sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
27c148819564477ae9921f460ad89057878a69173a38413d5a70e2cd69d35e5e | NEURON | 3,643 | 141 | TITLE R-type calcium current (Cav2.3)
COMMENT
neuromodulation is added as functions:
modulation = 1 + damod*(maxMod-1)*level
where:
damod [0]: is a switch for turning modulation on or off {1/0}
maxMod [1]: is the maximum modulation for this specific channel (read from the param file)
... |
f4fb82bd5b0ee1e36df2281dda9abc9ef5ca6e727d638d8c5b37eab0a2901d7d | NEURON | 3,681 | 192 | load_file("nrngui.hoc")
cvode.active(1)
cvode.atol(1.e-3)
mid=5
dist=15
secondorder=2
FARADAY=96520
PI=3.14159
Rm = 28000
RmDend = Rm/2
RmSoma = Rm
RmAx = Rm
Cm = 1
CmSoma= Cm
CmAx = Cm
CmDend = Cm*2
RaAll= 150
RaSoma=150
RaAx = 50
Vrest = -65
dt = 0.025
gna = .032
AXONM = 2
gkdr = 0.01
celsius = 34.0
KMU... |
01a8b3084ced1a4eea6d01afcae0241d99b262e753cbe808087314814015a5c9 | NEURON | 3,710 | 144 | COMMENT
The model of Glutamate transporter.
is based on two papers,
from the paper
1. Zhang Z1, Tao Z, Gameiro A, Barcelona S, Braams S, Rauen T, Grewer C.
Transport direction determines the kinetics of substrate transport by the glutamate transporter EAAC1.
Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18025-30... |
2dd398a777722f5e0de8fe7b1858f3493910453d7927e36616d2d110a9fb7c15 | NEURON | 3,830 | 93 |
COMMENT
Outside-In Diffusion Series Helper (artificial cell)
This auxiliary artificial cell helps the membrane mechanism "OutsideInDiffHelper" to do its job when there are some extracellular souces with "series" dynamics.
For each such source, we create a chain of type "NetStim -> NetCon -> OutsideInD... |
3da686aacc2d0fd8239d65f2eba8e4261e754df5ebccfa2cb5e2fae018e09acb | NEURON | 3,875 | 186 | TITLE Mouse sodium current
: Kinetics of Carter et al. (2012)
: Based on 37 degC recordings from mouse hippocampal CA1 pyramids
NEURON {
SUFFIX NaV
USEION na READ ena WRITE ina
RANGE g, gbar
}
UNITS {
(mV) = (millivolt)
(S) = (siemens)
}
PARAMETER {
gbar = .015 (S/cm2)
: kinetic parameters
Con = 0.01 ... |
3dc6481618d793945d2fae3cbfd48a81cf110648db22ee2499c3b07b19764407 | NEURON | 3,877 | 138 | : P2X47_microglia.mod
: Ionotropic purinergic P2X4 / P2X7 receptor for microglial compartments.
:
: KINETIC SCHEME (3-state Markov):
:
: C (closed) --kon*atpo^2--> O (open) --kdes--> D (desensitized)
: C <--koff-------- O <--krec-- D
:
: For P2X7: kdes=0, PCa_ratio=11, EC50_atp~0.7 mM
: For P2X4 (def... |
739ce84497b5fc3663973daa906fdbe749ad464738a7c668d5d4427eca8c20fd | NEURON | 4,053 | 161 | TITLE nethhwbm.mod interneuron sodium, potassium, and leak channels
COMMENT
This file is based on the original hh.mod file (see original comment
below). It was modified to match the model that was used in the
simulations of Wang and Buzsaki (1996, J. Neurosci. 16).
********************************************... |
262c851c884ecde8ba0f817258e7e544c00f1617b38f29bdda296c834b8d7390 | NEURON | 4,126 | 150 | TITLE N-type calcium current (Cav2.2)
COMMENT
neuromodulation is added as functions:
modulation = 1 + damod*(maxMod-1)*level
where:
damod [0]: is a switch for turning modulation on or off {1/0}
maxMod [1]: is the maximum modulation for this specific channel (read from the param file)
... |
4964f3701eb18578ef35845489416ed6a2ddbd12265113b6348224d223ea9633 | NEURON | 4,169 | 152 | TITLE HVA L-type calcium current (Cav1.2)
COMMENT
neuromodulation is added as functions:
modulation = 1 + damod*(maxMod-1)*level
where:
damod [0]: is a switch for turning modulation on or off {1/0}
maxMod [1]: is the maximum modulation for this specific channel (read from the param file)
... |
6d85c1b544c98ab7c3b5763c1eee882c4f3b1d2a155cddaeaf210231f38a6607 | NEURON | 4,310 | 134 | : AMPARec.mod
:
: Concentration-gated AMPA receptor for BrainCell
: Savtchenko / Rusakov Lab, UCL
:
: Reads extracellular glutamate concentration (gluo, mM) from the BrainCell
: ECS diffusion system (_OutsideInDiffHelper.mod / _InsideOutDiffHelper.mod)
: and produces a postsynaptic inward cation current iampa (mA/cm2).... |
1574f614b7195ca86e67545bd5881a7287f10f075fbd0808e457b5c6172a0f5a | NEURON | 4,372 | 157 | TITLE LVA L-type calcium current (Cav1.3)
COMMENT
neuromodulation is added as functions:
modulation = 1 + damod*(maxMod-1)*level
where:
damod [0]: is a switch for turning modulation on or off {1/0}
maxMod [1]: is the maximum modulation for this specific channel (read from the param file)
... |
808355a9c11bfff6e285b20ede1230ecfc92394721da02beab66aaebb2acbeb9 | NEURON | 4,416 | 181 | /********************************************************************
Create a spine with a spine neck
connected to the parant dendrite dendA1_00
*************************************************/
create s
access s
Numb=1 // Max number of spines per dendrites
Branches= 1
// ***********************Uniform distribut... |
e8aef35dc52351fb57cf3d373c834e767ac7bd2a11ff923b4097f02fdbe257a2 | NEURON | 4,452 | 170 | COMMENT
The model of Glutamate GLT-1 Transporters.
The kinetic scheme was from the paper
Comparison of Coupled and Uncoupled Currents during Glutamate
Uptake by GLT-1 Transporters
Dwight E. Bergles, Anastassios V. Tzingounis, and Craig E. Jahr
ENDCOMMENT
NEURON {
SUFFIX GluTransNew
RANGE C1, C2, C3, C4, ... |
cf074575ecdc40c45f3a380dbaa91554e4466a3f5822beb833ecc453222ebf50 | NEURON | 4,522 | 208 | COMMENT
Updated Exp2Syn synapse with Mg-blocked nmda channel.
Default 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... |
c8d2779b475928d2a599acc1ceb4fc2904cfe5be8cc3f7bda5590ff1af84b365 | NEURON | 4,883 | 94 | TITLE Slow Ca-dependent potassium current
:
: Ca++ dependent K+ current IC responsible for slow AHP
: Differential equations
:
: Model based on a first order kinetic scheme
... |
6f6223bace9b883380d6de0187cfc555a76a4f4bba4348ef9fb7efc7b47b16b7 | NEURON | 5,023 | 148 |
// !! maybe use AltRunControl to call "setIp3ToSomaAndDendrites" from "preRun" to avoid the jump of "ip3i" on the Graph on 1st iteration
isCaWaveSimActive = 0
{ load_file("Utils/CalciumParameters.hoc") }
begintemplate SimCalciumWave
public preShowCheck, show, advance, simDismissHandler
public biophysJson... |
6d3aedb35cf481f908900874521085e9c925a8b11af79acb5b256d26e48f09c3 | NEURON | 5,346 | 197 | TITLE Optic Nerve Nodal Membrane Channels - Complete Model
: Based on Oozeer et al. 2006 - Model of mammalian optic nerve fibre
: Includes: Fast Na (INa), Fast K (IA), Delayed Rectifier K (IKdr),
: Persistent Na (Ip), Slow K (Is), Leak
: Modified from RGC somatic model (Fohlmeister et al. 1990) and
: McInty... |
7a5c959a69fe41b2fdcc228896571bf6ae4e71dcf62bb1240e805697982241ae | NEURON | 6,305 | 186 | TITLE Glutamatergic synapses - distributed AMPA-like density mechanism
COMMENT
-------------------------------------------------------------------------------
GlutSynDens
-------------------------------------------------------------------------------
Density (distributed) mechanism that emulates AMPA-like glutamaterg... |
7e7bfd7d4fc49b300c6a018fb2f2082500c017f803c29342bc09be6d1c84d5c3 | NEURON | 8,367 | 379 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: P12-DEV176.CNG.swc
// Generated Tue May 30 13:23:24 BST 2017
{create soma[1]}
{create dendrite[32]}
{access soma[0]}
soma[0] {
pt3dclear()
pt3dadd(-1.02,2.15,0,8.357)
pt3dadd(-1.02,-2.02,0,8.357)
pt3dadd(-1.02,-6.19,... |
69aeb07bd8e5bd5d6fa38057d793d02f6afcda0f7fc7f81e373840a617c89084 | NEURON | 8,625 | 385 | // 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//... |
cb62d9c004be6fdf67178b6cc78b076eea45e2b01358a0c430c6a33666b1bbf9 | NEURON | 9,424 | 224 | COMMENT
================================================================================
gapFRAP.mod -- Gap junction flux for FRAP tracer ion
================================================================================
Origin
------
Derived from ifrap.mod (2018). Models the intercellular flux of a custom
fluore... |
65aec9c039e749bd57338abb89302a81ac91157e2def6705c964c5e8dae76e22 | NEURON | 9,520 | 403 | /*
Created by BluePyOpt(1.9.37) at 2021-03-04 08:10:05.491139
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
e6a8208254b367450b84d2c12f0d1db9ef9c5b60738a26f7993d3940b1556e13 | NEURON | 10,949 | 382 | 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... |
05fb167def1e7a3b968e1f17100f8813502b38f09e488bb27ecbafda7c806afd | NEURON | 11,699 | 269 |
COMMENT
Inside-Out Diffusion Helper (membrane mechanism)
Its job is to read "i{species}", then calculate and write "{species}o". Not used when user chooses "neuron.rxd" as the diffusion module.
If you want to add new species (or delete old ones), look for 5 blocks of code below marked as "Edit he... |
762abfba2dababce3f0df80af241d2a7be1452069a5ce5ca9509be5104fbf8fb | NEURON | 11,889 | 274 |
COMMENT
Inside-Out Diffusion Helper (membrane mechanism)
Its job is to read "i{species}", then calculate and write "{species}o". Not used when user chooses "neuron.rxd" as the diffusion module.
If you want to add new species (or delete old ones), look for 5 blocks of code below marked as "Edit he... |
0aecad2ce59c449fd876c76eec87a9200d5c547f406b48264650fcccd3c8721e | NEURON | 12,568 | 560 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: P9-DEV309.CNG.swc
// Generated Wed May 31 09:55:11 BST 2017
{create soma[1]}
{create dendrite[49]}
{access soma[0]}
soma[0] {
pt3dclear()
pt3dadd(0.37,6.03,0.03,11.534)
pt3dadd(0.37,0.27,0.03,11.534)
pt3dadd(0.37,-5.... |
d4e04341d65b0a0dc0f855bb48f8b2bd285ce55cf1e762f81597765d268640b6 | NEURON | 12,827 | 567 | // 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//... |
c61899a4d1bfe452fd9f845e9ade8f85ef0adb240b721c16f16301c851aacf51 | NEURON | 13,058 | 707 | load_file("nrngui.hoc")
load_file("cell_seed2_0.hoc")
cvode_active(1)
objref testcell, stim, stim2, apc, v1
testcell = new test_Wt()
testcell.init()
tstop=2500
celsius=25
proc distribute_distance(){local x localobj sl
strdef stmp, distfunc, mech
sl = $o1
mech = $s2
distfunc = $s3
testcell.soma[0] dista... |
5438b3b0e900f8d1bde34e3b1b8b0701e8b955ae006647a2d6a76664b5917c3a | NEURON | 17,271 | 436 | COMMENT
================================================================================
GAT1_Bicho.mod -- 8-state alternating-access kinetic model of GAT1
GABA treated as a tracked ion (VALENCE 0)
================================================================================
REFERENCE
Bicho ... |
fe3b3e5b44a735deb4697d73938725d66156b0ef5cb3f027c0b139dab1594dc8 | NEURON | 21,235 | 1,057 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: P12-DEV185.CNG.swc
// Generated Tue May 30 16:02:29 BST 2017
{create soma[1]}
{create dendrite[107]}
{access soma[0]}
soma[0] {
pt3dclear()
pt3dadd(-0.42,3.55,0,7.887)
pt3dadd(-0.42,-0.39,0,7.887)
pt3dadd(-0.42,-4.33... |
8b8644f3cc406bf87fc214ffc67b1eec35c5ef809f8381063d647801ec1b7e74 | NEURON | 21,494 | 1,064 | // 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... |
068691a7c1da395f86b8fea50b973b0abbbcf1beb94abc29d2f350a3a2c3b271 | NEURON | 24,098 | 571 |
COMMENT
Outside-In Diffusion Helper (membrane mechanism)
Its job is to calculate and write "{species}o" based on the extracellular sources created by user with the Manager of Extracellular Sources
If you want to add new species (or delete old ones), look for 7 blocks of code below marked as "Edit... |
ff622bb35bcf5031bcd35483d1a145fdd5623fa407d553449572443463a4b120 | NEURON | 24,262 | 1,245 | // NEURON hoc file generated from CVapp (NeuroMorpho.org version)
// Original file: P32-DEV136.CNG.swc
// Generated Wed May 31 09:53:21 BST 2017
{create soma[1]}
{create dendrite[125]}
{access soma[0]}
soma[0] {
pt3dclear()
pt3dadd(0.23,5.83,0,13.226)
pt3dadd(0.23,-0.77,0,13.226)
pt3dadd(0.23,-7.38,... |
21829da134a56727fd80959c526a801809dd15b61b76adf22cdc886b5955c8b5 | NEURON | 24,318 | 577 |
COMMENT
Outside-In Diffusion Helper (membrane mechanism)
Its job is to calculate and write "{species}o" based on the extracellular sources created by user with the Manager of Extracellular Sources
If you want to add new species (or delete old ones), look for 7 blocks of code below marked as "Edit... |
3b3e8e72b62c5188501803a6eda524e86ffa73bc6155867a0dd0471dbdb93c4c | NEURON | 24,520 | 1,251 | // 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... |
d5f9b52386343be8e3ca3a295a8a1aaf60846dbae3ef1b5acaf92304cdda9999 | NEURON | 24,825 | 718 |
create dendrite[55]
proc celldef() {
topol()
}
create soma[1]
proc topol() { local i
connect dendrite[1](0), soma[0](0.5)
for i = 2, 4 connect dendrite[i](0), dendrite[i-1](1)
for i = 5, 6 connect dendrite[i](0), dendrite[3](1)
connect dendrite[7](0), dendrite[2](1)
connect dendrite[8](0), dendri... |
70688f4476f3d4460c6b96d0d4366f9db8c49961b5babf043f4a4fbd10c6a40c | NEURON | 25,040 | 722 | OriginalDendrite=55
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 dendrite[NumberDendrites]
proc celldef() {
topol()
}
create soma[1]
proc topol() { local i
conne... |
8b7d269567a49bd2627a4dba638e1099fa4150773ec74899206c648c25042c89 | NEURON | 25,219 | 1,302 |
create soma[1]
create dendrite[133]
access soma[0]
soma[0] {
pt3dclear()
pt3dadd(0.23,5.83,0,7.226)
pt3dadd(0.23,-0.77,0,7.226)
pt3dadd(0.23,-7.38,0,7.226)
} // end of points list
{soma[0] connect dendrite[0](0), 0.5}
dendrite[0] {
pt3dclear()
// Note: not adding point: (0.23,-0.77,0,13.226) on... |
f517c50e83cbdc3299c897bc6425f3778393f31a37a35d850ec91a90e1ad599a | NEURON | 25,436 | 1,308 |
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]
access soma[0]
soma[0] {
pt3dclear()
pt3dadd(0.23,5.83,0,7... |
8cbf384d060d68e34a79a56657b3e2f57fa7a3597e711ab36b2f49520d063e65 | NEURON | 27,570 | 859 | //
//************************************************************************************************************
//
OriginalDendrite=101
NumberDendrites=OriginalDendrite//397 //265 133 397
SeedNumber=OriginalDendrite-1//132 // Number of extra seeds equal to the number of the central dendrites
create soma[1]
create ... |
c7c601b3bf3dc79c772a04ba4701dfc004d7bbde13bff556962f90f4b5660a87 | NEURON | 30,444 | 692 | COMMENT
================================================================================
cadifus.mod -- Calcium diffusion in astrocyte / neuron radial shell model
================================================================================
Origin
------
Derived from the canonical cadifus.mod in Chapter 9 of:
H... |
6c47f713926165269440ddae6df7da1be5696652f5fe327906c369350b99aac1 | NEURON | 36,224 | 1,142 | //
//************************************************************************************************************
//
OriginalDendrite=145
NumberDendrites=OriginalDendrite//397 //265 133 397
SeedNumber=OriginalDendrite-1//132 // Number of extra seeds equal to the number of the central dendrites
create soma[1]
create ... |
0f69708c5a7a082caf2638b5a9216fdbccdc4467ba46abd56ce65e81bda2e9d6 | NEURON | 48,295 | 1,206 | // Original File: /Volumes/research-data/PRJ-Hoferlab/icamplab/Phillip PhD/Imaris/20200515 Imaris analysis all ages/1 mo/WT/247318 IL6 WT/Cortex/247318 gfil6 wt 20x cortex iba1 1.ims
// Generated by Bitplane Imaris 9.9.0 [Mar 11 2022]
// Date: 2022-05-17
strdef neuron_name
neuron_name = "Filaments 2"
create filament... |
d4621aac47fdd7e49142a8522c305c5dc2e2df1ff7f63f536b64b063961a8525 | NEURON | 77,937 | 2,915 | // 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
{create soma[1]}
{create dendrite[172]}
{access soma[0]}
soma[0] {
pt3dclear()
pt3dadd(-3.49,7.12,0.02,15.88)
pt3dadd(0,0,0,15.88)
pt3dadd(3.49,-7.12,-0.02,... |
54e5563675ac2ceb7743c5a3b45ac9c913948016f10d1f0ac07fa33bfc048908 | NEURON | 78,196 | 2,922 | // 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/... |
1d3f17868f1dfcb5710b53c8e64e8901681c3412a0a2e46b684ca71d723d20b4 | NEURON | 200,000 | 2,513 | //////////////////// Table of contents ///////////////////////////////////
/*
Line 30: Version info
Line 47: Params
Line 57: Utils
Line 259: Sections
Line 288: Imported section names
Line 304: Section references
Line 351: ... |
2e49e5c99697d95e71fd91b854e95c3dd80715abafacf69e2d4b9893875f1d10 | NEURON | 200,000 | 4,497 | create soma
create dendrite[19057]
access soma
connect dendrite[0](0), soma(0.5)
connect dendrite[1](0), dendrite[0](1)
connect dendrite[2](0), dendrite[1](1)
connect dendrite[3](0), dendrite[2](1)
connect dendrite[4](0), dendrite[2](1)
connect dendrite[5](0), dendrite[4](1)
connect dendrite[6](0), dendrite[5](1)
conne... |
6505147fa38ef031c0064a1116edf49b72cc0aba070fe45bf6f3e889199ba415 | NEURON | 200,000 | 5,302 | /*
This is a CellBuilder-like file written for the simulator NEURON
by an automatic procedure "neuron_tree" part of the TREES package
in MATLAB
copyright 2009 Hermann Cuntz
*/
proc celldef() {
topol()
subsets()
geom()
biophys()
geom_nseg()
}
create soma[1]
create axon[879]
create dend[216]
proc topol_1() {... |
7612ddc99dc23811ec8db4cf49eb95423295f2355edab94108daa89dcb3f4da7 | NEURON | 200,000 | 5,362 | proc celldef() {
topol()
}
//************************************************************************************************************
//
OriginalDendrite=145
NumberDendrites=OriginalDendrite+2*(OriginalDendrite-1)//397 //265 133 397
print NumberDendrites
SeedNumber=OriginalDendrite-1//132 // Number of extra see... |
c5d7116d8427b6e4393581861fd6665a2b564f8e36b87716fedf5e60507927a5 | NEURON | 200,000 | 5,646 | proc celldef() {
topol()
geom()
geom_nseg()
}
create soma, dendrite[144], LargeGlia[10000], SmallGlia[10000]
proc topol() { local i
for i = 0, 10 connect dendrite[i](0), soma(0.5)
for i = 11, 12 connect dendrite[i](0), dendrite[1](1)
for i = 13, 14 connect dendrite[i](0), dendrite[2](1)
for i = 15, 16 c... |
d3feca55da279e8a47e8373fb6a79f73b686116bf345bfcd4cb2750516378b23 | NEURON | 200,000 | 2,508 | //////////////////// Table of contents ///////////////////////////////////
/*
Line 30: Version info
Line 47: Params
Line 57: Utils
Line 259: Sections
Line 288: Imported section names
Line 304: Section references
Line 351: ... |
d5d2b577654c463978ad55d14aba4e7aaf69051b65b90912a014df1022c9da9b | NEURON | 200,000 | 5,598 | /******************************************************************************
Cell morphology of a CA1 pyramidal cell taken from
Golding NL, Kath WL, Spruston N
Dichotomy of action-potential backpropagation in CA1 pyramidal neuron dendrites
J Neurophysiol (2001) 86:2998-3010
**************************************... |
f2e5a3a9d733d24200117b16311b00f83fbeacfeff2cc98b37560717cf105723 | Perl | 524 | 26 | #!/usr/bin/env perl
## Quick-and-dirty way to prepend copyleft.
$#ARGV >= 1 || die "usage: prepend-notice.pl <notice> <file 1> [<file 2> ...]\n";
$copying_src = shift @ARGV;
print "## applying notice in $copying_src\n";
$copying = `cat $copying_src`;
foreach (@ARGV) {
if (/^${copying_src}$/) {
print STDERR "... |
69c9bfa5e1617cc970e3ff73e7a70a72fbcf4f58edd2ba18a784a8b2009d7ec6 | Perl | 536 | 24 | #!/usr/bin/perl
# script to modify FASTQ header lines for Trinity program
# Hidemasa Bono <bonohu@gmail.com>
my $c = 0; # line count value
my $strand = shift(@ARGV); # 1 or 2
print STDERR "usage: % perl for_trinity.pl 1 (or 2) < SRA.fastq > processed.fastq\n" if ($strand eq '') ;
# STDIN: FASTQ file
while(<STDIN>) {... |
5af8f1ce38a0a2a48067310ee9f62f05eaedc54f4bbfb1a216b9195eb01e640e | Perl | 608 | 31 | #!/usr/bin/env perl
use strict;
use Getopt::Long;
my ($reference,$query,%Reference,$out);
# >>> GetOpts
GetOptions("r=s"=>\$reference,
"q=s"=>\$query,
"o=s"=>\$out) or die("Error in command line arguments");
# >>> Build Reference Hash
open(FILE,"$reference");
while(<FILE>){
if(/(chr.*)\t(\d*)\t(\d*)\t(\d*)/){ #$2... |
232f292d0aa062f737394469de8200463749196f13986c763701b84561454b00 | Perl | 671 | 19 | # Copy until the first xml comment, which leads into the annotation property section
while (<>)
{ last if /[<][!]-- / ;
# Add versionIRI
if (m'<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/iao/import-OBO.owl"/>')
{ s'OBO.owl"/>'OBO.owl">';
print $_;
print ' <owl:versionIRI rdf:resource="... |
cc6f3d88c569715d38a3c34327d87c57dab3d59afe6b797ae3c6219e4abd6eed | Perl | 995 | 31 | #!/usr/bin/env perl
sub p_inc {
$DateiName = shift;
if ( open (my $datei, "$DateiName") ) {
print "%%%---------- open: ", $DateiName, "\n";
while (<$datei>) {
if ((/^\s*\\include\{\s*(\S+)/i) or (/^\s*\\input\{\s*(\S+)/i)) {
my $include = $1;
chomp($include);
... |
76dcf09c2a93f34dd42c6188e234fe42a75dc482d932713d0502108d8e2b81d4 | Perl | 1,317 | 68 | # perl assemble.pl master_genotype_vcf query_bed expression_file covariate_file
$geno_vcf = $ARGV[0];
$query_bed = $ARGV[1];
open FILE, "$ARGV[3]";
while(<FILE>){
next if $_ !~ /\d/;
my @data = split /\s+/, $_;
shift @data until $data[0]=~/^\S/;
if (/\s*ID/){
shift @data;
@id_list = @data;
... |
1ba2a18ffa0cc8e158bdd8535f174f8415a2ea039f8564abb3fe5b1ca37bfee3 | Perl | 1,357 | 56 | for ($i=0;$i<=$#ARGV;$i++){
if($ARGV[$i] eq "-e"){
$expr_file = $ARGV[++$i];
next;
}
if($ARGV[$i] eq "-g"){
$geno_vcf = $ARGV[++$i];
next;
}
if($ARGV[$i] eq "-c"){
$covar_file = $ARGV[++$i];
next;
}
if($ARGV[$i] eq "-t"){
$tissue = $ARGV[++$i];
next;
}
... |
639de660b4961741082d08d7acf0b87e3fed870519512702c639179044606986 | Perl | 1,912 | 56 | # The script used to replace the IRIs of BFO 1.1/RO terms with those in BFO 2.0. Since the replacement using the pattern,
# be careful for the terms which shared the same pattern, such as
# http://www.obofoundry.org/ro/ro.owl#has_participant
# http://www.obofoundry.org/ro/ro.owl#has_part
# Need to replace "has_par... |
540d5be7e1c00095da2812d77725a4a6927501ac2d7f773637dfc6aca53e956c | Perl | 2,186 | 93 | #!/usr/bin/perl
use strict;
use Getopt::Std;
our ($opt_h,$opt_v, $opt_c, $opt_l, $opt_f);
getopts("hf:vlc") ;
&usage if $opt_h;
sub usage {
die "RunMeta.pl -f <fofn>
runs metasoft twice, second time processing the log file to acquire mean and hetero corrections
\n";
}
sub SpawnProcess {
my ($command) = @_[... |
3e8722f7397746ea9ad12707a000411ed1503480a1e369903c80d82efcf66814 | Perl | 2,210 | 102 | #!/usr/bin/perl
use strict;
use Getopt::Std;
our($opt_h, $opt_p, $opt_o, $opt_s, $opt_d, $opt_f, $opt_v, $opt_m, $opt_c, $opt_P);
getopts("hp:f:cm:vP:o:d:s:");
&usage if $opt_h;
my $fofn = $opt_f;
my $option = 0;
if ($opt_v) {
$option = 1;
}
if ($opt_c) {
$option = 2;
}
my $AllowedPhenotypes = {};
$AllowedPhen... |
abec48ef05921667d4dee22485fb9388599b501e63067413b2cc9c50c8bf327e | Perl | 2,928 | 98 | #!/usr/bin/perl
# check_spaces.pl : Check source files for tabs and trailing spaces
#
# Author : Rob Davies <rmd@sanger.ac.uk>
#
# Copyright (C) 2018-2019, 2022 Genome Research Ltd.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation f... |
530d50deaae8174bbba0bfbf332993240404021329cfbbc341606ad1d50ceb53 | Perl | 3,206 | 114 | ###############################################################################
#
# Filter tandem polyA sites by length
#
# AUTHOR: Ralf_Schmidt
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: mihaela.zavolan@unibas.ch
# CREATED: XX-XX-XXXX
# LICENSE: Apache_... |
c14e8677939bc72682027679f7f7938e79c4905337b2afb62e213a76de86dcc0 | Perl | 3,237 | 99 | #!/usr/bin/perl
# check_copyright.pl : Basic source file checks for copyright boilerplate
#
# Author : Rob Davies <rmd@sanger.ac.uk>
#
# Copyright (C) 2018-2019 Genome Research Ltd.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation f... |
14072cea506966080ccc0981b5d306e9033a1be137d0466a76c81443ca404a59 | Perl | 6,259 | 181 | use strict;
use File::Copy;
# Rewrite the old OBI namespace into new purls. Beware UGLY HACKS below
# Policy here. TBD.
my $idNamespace = "http://purl.obofoundry.org/obo/"; # conservative, but less elegant: http://purl.org/obo/OBI/. Current OBO practice: http://purl.org/obo/OBI#
my $namedclassNamespace = "http://purl... |
7c82739eaa9e94c732b2ad0c47012a281a5eb546f7c2652a1e0273b603858ce1 | Perl | 7,981 | 330 | #!/usr/bin/perl -w
use warnings;
use strict;
use POSIX;
use Getopt::Long;
use File::Path;
use File::Basename;
use Pod::Usage;
=head1 NAME
Generate SFBA Makefile
=head1 SYNOPSIS
./gen_mkf.pl [options]
Options:
-h help messages
-d degub
--mf output make file
=head1 OPTIONS
=over 8
=item B<-he... |
2120f3c27856e8af5b8bafea8fcc4dbdee27a6b0cb4677edad0ec35b9a48e8e1 | Perl | 8,261 | 270 | ###############################################################################
#
# Intersect tandem poly(A) sites of terminal exons with the annotation.
# Only retain exons that can be associated to a gene unambiguously.
#
# AUTHOR: Ralf_Schmidt
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institu... |
f9546113e7d83a97b5cd95749dc355a309fe568b254eb3c816b7ee0e5ed90555 | Perl | 8,879 | 290 | ###############################################################################
#
# Intersect tandem poly(A) sites of terminal exons with the annotation.
# Only retain exons that can be associated to a gene unambiguously.
#
# AUTHOR: Ralf_Schmidt
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institu... |
f9d2829f5e487e3b6cf3857b2eb7a727839e0ff2ad5f11cbfeda61f84ed0f7b9 | Perl | 9,964 | 323 | #!/usr/bin/env perl
#
# Copyright (C) 2012-2013 Genome Research Ltd.
#
# Author: Petr Danecek <pd3@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, i... |
da85d23a15e9b9f86b2f7c9d13de614cb8fdb4c0ef63861fb4d9be54166b27e3 | Perl | 11,341 | 327 | #!/usr/bin/env perl
# The MIT License
# Copyright (c) 2014, 2020 Genome Research Ltd.
# Author: Rob Davies <rmd+sam@sanger.ac.uk>
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without re... |
d074de7fec8270afd6a68b9aaae70add53eddca0031217ebd092b46b8cc7a93c | Perl | 13,503 | 339 | #!/usr/bin/perl -w
use strict;
use Getopt::Long;
use Pod::Usage;
use FindBin qw($Bin);
my $NES_profile = "$Bin/NES_profiles_trained.txt";
my $threshold_score = 2;
my $cut_off = -10;
my $notout_predicted_NES = 0;
my $help;
print STDERR "$Bin\n";
GetOptions(
'profile|p=s' => \$NES_profile,
'minscore|ms=i' => \... |
a88264b08da637a7ec1dd29eaa5c0491845c86783a21d22670fad573a866549d | Perl | 15,095 | 455 | #!/usr/bin/perl -w
use warnings;
use strict;
use POSIX;
use Getopt::Long;
use File::Path;
use File::Basename;
use Pod::Usage;
=head1 NAME
Generate bfGWAS Makefile
=head1 SYNOPSIS
./gen_mkf.pl [options]
Options:
-h help messages
-d degub
--mf output make file
=head1 OPTIONS
=over 8
=item B<-h... |
c586f0d7b3a327a43cea2e9c8e32a152873409b695e71131b83007c2776256d5 | Perl | 15,158 | 517 | ###############################################################################
#
# Select only poly(A) sites which may be categorized as proximal/distal.
#
# AUTHOR: Ralf_Schmidt
# MODIFIED BY: Mihaela Zavolan
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: mi... |
4609a10fd62628af4c8722d29cbe7e6c6d76d8ecf3be15551bbe211901d1091f | Perl | 16,479 | 552 | #!/usr/bin/env perl
#
# Copyright (C) 2009, 2010 Genome Research Ltd.
# Portions copyright (C) 2010 Broad Institute.
#
# Author: Heng Li <lh3@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to... |
b83e888e8062e7dccb0d2ac45b6c0137f12e9b670bcb033aac59cd69f7dc799a | Perl | 96,931 | 2,452 | #!/usr/bin/env perl
#
# Copyright (C) 2013-2015 Genome Research Ltd.
#
# Author: Petr Danecek <pd3@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, i... |
f2ac6ce2aaac1a529cd00e0aafb055fb6d67017f2043438aa328bad161ba907f | Perl | 200,000 | 4,058 | #!/usr/bin/env perl
#
# Copyright (C) 2013-2026 Genome Research Ltd.
#
# Author: Petr Danecek <pd3@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, i... |
76a71fbef8a8339fcbcaff8c9aadfb85c834bc3cc0c07069a5ebb2eea3d90d68 | Python | 2 | 1 | ## |
b6a6598d4bc7516d17d5d90c04410b5071a91690d2defd156466fb2af813643d | Python | 15 | 1 | u = "🦜🔗"
|
353ec15e9a6fb6c64c9be1a25201667c5bfd8bfda9395d9e83b737f2341b6fd0 | Python | 16 | 1 | import psycopg2
|
5721bcabb657f2d626f68f7b64b6b286765474d72d23a7ffcab1b5426b1808e2 | Python | 17 | 1 | from . import pde |
673e86cb990614521f5409c6d1ae9ce28be2e5733d29985e18a699fdf15b9866 | Python | 17 | 1 | """Jira Tool."""
|
7aaaaef477792a263dfb4e17dbff5a7082c8d9b4a1812a8dc4916c43b726f43c | Python | 17 | 1 | """SQL agent."""
|
02865a7239b3673b520cd8a9b3d0a0d18c91df7aa43aaa9b84dcc843ef31541b | Python | 18 | 1 | from . import loss |
3b77e7fc048313e783714dc5b0168f4e62c757be6184c4b873abf6ab3ada9391 | Python | 18 | 1 | """Sleep tool."""
|
4fb67dcf0f7f6b07f9fabd24131bebcb66b26f3c449e90dbe52c8b3a9042d9dd | Python | 18 | 1 | """Json agent."""
|
5dbbbbcd0b87c9a57dd1c095945b75c93288a95ce9cf888962db8bd756983f57 | Python | 19 | 1 | from .opt import *
|
8b090ec972a3fc7f8f52a81e78947b22eded98e0aecb90ef71b7b7f41560396f | Python | 19 | 1 | """GitHub Tool."""
|
ea64d626b9e7bf400e237c69e81c1a743d4c925edfdc43b9e96e41953eab01be | Python | 19 | 1 | """GitLab Tool."""
|
20904f6e91d45cf145976fa962f442683833e8d2927e92847937b3ae15be4901 | Python | 20 | 1 | """NASA Toolkit."""
|
55e7bcac44acbad96c0f0e202c45124f85fe0875d2d03c12953cda39b3691664 | Python | 20 | 1 | from . import solver |
83b97c10f09751d74ffbf0223bd86e111702ff1da40fe75fae862651ef0ef08d | Python | 20 | 1 | """Jira Toolkit."""
|
2d296b601bb10f9c098b66ba4e07e8f9796610b9366423007c5e7b31843179f9 | Python | 21 | 1 | from .gcl import GCL
|
4917c5ee80d594e3808ba9c62a224850ae81fdaaea60b3bd892329fb6219669b | Python | 21 | 1 | from .models import * |
88e320c560add054cd2cc36ad3049c81237f61d041abee7a54cea3d1477c1a92 | Python | 21 | 1 | """Steam Toolkit."""
|
94f66fac5aef5b5da0bb0ec17faf2031ee4eb1f1eb44fb6b6851159a3e9fcada | Python | 21 | 1 | from vmdpy import VMD |
d18d8fd5de54172b1f583c705266fdf092c260d1e8401b351a7c729d6192473f | Python | 21 | 1 | """Gmail toolkit."""
|
e99ec6a5c243e85c2e14a75cbca26f21f845bc98a2cbd23b19cd4c48428995cc | Python | 21 | 1 | """Slack toolkit."""
|
141c50c6c93c3bd9f84d70995c7416ffed35d697552b7ff774dfb278b18f4231 | Python | 22 | 1 | """GitHub Toolkit."""
|
3c51af34c9cc617c8591359785a535839e09cab4a6553bdf0abc8ec0b572b03f | Python | 22 | 1 | from .escn import eSCN |
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