 2017
OriginalDendrite=32
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
print "NumberDendrites=", NumberDendrites
SeedNumber=OriginalDendrite-1//... |
95f84e7ba0acd3ca751496c5d7970599a7e7f223b4aaadfff8c4ab0d32e8a487 | NEURON | 9,106 | 195 | load_file("CalciumParameters.hoc")
// UI
objref vBoxCalciumDynamics, plotShapeCai, graphDendrites
// Calcium stimulation sets
TotalNUmberGapJunction = 50 //Total number of noisy Ca channels
objref inputSt[TotalNUmberGapJunction+2], StimTrigger[TotalNUmberGapJunction+2], NetInput1[TotalNUmberGapJunction+2]
// Statistic... |
e6556f5dd7976dfcf02e28e7a4c1ca568f4dee872137f1ea990438fd2212aace | NEURON | 9,326 | 324 | COMMENT
Calcium ion accumulation with radial and longitudinal diffusion, pump,
and SERCA.
Diffusion geometry based on Ca accumulation models from chapter 9
of The NEURON Book.
Mechanistic details of calcium pump and SERCA as described by Fink et al. 2000.
alpha = relative abundance of SERCA.
Current implementatio... |
a3675888ba416de4e3fbd1175a251d3bbe87d2c724ff7e9d41a81767fd978e67 | NEURON | 9,364 | 312 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
c998d305ad37539e24bf33a5a6f5d929698e54827703b8aebea0184cf89f818e | NEURON | 10,225 | 311 |
TITLE simple NMDA receptors
COMMENT
-----------------------------------------------------------------------------
Essentially the same as /examples/nrniv/netcon/ampa.mod in the NEURON
distribution - i.e. Alain Destexhe's simple AMPA model - but with
different binding and unbinding rates and with a magnesiu... |
7be97ff0a7f18fd0549d9cdf53dfa4182ffd70765b5813c7e5edd43cc1c27c6c | NEURON | 10,851 | 375 | COMMENT
This file was modified from basic cadifus.mod from Chapter 9 Hines and Carnevale NEURON
the computation of fluorescence was added
two types
The fluorescence relates to the cocnetration of bound mobile buffer
fluo = cabufm[0]
fluoNew = (BufferAlpha * cabufm[0] + ca[0] - BufferAlpha*(TBufm - bufm_0) - cai0)/(Bu... |
3eb5e3f93081732aedd6c837aa93521acf375cb6f97f85f409160bf7dc0a5dfc | NEURON | 11,659 | 429 | access soma
area(0.5)
distance()
proc geom_nseg() {
soma area(0.5) // make sure diam reflects 3d points
forall {nseg = int((L/(0.1*lambda_f(10000))+0.9)/2)*2+1}
}
//--------------------------------------------------------------
// Initialise user-defined membrane parameters
// ----------------------------------... |
bcfbdf11373a1bbe434a0430540d7fd32c3bc773a77d3801cc4ed82559693ca7 | NEURON | 11,659 | 429 | access soma
area(0.5)
distance()
proc geom_nseg() {
soma area(0.5) // make sure diam reflects 3d points
forall {nseg = int((L/(0.1*lambda_f(10000))+0.9)/2)*2+1}
}
//--------------------------------------------------------------
// Initialise user-defined membrane parameters
// ----------------------------------... |
48d1dcff91dbf80f0db5eae779b97fa43901a51860c06528b16d7a920831a266 | NEURON | 11,727 | 431 | access soma
area(0.5)
distance()
proc geom_nseg() {
soma area(0.5) // make sure diam reflects 3d points
forall {nseg = int((L/(0.1*lambda_f(10000))+0.9)/2)*2+1}
}
//--------------------------------------------------------------
// Initialise user-defined membrane parameters
// ----------------------------------... |
b1136c87b1e1c3a20ee8353943259ece43ee679026dc0a3138f7627d5e09e173 | NEURON | 11,727 | 431 | access soma
area(0.5)
distance()
proc geom_nseg() {
soma area(0.5) // make sure diam reflects 3d points
forall {nseg = int((L/(0.1*lambda_f(10000))+0.9)/2)*2+1}
}
//--------------------------------------------------------------
// Initialise user-defined membrane parameters
// ----------------------------------... |
0aea616577ffdd39ecf027126a0f9d1aa0e41c71d60e07b63a90a5a31ef825fa | NEURON | 11,728 | 431 | access soma
area(0.5)
distance()
proc geom_nseg() {
soma area(0.5) // make sure diam reflects 3d points
forall {nseg = int((L/(0.1*lambda_f(10000))+0.9)/2)*2+1}
}
//--------------------------------------------------------------
// Initialise user-defined membrane parameters
// ----------------------------------... |
78f8e690dacadefb56847062fc3918d7bf47b539b4c36e03ac3a427f9fec27bc | NEURON | 11,728 | 431 | access soma
area(0.5)
distance()
proc geom_nseg() {
soma area(0.5) // make sure diam reflects 3d points
forall {nseg = int((L/(0.1*lambda_f(10000))+0.9)/2)*2+1}
}
//--------------------------------------------------------------
// Initialise user-defined membrane parameters
// ----------------------------------... |
9ac2407b74773c8bdf24a786bac97c2304109a481121e30eef2af87c083ba7c5 | NEURON | 11,820 | 422 | // .hoc file for simulating WT SCN2A
// corresponds to adult model from (Ben-Shalom et al., 2017)
// ----------------------------------------------------------------------------
// Channel densities and parameters
// ----------------------------------------------------------------------------
na_ais = 7000 // nav1.... |
65fe125809d67ac46c7c7eef38ae617f76f1f5024bfe10fb5df0d0695d760cc4 | NEURON | 12,011 | 425 | // .hoc file for simulating E1803G
// activation/inactivation shifts = 2/10
// ----------------------------------------------------------------------------
// Channel densities and parameters
// ----------------------------------------------------------------------------
scn2a_scale_factor = 1.0
na_ais = 7000 // n... |
f06cdc91cc6764bbd1c4350411bd324080ad379c8a3250ab7a2b7bebb92c1cee | NEURON | 12,012 | 425 | // .hoc file for simulating E1803G
// activation/inactivation shifts = 0/10
// ----------------------------------------------------------------------------
// Channel densities and parameters
// ----------------------------------------------------------------------------
scn2a_scale_factor = 1.0
na_ais = 7000 // n... |
2872ea5c46ea004644a5de3a1a2306446fc7bbcb36d6fd3dcc6387dd633c40a7 | NEURON | 12,061 | 426 | // .hoc file for simulating WT SCN2A
// corresponds to developing model from (Ben-Shalom et al., 2017)
// ----------------------------------------------------------------------------
// Channel densities and parameters
// ----------------------------------------------------------------------------
na_ais = 7000 // ... |
fd8b8089695bacddbc2d9ae8b37a916d01c66d57de2d0bac16f7227054be0e09 | NEURON | 12,106 | 427 | // .hoc file for simulating non-conducting SCN2A
// SCN2A conductance = 0% of WT
// ----------------------------------------------------------------------------
// Channel densities and parameters
// ----------------------------------------------------------------------------
scn2a_scale_factor = 0.0
na_ais = 7000... |
7cb18cad4fc7f303f6c23070f7bbb1ca6f4da1f5a6a46d38e55b7e0b67a2071c | NEURON | 12,108 | 427 | // .hoc file for simulating non-conducting SCN2A
// SCN2A conductance = 25% of WT
// ----------------------------------------------------------------------------
// Channel densities and parameters
// ----------------------------------------------------------------------------
scn2a_scale_factor = 0.25
na_ais = 70... |
e97934982b144b78c6023aa6e9a1de8314652c56b2f036f61d54edbcb60c8f78 | NEURON | 12,108 | 427 | // .hoc file for simulating non-conducting SCN2A
// SCN2A conductance = 75% of WT
// ----------------------------------------------------------------------------
// Channel densities and parameters
// ----------------------------------------------------------------------------
scn2a_scale_factor = 0.75
na_ais = 70... |
3d4f6e066c16fa63c2d595afdcc5a33421a95c2fcb52b554c9d39ed70bd80d08 | NEURON | 12,131 | 427 | // .hoc file for simulating non-conducting SCN2A
// SCN2A conductance = 50% of WT (i.e. heterozygous LOF)
// ----------------------------------------------------------------------------
// Channel densities and parameters
// ----------------------------------------------------------------------------
scn2a_scale_fac... |
2b6ae69107ebb618a8303c293c30b7f8f300790864947d9a55598a283736d9ec | NEURON | 12,835 | 568 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: P9-DEV309.CNG.swc
// Generated Wed May 31 09:55:11 BST 2017
OriginalDendrite=49
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
print "NumberDendrites=", NumberDendrites
SeedNumber=OriginalDendrite-1//... |
54b77638a803fc6a11f4e4f809e1489d0f30ee868cfaeb0729291d7d9e270d6f | NEURON | 14,300 | 273 | // UI
objref vBoxMainPanel, vBoxLeftPanel, vBoxCentralPanel, vBoxRightPanel, plotShapeMainV, graphMainSomaV
// 0 - Uniform distribution selected, 1 - Distribution from file selected
// Diameter distribution of leaves
distrStatusLeaves = 0
// Diameter distribution of stalks
distrStatusStalks = 0
// change the volume of... |
44369ad7b893c37be92897f69a053966effe18024c4157541d139f2ab9a27e51 | NEURON | 14,662 | 378 | TITLE Multisite synapse
COMMENT
-----------------------------------------------------------------------------
Multi-site synapse with independent release sites. Each site operates independently
and releases a vesicle upon presynaptic depolarization with a probability
determined by the history of activity, using the D... |
b4f48e84d39d2e3a4609286ed22dfd4c60858df424ef250334fa012f06be830c | NEURON | 21,502 | 1,065 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: P12-DEV185.CNG.swc
// Generated Tue May 30 16:02:29 BST 2017
OriginalDendrite=107
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
print "NumberDendrites=", NumberDendrites
SeedNumber=OriginalDendrite-1... |
d3a7d5abe487bb06e1ac94597212a222bc61355476f3c1bbc2a01923186400ad | NEURON | 24,528 | 1,252 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: P32-DEV136.CNG.swc
// Generated Wed May 31 09:53:21 BST 2017
OriginalDendrite=125
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
print "NumberDendrites=", NumberDendrites
SeedNumber=OriginalDendrite-1... |
404cfbcf3e7298376a512952ce2700b58002f29400309c988a424f4e34d50696 | NEURON | 25,445 | 1,309 |
OriginalDendrite=133
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
SeedNumber=OriginalDendrite-1//132 // Number of extra seeds equal to the number of the central dendrites
create soma[1]
create dendrite[NumberDendrites]
scp = 1
access soma[0]
soma[0] {
pt3dclear()
pt3dadd(0.23,... |
944bc28d8162baed72d8106889345a25ea4442abee52972e849df2858c1fc21e | NEURON | 25,453 | 1,309 |
OriginalDendrite=133
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
SeedNumber=OriginalDendrite-1//132 // Number of extra seeds equal to the number of the central dendrites
create soma[1]
create dendrite[NumberDendrites]
scp = 1
access soma[0]
soma[0] {
pt3dclear()
pt3dadd(0.23,... |
5a8d1710eb77ae51fdc3a40c3ddb2abfcd7e2cb1cc721b2e01018ea40953c39d | NEURON | 29,255 | 861 | //
//************************************************************************************************************
//
OriginalDendrite=101
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
SeedNumber=OriginalDendrite-1//132 // Number of extra seeds equal to the number of the central dendrites ... |
037023395644f8204082e501c376ca7f682552f4691145818aaaf6621d75f0e3 | NEURON | 37,037 | 1,142 | //
//************************************************************************************************************
//
OriginalDendrite=145
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
SeedNumber=OriginalDendrite-1//132 // Number of extra seeds equal to the number of the central dendrites ... |
0de1746ba310312c5fc814296aad90033b76af3776067a648acaac7fdf74c862 | NEURON | 42,620 | 955 | proc celldef() {
topol()
}
create hillock[1], initialsegment[1], unmyelinatedaxon[1], soma[1], primarydendrite[100]
proc topol() { local i
connect soma(0), hillock(0)
connect initialsegment(0), hillock(1)
connect unmyelinatedaxon(0), initialsegment(1)
connect primarydendrite(0), soma(1)
for i = 1, 7 conne... |
9ff8ac8f31e939e015b8b6c7f0db96890a8f3495d5d8377cd052062db79c9e5a | NEURON | 78,204 | 2,923 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: 185-1-3dk.CNG.swc
// Generated Tue May 30 16:10:10 BST 2017
OriginalDendrite=172
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
print "NumberDendrites=", NumberDendrites
SeedNumber=OriginalDendrite-1/... |
5e320525d2ff3c5ace6e2f13508d434d33e1cf4717bcdade721adbd78a0b5fc9 | NEURON | 200,000 | 5,271 | //--------------------------------------------------------------
// morphology of layer 5 pyramidal neuron
// corresponds to 28_04_10_num19.hoc from Hallermann et al. 2012
// doi: 10.1038/nn.3132
//--------------------------------------------------------------
proc celldef() {
topol()
subsets()
geo... |
c444ddfce91451b2fdd907087f0ebe96ce1f631810ecff8235e52fa8be92890e | Perl | 513 | 21 | #!/usr/bin/perl -w
my $arg_output_homo = shift @ARGV;
my $arg_output_orf = shift @ARGV;
open FH_HOMO, ">$arg_output_homo" or die "Can't open file ($arg_output_homo) for writting";
open FH_ORF, ">$arg_output_orf" or die "Can't open file ($arg_output_orf) for writting";
while (my $l = <STDIN>) {
chomp $l;
my $sour... |
043e3be1a5549f79f10796093807329f7e235845f09826f0f68bcf108b85910c | Perl | 612 | 25 | #!/usr/bin/perl -w
use strict;
use warnings;
print join("\t", "QueryID", "CDSLength", "Score", "Used", "Strict"), "\n";
# >gi|344283|emb|A01270.1| T.ovis mRNA for 45W antigen (partial) \\
# [framefinder (0,702) score=55.32 used=75.65% {forward,local} ]
while (my $l = <STDIN>) {
chomp $l;
if ($l =~ /^>(\S+)/) {... |
abc1463a827233ed0a92a65aa5c0aadc76669ed601d9136545fdc5935190c862 | Perl | 617 | 33 | #!/usr/bin/perl -w
use strict;
use warnings;
my @output_lines;
while (my $f = shift @ARGV) {
open FH, "<$f" or die "Can't open file($f): $!";
my $curr_line_index = 0;
while (my $l = <FH>) {
chomp $l;
next if $l =~ /^\s*$/;
next if $l =~ /^\s*#/;
next if $l =~ /^labels/; # skip possible "labe... |
d2aff17dafd9fef10c7722851119339f875b407f9227aee515a7076adf3174fa | Perl | 680 | 22 | #!/usr/bin/perl -w
if ($#ARGV >= 0) { $who = join(' ', $ARGV[0]); }
opendir(DIR, $who);
@filelist = glob("$who");
# @filelist2 = glob("$who2");
$ct=0;
$dir = `pwd`;
$dir=substr($dir,0,length($dir)-1)."/";
$pathpre="/mnt/aibs1/avants/bin/ants/";
foreach $name (@filelist)
{
$exe = $p... |
65185e070c67287e898c0f59023e8a523adf4675b381eb5422b42a4985d77940 | Perl | 742 | 30 | #!/usr/bin/perl -w
use warnings;
use strict;
my $arg_input_blast_report = shift @ARGV;
open FH_BLAST, "<$arg_input_blast_report" or die "Can't open BLAST input file ($arg_input_blast_report): $!";
my ($curr_query_id, $curr_record_start, $curr_record_end);
while (my $l = <FH_BLAST>) {
if ($l =~ /^BLASTX/) {
m... |
d6df845b191981f1be1d886fb9410d2991e29440a3227aca49398e679eb4b3ba | Perl | 835 | 38 | #!/usr/bin/perl -w
use strict;
use warnings;
my $arg_input_blast_report = shift @ARGV;
my $arg_input_index = shift @ARGV;
my %index;
open FH_INDEX, "<$arg_input_index" or die "Can't open index ($arg_input_index): $!";
while (my $l = <FH_INDEX>) {
chomp $l;
my ($query_id, $start, $end) = split /\t/, $l;
$index... |
96a22085d887244aacd95a6715ea74a96eea16c41c1d5118518b8541f46914ba | Perl | 876 | 43 | #!/usr/bin/perl -w
use strict;
use warnings;
my $arg_feat_file = shift @ARGV;
my %existed_feat; # QueryID ==> whole line
open FEAT, "<$arg_feat_file" or die "Can't open file ($arg_feat_file): $!";
while (my $l = <FEAT>) {
chomp $l;
next if $l =~ /^\s*$/;
next if $l =~ /^\s*#/;
my $query_id = (split /\t/, ... |
f1bb8fcbe2a9f36f72d4248cf23c73c835f7d1c29b4d387d3da5f5b5b9401d34 | Perl | 926 | 36 | #!/usr/bin/perl -w
use strict;
use warnings;
use Bio::SeqIO;
######################################################################
#
# FIXME: Well, I know, the code is low-performance, fat, dirty and
# ... suck, but what would you expect a man with damned flu-fever to
# write in less than 10 minutes, anyway?
#
# ... |
cd37a7be679a94d9043adfe04a3769ec86506e7bf158dda61d221730b133e357 | Perl | 1,049 | 54 | #!/usr/bin/perl -w
use strict;
use warnings;
my $arg_seq = shift @ARGV;
my @query_ids;
my @seq_len;
my ($curr_query_id, $curr_query_seq_len);
open FH, "<$arg_seq" or die "Can't open file ($arg_seq): $!";
while (my $l = <FH>) {
chomp $l;
next if $l =~ /^\s*$/;
next if $l =~ /^\s*#/;
if ($l =~ /^>(\S+)/) {
... |
df6d007a279715803e0c4d0f8dcbcf390a11c26d3aa6717ad8fee1c431779ab8 | Perl | 1,109 | 35 | #!/usr/bin/perl -w
if ($#ARGV >= 0) { $who = join(' ', $ARGV[0]); }
if ($#ARGV >= 1) { $imagedimension = join(' ', $ARGV[1]); }
if ($#ARGV >= 2) { $outputname = join(' ', $ARGV[2]); }
if ($#ARGV < 2) {
print " usage: \n perl weightedaverage.pl *files.jpg imagedimension weight1 ... weightN \n ";
exit... |
79bda4768e897445f0501f718cb95d0b25563d064dbb8a61dee2528e7c5bbf4f | Perl | 1,168 | 22 | #!/usr/bin/env perl
# Decoy shuffles and strata: golden values shared with PyTransDecoder (tests/test_decoys.py).
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Decoys;
my $fail = 0;
sub check { my ($ok, $what) = @_; print(($ok ? "ok" : "FAIL"), "\t$what\n"); $fail++ unless $ok; }
&c... |
86a8fb90b9eaf3e5c99d15d938ac57f0b976783ebe052aca911375b53201d927 | Perl | 1,313 | 60 | #!/usr/bin/perl -w
use strict;
use warnings;
my $arg_seq = shift @ARGV;
my @query_ids;
my @seq_len;
my ($curr_query_id, $curr_query_seq_len);
open FH, "<$arg_seq" or die "Can't open file ($arg_seq): $!";
while (my $l = <FH>) {
chomp $l;
next if $l =~ /^\s*$/;
next if $l =~ /^\s*#/;
if ($l =~ /^>(\S+)/) {
... |
b1d7eb80d0a292ef9bdf36bcaad1a1daa9372b4383f9fa2f68a3d84e6081165a | Perl | 1,403 | 79 | use strict;
use warnings;
use POSIX;
my $sample = "hip142079";
my $nb = 2500;
#my $sample = "hip142078";
#my $nb = 2560;
#my $sample = "mob164315";
#my $nb = 918;
open(IN, $sample.".snp100838.RN3.QV6_snpmatrix.txt") || die $_;
my $header=<IN>;
$header=~ s/\t/,/g;
my %ai=();
while(my $ligne=<IN>){
chomp($ligne);
... |
2ea2a7e3ce282a6f517c4a446ea8ccc65e7207ca9de6f4d06aecc472a86f0bbe | Perl | 1,542 | 55 | #!/usr/bin/perl -w
if ($#ARGV >= 0) { $who = join(' ', $ARGV[0]); }
if ($#ARGV >= 1) { $template = join(' ', $ARGV[1]); }
if ($#ARGV >= 2) { $dim = join(' ', $ARGV[2]); } else { $dim=0; }
if ($#ARGV >= 3) { $outnaming = join(' ', $ARGV[3]); } else { $outnaming=""; }
opendir(DIR, $who);
@filelist... |
cf63b5e070bd0bc7068ca0aa2502cb4640194490cc85102014c04351d6cb2b09 | Perl | 1,686 | 54 | #!/usr/bin/perl -w
use strict;
use CPAN::MyConfig;
use CPAN;
use CPAN::HandleConfig;
use CPAN::Shell;
my $root;
BEGIN {
$root = $INC[0];
if ($root !~ s:/_cpan$::) {
die "Please invoke this script via .../setup.sh."
}
if ( ! exists $CPAN::Config{cpan_home} ) {
$CPAN::Config = {
... |
4f24fb6b91c89c7788bdf479dd6f529c7fae6c85972f400b06e79632102c9f72 | Perl | 1,760 | 59 | #!/usr/bin/perl -w
use File::Basename;
if ($#ARGV >= 0) { $who = join(' ', $ARGV[0]); }
if ($#ARGV >= 1) { $template = join(' ', $ARGV[1]); }
if ($#ARGV >= 2) { $params = join(' ', $ARGV[2]); } else { $params=0; }
if ($#ARGV >= 3) { $outnaming = join(' ', $ARGV[3]); } else { $outnaming=0; }
if ($#A... |
621bafc201f810affa5a502fd37b7bf40f9cb82bb4fb450b9f7528614d39f566 | Perl | 1,807 | 70 | #!/usr/bin/env perl
#
# Google Drive direct download of big files
# ./gdown.pl 'gdrive file url' ['desired file name']
#
# v1.0 by circulosmeos 04-2014.
# v1.1 by circulosmeos 01-2017.
# http://circulosmeos.wordpress.com/2014/04/12/google-drive-direct-download-of-big-files
# Distributed under GPL 3 (http://www.gnu.org/... |
fd4f910d856a43905ee0208b0cb2cc128e9f20a79bb36dbbe1b0f578652732b3 | Perl | 2,100 | 71 | #!/usr/bin/perl -w
use Getopt::Long;
my @opt_output_columns;
GetOptions ("c=s" => \@opt_output_columns,
);
my $arg_positive = shift @ARGV; # Coding
my $arg_negative = shift @ARGV; # Noncoding
my $arg_unknown = shift @ARGV; # Unknown, just as a placehold
# XXX: allow comma-separated lists, see Getopt::Long doc... |
12fd9ab0372f57ae2b99969e00152a7c842d89aa1cfa38e695bfd4b9c4e1ce0c | Perl | 2,373 | 94 | #!/usr/bin/perl -w
use strict;
use warnings;
# combine two lsv file, columns by columns
#
# NOTE: the code is rather d00dle: currently, only lsv generated by
# feat2libsvm.pl could be tested, USE IT CAREFULLY!
my $arg_lsv1 = shift @ARGV;
my $arg_lsv2 = shift @ARGV;
# (from libSVM README)
# <label> <index1>:<value1... |
64be96822272cf1a942b5d563f2b1b1d45dfbc9c3c1663eee4c099556bd929a5 | Perl | 2,638 | 101 |
#!/usr/bin/perl -w
use strict;
use warnings;
############################################################
#
# FIXME: THE CODE IS RATHER DIRTY (AND SUCK)....
#
############################################################
my $arg_blastx_table = shift @ARGV;
my $arg_ff_result = shift @ARGV;
my %blastx_table;
open ... |
f19d8de9efb7cc065683f0aa407ada3ca8ff6d594d8647142848544053d398ec | Perl | 2,805 | 133 | #!/usr/bin/perl -w
use strict;
use warnings;
use Data::Dumper;
my $curr_query_id;
my $curr_sbjct_id;
my ($curr_hit_seq_count, $curr_hit_HSP_count);
my @curr_hit_score;
my @curr_hit_frame_scores; # [0|1|2] ==> \(100, 200, ...,300)
# Banner
print join("\t", "QueryID", "hit_seq_count", "hit_HSP_count", "hit_score", "... |
56b88a7ad49b0fea04244b9ea826718c6c3844523669e54da5a1e4a4f4339b47 | Perl | 2,890 | 86 | #!/usr/bin/perl -w
# The code is downloaded from
# http://safari5.bvdep.com/0596002998/blast-APP-E, as the appendix E
# of book "BLAST" by Joseph Bedell, Ian Korf, Mark Yandell, published
# by O'Reilly.
# Pub Date: July 2003
# ISBN: 0-596-00299-8
# Pages: 360
use strict;
use Getopt::Std;
use vars qw($opt_p $opt_b ... |
1c0844290cf2ed879bdc75f9e25665b30cb3b02a1213049e69bdffc35f0a78c3 | Perl | 3,032 | 125 | #!/usr/bin/perl
use strict;
MAIN : {
my ($read1_bam, $read2_bam) = @ARGV;
if ((not defined $read1_bam) ||
(not defined $read2_bam)) {
die ("Usage: ./two_read_bam_combiner.pl <read 1 bam> <read 2 bam>\n");
}
open(FILE1,"samtools view -h $read1_bam |");
open(FILE2,"samtools view -h $read2_... |
00db280b71ea1bc0d8dd0de2597b40d9b278bb583de88e0346b1cf6ef8a2066f | Perl | 3,050 | 125 | #!/usr/bin/perl
use strict;
MAIN : {
my ($read1_bam, $read2_bam) = @ARGV;
if ((not defined $read1_bam) ||
(not defined $read2_bam)) {
die ("Usage: ./two_read_bam_combiner.pl <read 1 bam> <read 2 bam>\n");
}
open(FILE1,"/usr/bin/samtools view -h $read1_bam |");
open(FILE2,"/usr/bin/samtoo... |
72c81e0c1f44a6a0ea2db2d047385b239edefe28cdab1ba0b652be3fcced34c2 | Perl | 3,191 | 129 | #!/usr/bin/perl -w
use strict;
# Usage: waitForSlurmJobs.pl <verbose [1 or 0]> <delay in seconds in range 10-600> [job IDs]
#
#
# Takes as args a string of sbatch job IDs and periodically monitors them. Once they all finish, it returns 0
#
# If any of the jobs go into error state, an error is printed to stderr and th... |
71faf1e499f344951eddf04b794038e5017ff0be4a64c94b41f20782b1ce1893 | Perl | 3,243 | 109 | #!/usr/bin/perl
use strict;
use warnings;
my $prev_id = "";
my @five;
my @three;
my @unmap;
my @mid;
my @all;
my $counter = 0;
while (<STDIN>){
chomp;
if (/^@/){
print $_."\n";
next;
}
my ($id, $flag, $chr_from, $loc_from, $mapq, $cigar, $d1, $d2, $d3, $read, $read_qual, @rest) = split /\t/;
my $bin = revers... |
62ab8098579fb6efb43c2373a8bc2ffb98caefcf6a27b32b28e6914f246b2a57 | Perl | 3,277 | 108 | #!/usr/bin/perl
use strict;
use warnings;
my $prev_id = "";
my @five;
my @three;
my @unmap;
my @mid;
my @all;
my $counter = 0;
while (<STDIN>){
chomp;
if (/^@/){
print($_ . "\n");
next;
}
my ($id, $flag, $chr_from, $loc_from, $mapq, $cigar, $d1, $d2, $d3, $read, $read_qual, @rest) = split(/\t/);
my $bin = re... |
6745ca2a95d926984d1af5d023176eaf2a1355b832c937c9882cacc85f68c6db | Perl | 3,301 | 122 | #!/usr/bin/perl
#
# Usage: waitForXGridJobs.pl [-verbose] [-delay N] [-xgridflags string] job_IDs
#
# Minimal call would be (e.g., to wait for a single job ID #200):
# waitForXGridJobs.pl 200
#
# delay: Poll interval in seconds (default is 30)
# verbose: Be verbose
# xgridflags: Flags to pass to XGrid. Odds are you... |
3c287af92444f5405885625b2880c3454a168d021006cc00e3a2e74be14f93f9 | Perl | 3,431 | 156 | #!/usr/bin/perl -w
use strict;
$SIG{INT}=\&myCleanup;
# Usage: waitForSGEQJobs.pl <verbose [2 or 1 or 0]> <delay in seconds in range 10-3600> [job IDs]
#
#
# Takes as args a string of qsub job IDs and periodically monitors them. Once they all finish, it returns 0
#
# If any of the jobs go into error state, an error ... |
7a2ed29de740939cfa41bd4aa6bd295bce38230e187b9a042f1a2dd1e1711bd2 | Perl | 3,469 | 150 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
use Getopt::Long qw(:config pass_through);
use List::Util qw(min);
my $usage = "usage: $0 CDS hexamerScores [--genetic_code name]\n\n";
my $genetic_code = "Universal";
&GetOptions('... |
3300eb859660fe5a2ea7d24fd72bdeb69f71b749c45ae48efb8bbf42f68a0545 | Perl | 3,632 | 95 | #!/software/bin/perl -w
use strict;
use Bio::SeqIO;
use DateTime;
$|=1;
my $file = shift;
my $outfile = shift;
my $seqin = Bio::SeqIO->new('-format' => 'fasta',
'-file' => $file);
$outfile = "./trimreport.txt" unless ($outfile);
# parameters
my $minleftover = 100; # af... |
debacbf6a1bcbb37383985a7cd30c0ae20d4deb7279bf09dc8fa7793af7107bf | Perl | 3,737 | 159 | #!/usr/bin/perl -w
use strict;
# Usage: waitForSGEQJobs.pl <verbose [1 or 0]> <delay in seconds in range 10-600> [job IDs]
#
#
# Takes as args a string of qsub job IDs and periodically monitors them. Once they all finish, it returns 0
#
# If any of the jobs go into error state, an error is printed to stderr and the p... |
1587b36d8d7d93d397cf58f866e8b80a67b4346ce3d5295955f4dc85e75bdecd | Perl | 3,739 | 117 | #!/usr/bin/perl
use strict;
MAIN : {
my ($read1_bam, $read2_bam, $samtools, $mq) = @ARGV;
if ( (! defined($read1_bam)) || (! defined($read2_bam)) ){
die ("Usage: ./two_read_bam_combiner.pl <read 1 bam> <read 2 bam> <path to samtools> <minimum map quality filter>\n");
}
open(FILE1, "$samtools vie... |
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