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50f766ba33c6110184b09217badf97efb6a25b74c17bd390af2c12a789dfaf03 | Text | 660 | 19 | # GNN Parametrized Forcefields
## Description
Repository for the models used in the publication ['Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions'](https://arxiv.org/abs/2206.00355).
## Multipoles
The model was trained to be used in conjunction w... |
bb3a6adcf368b867c8935558c4e140d4307037a1eef7521afaa7324cba05b8c7 | Text | 662 | 7 | # BrainWAVE
Code to program and run flicker stimulation on a BrainWAVE stimulator device.
The Arduino folder contains code that can be used with an Arduino Uno or modified for use with another Arduino.
The NIDAQ folder contains code that can be used with a National Instruments Data Acquistion (NIDAQ) device.
The Beha... |
3bc12c82b0792dec429ca85867de31259a659e2249302cf25c60b86d800285f8 | Text | 674 | 8 | # topological-bone-analysis
This code can be used for topological microstructure analysis of greyscale images.
The method binarizes the images (Otsu method), cuts the images into non-overlapping patches (discards fully blank patches) and uses persistent homology with a signed Euclidean distance transform (SEDT) filtra... |
278f686a76d9b93505d4c2d380d240acc6ccdf6c7efd94a218c07de27445e463 | Text | 678 | 42 | # PCR-Prediction
## Introduction
Predicting dynamic trends in PCR amplification curves in advance using a deep learning model.
## Prerequisites
- Linux/MacOS/Windows
- Python 3.6+
- CUDA
- Tensorflow-gpu Keras
## Installation
1. Create a conda virtual environment and activate it.
```shell
conda create -n pcr_predi... |
1f149cc6e2d4c5980847291a1424427f7f1f244ed5c06a2963fbe0e796de2eb6 | Text | 679 | 6 | # Coding_gene_function_annotation
This script was used to annotate the function of coding genes in our "Genetic mapping and molecular mechanism behind color variation in the Asian vine snake" research. (Chen-Yang Tang†, Xiaohu Zhang†, Xiao Xu†, Shijie Sun, Changjun Peng, Meng-Huan Song, Chaochao Yan, Huaqin Sun, Mingfe... |
c4952b143574e95b0ae009b242a4838d6a878ad07015297b667f486f9608802a | Text | 687 | 11 | <!-- badges: start -->
[](https://zenodo.org/badge/latestdoi/490042485)
<!-- badges: end -->
# ASD_PPI
Documentation for analysis scripts used in the ASD PPI paper:
Pintacuda G*, Hsu YH*, Tsafou K, Li KW, Martín JM, Riseman J, Biagini JC, Ching JKT, Mena D, Gonzalez-Lozan... |
f6d3d8ffccabb1ae3f41a6116af518b831bbdf6c5600441fb6f16f7d907107fc | Text | 690 | 9 | # Zvolanek_2022
Code to accompany manuscript: "Comparing end-tidal CO2, respiration volume per time (RVT), and average gray matter signal for mapping cerebrovascular reactivity amplitude and delay with breath-hold task BOLD fMRI"
doi: <https://www.biorxiv.org/content/10.1101/2022.11.28.517116v1>
_Please Note:_ The cod... |
6c170f756def08bc100dcb4850c3f4edba7a3faaa1ac3b91919b5d434db2e3b4 | Text | 704 | 7 | # This repository contains code used in the following paper:
# Title: Multimodal brain age estimates relate to Alzheimer disease biomarkers and cognition in early stages: a cross-sectional observational study
# Authors: Peter R Millar,1* Brian A Gordon,2 Patrick H Luckett,3 Tammie LS Benzinger,2,3 Carlos Cruchaga,4... |
cac850cded2d41ab406653a1b3dd8b66ff640c6581e560c92c46e0ea01b20716 | Text | 705 | 11 | # OptEpiDeepL
Codes for "Shuangshuang Yin, Jianhong Wu, Pengfei Song. (2022) Optimal epidemic control by deep learning techniques and its applications on epidemic models, Journal of Mathematical Biology."
All the source codes are in `src` folder.
The output is in `output` folder.
To run the codes, install ... |
29598ba577b98402f1a72b756a3af5ab37dcd1c1d01c848948dc07d1b82795b6 | Text | 716 | 19 | 
# StarLZW
LZW code and demos to show how to extract compression index from binary data. Updated March 2018 (May 2017, Feb 12 2017) to match TN00344 ... extended to Python 3 and can be used as a library.
For more info see: https://arxiv.org/abs/1707.09848
_______... |
89e353c8e6528625bb3a708a8771d1c2d4a7a04e36f367b1074d1d2f18172900 | Text | 725 | 6 | ### Circadian parameter analysis and data visualization
This is the GitHub repository for the calculation and visualization of circadian parameters used in Asano et al., PNAS in press.
Code provided here is specified to the dataset used in Yanagisawa/Funato lab in IIIS, but may be helpful for those interested in casua... |
1998e6784456b9876f9d8cf57a79d8b289442890cf41946f432dc72ee98f1633 | Text | 727 | 12 | # NM-Competitive-Dynamics-Simple_Release
CD model simulated in Ali, Decker & Layton (Journal of Vision)
To get started, [download the Switch Experiment optic flow dataset](https://osf.io/td4as/?view_only=204c48fdb03e4452b41dd5a7fce79ceb) (1.2G). Unzip data.zip to the base project directory, replacing the data subd... |
d3d0cd87f4f009c071fad0129c5a0ee12ffe4b2d166a9b9ce0b10f7757602e2a | Text | 731 | 14 | # SeahorseR
This package contains code used in the manuscript:
Videlock et al. *Distinct patterns of gene expression changes in the colon and striatum of young mice overexpressing alpha-synuclein support Parkinson Disease as a multi-system process*, Journal of Parkinson's Disease
This code draws heavily on code deve... |
e7b760ac495f936738a0899387e19900a9c967d04470abf65207af9a19a5dc93 | Text | 753 | 25 | [](https://zenodo.org/badge/latestdoi/594055438)
# Neural knowledge assembly in humans and neural networks
This repository contains the official implementation of the neural network simulations of the [Neuron](https://www.cell.com/neuron/home) paper "Neural knowledge asse... |
2232773476bf2d9e12bc99a1e9626295952cf4cc0f79b14311c38844909d2f2d | Text | 759 | 4 | # separationRNAseq
Code for behavioral and transcriptional analysis associated with "Prolonged partner separation erodes nucleus accumbens transcriptional signatures of pair bonding in male prairie voles" published at eLife [doi:10.7554/eLife.80517]. All code was produced by the first author Julie M. Sadino in R for us... |
763f600ad885f0217d8c6d1eece634da6d542c918623dbdef38e838e999f74cb | Text | 769 | 14 | # Code accompanying Bimbard et al., Nat. Neuroscience, 2022
Code to reproduce the figures from Bimbard et al., 2022, "Behavioral origin of sound-evoked activity in mouse visual cortex".
Companion data is available on [Figshare](https://doi.org/10.6084/m9.figshare.21371247.v1), and follows the [ONE filename convention]... |
40e1ffcc7ff6c0f14c3f764db0db787ab3cbb25449bdb7b933a49e3dd05fa7b5 | Text | 780 | 28 | # COVID-19 MLP
The repository contains code for modeling the COVID-19 spread, using location and time data, by using a Multilayer Perceptron (MLP) Artificial Neural Network (ANN).
The repository is split into four directories:
## Input Data
[Data as used for training, obtained from COVID-19 Data Repository by the C... |
08ad304556a36fa587e5df42abe710cdbee136107b99a126f29edaf0d8094747 | Text | 787 | 20 | # HF_iScience
Scripts for "Single-cell RNA sequencing identifies hippocampal microglial dysregulation in diet-induced obesity"
## Description
Data were collected after mapping all fastq files to the mm10 genome with the cellranger version 4.0.0 software with default paramaters by using "cellranger count".
## Required ... |
3412fbe0f1a5a94f8dff1eabf2d880ab369de66e34c5f5e51d6fb0d616634c98 | Text | 800 | 15 | # CZI spectral imaging: loading into MATLAB
Loading and handling of spectral imaging data from CZI format using bioformats.
Project developed for user support at the [Centre for Cellular Imaging](https://cf.gu.se/english/centre_for_cellular_imaging) of [Gothenburg university](https://www.gu.se/english).
# What is in... |
7665c3e52279cf14afbbaf8f7e203b45e064284bcc6b382f8dcbe5dd9d3986a5 | Text | 800 | 11 | # BPARC
Supervised brain parcellation framework for encoding spatiotemporal brain dynamism using fMRI data.
Note: This repo will be update very soon.
## References
<a href="https://ieeexplore.ieee.org/abstract/document/9288154">[1] Kazemivash, B., & Calhoun, V. D. (2020, October). BPARC: A novel spatio-temporal (4... |
45574bdcc5faa66ac596bada0fde5a5198728023139d456a48d2de2b0a4ec3ac | Text | 806 | 11 | # palamedes_wrapper
A handy wrapper function for the Palamedes toolbox, with a focus on using its adaptive procedures.
You must have the Palamedes toolbox (http://www.palamedestoolbox.org/) installed and in your MATLAB path.
With these functions you will be able to flexibly choose the threshold level of task performan... |
49c41aa6be9a76bdf06873978c4fa101ca23b9ba4f55c49639f3b5db16e0b91a | Text | 817 | 20 | # HBCP Semantic Prediction
The repository for the HBCP semantic-enhanced prediction system.
We aim to develop an interpretable system for prediction of outcomes from behaviour change interventions using the Behaviour Change Intervention Ontology and a corpus of annotated literature.
# How to run the rule prediction... |
6e7e962d00f23765090006720e1ddac487375007e81ccb1cf717b0a4337d1622 | Text | 823 | 14 | # Code accompanying Bimbard et al., Nat. Neuroscience, 2023
Code to reproduce the figures from [Bimbard et al., 2023, "Behavioral origin of sound-evoked activity in mouse visual cortex"](https://www.nature.com/articles/s41593-022-01227-x).
Companion data is available on [Figshare](https://doi.org/10.6084/m9.figshare.2... |
7b204f6eda34c1709340471f1963616912fdf3f410bb50c44da5e29f8a8e0cdb | Text | 832 | 21 | # Feature Aligment
Code for the paper: *Feature Alignment for Approximated Reversibility in Neural Networks*
https://arxiv.org/abs/2106.12562
Each folder has the same files, but shaped for different data sets.
The file *training.py* contains the main code which should be executed.
The file *networks.py* contais the ... |
71f99d6732a18e1ba8c1690425157c53899daa139d087ac49bcb7960a3199383 | Text | 843 | 25 | # Neurons learn by predicting future activity
This is code to reproduce our results from manuscript: "Neurons learn by predicting future activity":<br/>
https://www.biorxiv.org/content/10.1101/2020.09.25.314211v2
To run CHL_clamped.py, go:
```
python CHL_clamped.py
```
*for this code, please install pytoch.
*This ... |
3639c174fba21b2fb776fbdbd6201219e8e8b3a0c10c0b351f2bf02f3f221503 | Text | 858 | 18 | # MultiAreaOptoMarmo
Code to reproduce figures from our manuscript "Multi-area recordings and optogenetics in the awake, behaving marmoset".
https://www.biorxiv.org/content/10.1101/2021.10.30.466578v1
## Software requirements
- Matlab (R2020b and R2018b tested on Linux and Windows)
- [CircStat toolbox for Matlab](http... |
7168b202440d694764a140dc072e358c4e3000a3e6ad0a07b9a1d939166c7668 | Text | 874 | 9 | ### Data and code for [Tran-Van-Minh et al. 2023](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0278053)
Do you have rabies tracing data? Are you planning to acquire some? Read the paper and try our code. The [pdf version included here](https://github.com/ranczlab/Tran_Van_Minh_et_al_2023/blob/main... |
d5bd6ce1e64facdf9907dc16b4c9f8fe6ebab1b21b2271cbe806923464abb423 | Text | 883 | 20 | # Application-of-neural-network-based-image-analysis-to-detect-sister-chromatid-cohesion-defects
This repository will be the sample code for the title paper.
It includes the following
1. Data : Chromosome images of WT cells and CTf18 -/- cells for classification
2. Models : Trained models to classify three classes ... |
e23652ab16a37bfe83d7e76cc8b43b1213ad3d3d637e01f119e2a265c6bb13f3 | Text | 902 | 16 | This is a brief introduction to how to use the kinematics classification model based on random forest classifier.
1. Firstly, prepare the kinematics file of your impacts, follow the example_kinematics.mat.
The file should contains a structure variable (1*N, N is number of impacts) named impact, each including at l... |
73666c16f3bd8301dde361343d44505e6b77c1f0068da08ab944ad02f5acbb87 | Text | 923 | 14 | # DeepHybridLearning_RadiotherapyQA_Depository_ManuscriptID_Diagnostics
The python codes above are the one used in the manuscript "Deep Hybrid Learning prediction of patient specific quality assurance in radiotherapy: implementation in clinical routine" published in Diagnostics.
PMID: 35008198.
- "Complexity_index"... |
193cfa15727db3bd35827408372aa34bbc8f7619177f3b9f8a6c67994b2a1f7d | Text | 937 | 30 | # raman-fitting
Uses `skimage`, please install it with pip:
```
pip install scikit-image
```
If you want to run the demo, you will also need `matplotlib`:
```
pip install matplotlib
```
## Usage
```
from fitting import fit_spectrum
fit_spectrum(spectrum, ref)
```
where `spectrum` is the spectrum we would like to tra... |
78b00969691708a54f8bcbe80e6c3ad5b58918e1b31bdfb2362a684f69a3f29a | Text | 952 | 13 | # Analysis pipelines for fungal genomic analysis
This repository contains workflows used by the Fungal Genomics group in the Infectious Disease and Microbiome Program (IDMP), the Broad Institute of MIT and Harvard.
Each directory in this repository corresponds to a workflow. Workflows are written in [Workflow Descript... |
2e8c2c62fb1805c19d0995bc0aa3ae8ba2fd52627ffbe77aff7a300b359c5887 | Text | 953 | 20 | # Functionality of the time resolved partial directed coherence (TPDC) code
System requirements:
- Windows 7 and newer.
- Tested on Matlab2011 or later
- Matlab should have the Signal processing and Communication, Math, Statistics and Optimization toolboxes (with Licenses).
- The arfit tollbox is also required (htt... |
947e4117f9fb1b02c137b972850beb66f85de7da730cda465838cd8a256c11b8 | Text | 955 | 15 | # 4DFlowNetv2
Refined adaptation of Super Resolution 4D Flow MRI using Residual Neural Network. This repository supplements the article [Super-resolution 4D flow MRI to quantify aortic regurgitation using computational fluid dynamics and deep learning](https://doi.org/10.1007/s10554-023-02815-z).
This is a refinement ... |
f5bfe9ef9adca1471086514e884b6fba4a4c657946473891d7f5fb6689984a0c | Text | 955 | 19 | # BIDSKIT
Python utilities for converting from DICOM to BIDS neuroimaging formats.
The *bidskit* console command takes a directory tree containing imaging series from one or more subjects (eg T1w MPRAGE, BOLD EPI, Fieldmaps), converts the imaging data to Nifti-1 format with JSON metadata files (sidecars) and populate... |
3f4a32454d4c2d0abf4f3c1b438c8d72ffe0ee2747c03a39667e11d069dc2c6a | Text | 960 | 23 | # MI-OpenBCI
You will find here the raw EEG and EMG data acquired by using the OpenBCI kit, as well as the OpenViBE scenarios and the Matlab Codes used for the protocol display and post-processing, respectively.
# Database
The clean database, ready to use for further decoding algorithms can be found [here](https://gi... |
7e0f813a4dea1664d3d85d9920028b197345823822a1b8ee3421fd389ff5e935 | Text | 963 | 31 | # PV-RNN
The simulation experiments of flexibility task using PV-RNN model.
## How to run.
```
python main.py
```
## Hyper parameter setting
You can change learning and test conditions by editing `config.py`.
Don't forget to change the output directory. The setting of output directry is in `out_dir_name` in `conf... |
3188ec786e744f4c65ecef0519d29994871493c1996aced7267fa99e7886ed4b | Text | 964 | 26 | # sleep_net
ANN models trained to predict sleep stage based on z-scored LFP power spectra bands
## MATLAB Installation
Download the models packaged as a MATLAB toolbox(.mltbx) from [Releases](https://github.com/UH3-RestoreSleepPD/sleep_net/releases)
> Requires the Deep Learning Toolbox
## Usage
- [importSleepNetHyb... |
38ec14b60edc3b961c521a79129d04f06638ba586117b316011c2dadad8ba897 | Text | 968 | 14 | This is the data and code to accompany the article title "The effects of developmental and acquired brain injury on finger coordination in children ages 4-12 years", by Mimouni-Bloch et al.
The data from the control group is from a previous experiment (Shaklai et al., 2017), while the data from the CP and TBI groups a... |
41959dbdc908e31152d7899177376dbdf40db79703258a94b0db2005d9af72de | Text | 973 | 27 | # Training Neural Networks with Mixed Integer Programming
This repository contains code that was used for experiments for Tómas Þorbjarnarson's Master's thesis at TU Delft which can be accessed here: http://resolver.tudelft.nl/uuid:27875d51-672a-4a78-9aad-c44236992518
## How to run
To run experiments:
<code>python ... |
303276ef915e7dcef00fc5f2c5dfce29d97863916ef3c30a21d74bb9ce399042 | Text | 976 | 19 | # Functional organization of social perception networks in the human brain
This repository contains scripts used for analyzing the fMRI data in the article:
"Functional organization of social perception networks in the human brain"
https://doi.org/10.1016/j.neuroimage.2023.120025
Consensus clustering anlaysis was pe... |
dd52e1e286591b2adeb62555a951471ca91f354d7af37738d7edcaffdd3d4639 | Text | 986 | 11 | %%% 27-01-22 first revision
%%% Benoit Duchet, University of Oxford
*************************************************
This package can be used to compute entrainment metrics in the sine cicle map and Kuramoto model, with periodic stimulation or dithered stimulation. The toggling approach is implemented in the Kuramot... |
63b203091d5927d1bac1d481bb4fdf58a9b878879263fbe0984c9634cec7f0e0 | Text | 988 | 17 | # ArtifactScanTool
## A MATLAB wrapper program for artifact rejection in the [Brainstorm Software Suite](https://neuroimage.usc.edu/brainstorm/Introduction)
### Documentation
[ArtifactScanTool Documentation](https://brainstorm-artifactscantool.readthedocs.io/en/latest/)
### Authors & Affiliations
Nicholas Christopher... |
a46496225fa50f0d8f9c769f8574143780ff73cc67bec305c6e9825337d1038b | Text | 989 | 14 | # deepdream
This repository contains IPython Notebook with sample code, complementing
Google Research [blog post](http://googleresearch.blogspot.ch/2015/06/inceptionism-going-deeper-into-neural.html) about Neural Network art.
See [original gallery](https://photos.google.com/share/AF1QipPX0SCl7OzWilt9LnuQliattX4OUCj_8... |
1c2cdd51aa25fea7616f8e92d18c475e9b73b02a66700577b67f2b99b19ce026 | Text | 998 | 21 | Metabrain
========
This repository contains code related to the MetaBrain project.
Contents
--------
**2021-deKleinEtAl/** contains code for the de Klein _et al._ 2021 manuscript "Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases... |
2d0a21254e2690daa9a678f3feb79b27a98ba501a2421a7f40834b1a23a11055 | Text | 1,008 | 19 | # Code for Van der Plas*, Tubiana* and colleagues, 2023 eLife
### Source:
https://elifesciences.org/articles/83139
and former bioRxiv preprint:
https://www.biorxiv.org/content/10.1101/2021.11.09.467900v1
**We welcome you to reuse this code, and ask you to please cite our eLife article if you do.**
### Instruction... |
08fb5d7ea2741c48b00e85a625aa276a6bed4d4f4c30e70646440912511ca070 | Text | 1,009 | 15 | All scripts and data used for CNN training on MD data studying curvature sensing by helical peptides.
When using this code, please cite:
Van Hilten, N.; Methorst, J.; Verwei, N.; Risselada, H.J., Science Advances. 2023, 9(11). DOI: 10.1126/sciadv.ade8839
This repo contains:
- data.txt The original data set with seq... |
bfe8ad1b7c885dca8f14e776a72187c0a7fa80d784da6349d8d1ad5c9b8770b3 | Text | 1,013 | 11 | # Documentation
Codebase for manuscript "Propagating spatio-temporal activity patterns across macaque motor cortex carry kinematic information"
To replicate the environment, you can either build your own image by using the Dockerfile_copy in the github repo (probably quicker, but their latest gpu environment might hav... |
f889a8b9b554626112aef30cc143566cf75c36d8fee8dbe69615641b6232ce50 | Text | 1,015 | 19 | # Deep Picker Suite
A bunch of programs that belong to the Deep Picker suite. Dawei can fill this in with something useful.
# Build
For local building of this application, please utilize the ccic/spindocker project and the associated
image at `code.osu.edu:5000/ccic/spindocker/spindev:latest`.
# Deployment
As th... |
84a070907ea6e57adafa362c19258f4cb0d86c0eb09145441882203c6a2e1a9b | Text | 1,017 | 20 | # gnn-fracture
Prediction and control of fracture paths in disordered architected materials using graph neural networks
## Pipeline
- To generate the Voronoi networks and their corresponding finite element meshes, run **generation/generateVoronoiLattices.py**. Adding the flag **--plot=1** plots each Voronoi network as... |
7b9d416f5f82a6dae880387d3a1da3e6eb3f1f5bd2fae826f48931bcaf1e2bd3 | Text | 1,021 | 10 | # BCI-beta-desynchrony_2021
This repository contains Matlab scripts to run a non-overlapping temporal window DICS beamformer source analysis on the MEG trial responses of a mental imagery BCI task. Scripts were prepared for a research work titled "Mapping & decoding cortical engagement during motor imagery, mental arit... |
654eab13ed956394ef701e3c253388767c2559d2aa4adfe5aa58531756f7b713 | Text | 1,026 | 21 | The tasks corresponding to each TTL window correspond to the CyberGlove filenames with task name and timestamp.
Example: Fourth TTL window corresponds to the task nHOC2 (no stim Hand Open Close Task).
First TTL window starts on the sample in the ECoG mat file.
ECoG_TTL.mat vars
- TTL contains TTL voltages ext... |
0b5fd2bf4027a5d665bf8dde3aa27deafc16e209efd4054ac511fda7bf9b7dbd | Text | 1,029 | 14 | # projection-scrubbing-paper
Public repository for code and selected results for the projection scrubbing paper.
`/code`: R source code for the analysis.
* `/analysis`: Analysis scripts contributing to manuscript. Numbered in order of execution.
* `/exploratory`: Analysis scripts which did not directly contribute t... |
44da3739a844e24c5c44ec1d98b750c1b871524d816a2fa66ca26e998ee53f28 | Text | 1,031 | 35 | Aalto ASR Tools
===============
Aku
---
Aku is the acoustic modeling toolkit of Aalto University.
Aalto Decoder
-------------
Decoder is a C++ library that reads a language model and a pronunciation dictionary, builds the search tree, and performs the actual speech recognition. It can be linked to a C++ program, o... |
d4ac2d44fff5e93f5c504f1d59bdc3b0a1bbf52b6ea2872720960ec8d7abbaca | Text | 1,031 | 43 | BIAS
*****
BIAS is a software application for recording video from IEEE 1394 and USB3
Cameras. BIAS was intially designed as image acquisition software for
experiments in animial behavior. For example, recording the behavior of fruit
flies in a walking arena.
|
.. figure:: https://bitbucket.org/iorodeo/bias/raw/de... |
b705c2d905a3942e697361aff06720366135f7d2630ea66569f9153311a2e453 | Text | 1,035 | 37 | # CNN-Siam: Multimodal Siamese CNN-based deep learning approach for drug‒drug interaction prediction
- `DDI.ipynb`: The code for DDI prediction task.
- `/Ranger-Optimizer`: Ranger optimizer sourece codes for PyTorch.
- `/data`: Contains `event.db` file, which includes 572 drugs with chemical substructure(smile for... |
8369366000400fde2530d3ed25aa8a729c98cd9ca2dd93cfc50acb4d0c02205e | Text | 1,053 | 15 | # NerualMassModellingToolbox
This repository contains code to generate figures and run the algorithms described in Dunstan et al. (2023) Global nonlinear approach for mapping parameters of neural mass models. doi: https://doi.org/10.1371/journal.pcbi.1010985.
The repository comes in two parts.
1. To provide a platfo... |
b532ac884874dad91168a88af669ba69081e8d0f624b1c8423670e7d81884a0b | Text | 1,054 | 12 | # TRACER - 3D
TRACER-3D is a useful toolbox for visualizing the trajectories of recording electrodes(e.g Neuropixels) through different sub-regions of the rat brain. Anatomical delineations are referenced from the Waxholm Space atlas of the adult Sprague Dawley rat brain (https://www.nitrc.org/projects/whs-sd-atlas). T... |
49c5614f67ce03d9ca2652cf5c70bb6f1c577de06074c590d22f0f033dc175d0 | Text | 1,065 | 9 | ## Code for reproduction of "Relating local connectivity and global dynamics in recurrent E-I network", Shao \& Ostojic
This repository provides the code to qualitatively reproduce the corresponding figures in the paper - create, simulate, analyse and visualize the locally-defined connectivity, low-rank approximation,... |
0f554e54eb25a3e5b3be561fc42828c3aaf0b1405ac1d66f7bd2969842b0fbc5 | Text | 1,067 | 21 | # !Repository Under Development!
<p align="center">
<img src="https://user-images.githubusercontent.com/56682642/156801158-44567c7d-85e0-4b08-ab52-2b01e710fa06.jpg" />
</p>
## automated-clavicular-epiphysis-localization
This repository contains Python scripts and Jupyter notebooks to localize the medial clavicular... |
2a7a57448eafb4f0e078abe901f0d507ffad6f3155b805968a770515ddd05670 | Text | 1,076 | 17 | This set of files contains the raw data generated by the study titled:
'Electronic excited states in deep variational Monte Carlo'.
The data for each results section (Sections II A - D in the main paper) is located in the respective *.tar.gz file.
For each calculation we have included the following data:
- hyperpa... |
05a41a694ead5d73ce56bc6a259b4fbc5547b53a249a659ff3a9e6594d691138 | Text | 1,077 | 25 | ## Supporting code for Multi-Plasticity Networks.
To reproduce results from the paper, see the directory "paper".
The code contained here can be used to construct networks with mutli-plasticity layers, including the two-layer MPN analyzed in the paper. The notebook `mpn_demonstration.ipynb` demonstrates the following... |
73d2aed1035c8f422f21ce14349b8bbc5ca96799afa94c0a7959096057f963f6 | Text | 1,088 | 31 | # NeuroML Websites
Source code and documentation for NeuroML-DB.org and NeuroML-DB Curator.
# Steps to start website:
## On dendrite
1. `cd /var/www/NeuroML-DB.org_Docker/`
2. `sudo -u www-data ./run.sh` This will (re-)build the docker image and start the website on port 8000
3. `/etc/apache2/httpd-nml2.conf` fil... |
03cd1e6c1d5316f44a6606307108c003e875f050850e83267387fb9ad8733afa | Text | 1,096 | 12 | # Sleep in the Intensive Care Unit through the Lens of Breathing and Heart Rate Variability: Code Repository.
This repository contains code and data used in the research paper "Sleep in the Intensive Care Unit through the Lens of Breathing and Heart Rate Variability: A Cross-Sectional Study".
Preprint:
In /sleep_s... |
e6295115bea8c48d0c11a5b7731b589aea2f5db77d2caa7b304c2e2d9b025dbe | Text | 1,107 | 18 | # stSCA_scripts
Analysis scripts used for stSCA manuscript
signal_proc_functions is a folder that contains custom scripts for various signal processing procedures used throughout the scripts
utah_maps is a folder containing spatial map of the utah array channels. They are specific to the site of data collection (i.e.... |
00f071f56cbbd095d3509fe6c762fe7755e6bc8e84716a3aa388e8e476c732ad | Text | 1,117 | 10 | # LocoMUA_MLR_SCI
Import EMG data from Spike2 for analysis in MATLAB 2013b.
These scripts were written for MATLAB by Maxime Lemieux, research assistant in the laboratory of Prof. Frédéric Bretzner at Université Laval, Québec, Canada. They process data sampled and processed by Spike2 (CED). Data were acquired with a Po... |
f6f3a24372b1f92eeae9e303669654fa785ad91aa638cced8d4259188fa66281 | Text | 1,125 | 19 | # DREiVe
DREiVe is developed by Alona Sosinsky.
DREiVe stands for Discovery of Regulatory Elements in Vertebrates and it was originally developed by Alona Sosinky. However, the Perl scripts are very badly annotated (hardly any comments in the scripts) and the code has not been optimised for performance (hence in its ... |
b607160fe809c7433ae18f4d917fa206908cd542af12bd514ef154522969db47 | Text | 1,139 | 14 | This directory contains the various test data used to generate the scatterplots for evaluating the model performances throughout the manuscript.
### The notebook in this directory takes the reader through all the test data for model prediction performance validation (shown as scatterplots) used throughout the manuscri... |
15344a3f703cd8b24da1f043cd5973a934c16ceb566dc6aab8333cf86773aacc | Text | 1,152 | 29 | Copyright for this implementation:
2016 - John Barton, Eleonora de Leonardis, Alice Coucke, Simona Cocco
jpbarton@gmail.com, eleonora.deleonardis@gmail.com, alice.coucke@gmail.com, cocco@lps.ens.fr
Permission is granted for anyone to copy, use, or modify this
software and accompanying documents for any uncommercial
pu... |
56547464c258a25d3a58f525b44669b34c085253926bf710198c4dd5c3abeedb | Text | 1,161 | 32 | <div align="center">
<h1>[BMC Bioinformatics'23] cnnLSV: detecting structural variants by encoding long-read alignment information and convolutional neural network</h1>
</div>
# Installation
### Clone
```
git clone https://github.com/mhuidong/cnnLSV.git
```
### Dependencies
python3, cv2, numpy, torch, torchvision, pys... |
9a73ac5f4e4fbb983c52d4a0dfbaff7ca568e6728838fbb9ef0ab424a8544c96 | Text | 1,163 | 38 | ### [MobileFaceSwap: A Lightweight Framework for Video Face Swapping (AAAI 2022)](https://arxiv.org/abs/2201.03808)
---
**Dependencies**
- paddlepaddle==2.1.2
- insightface==0.2.1
- opencv
- numpy
**Getting Started**
1. The pretrained models can be downloaded from [Baidu Drive](https://pan.baidu.com/s/14_Wat-OA6lj... |
114bae3e6d04e017547bc62a143a6213d3d73b533fa02ae6ea070519751b28b4 | Text | 1,171 | 16 | ## Homogenisation for arbitrary arrangements of obstructions in cardiac fibrosis
This MATLAB code accompanies the journal article "Homogenisation for the monodomain model in the presence of microscopic fibroticstructures",
by Brodie Lawson, Rodrigo Weber dos Santos, Ian Turner, Alfonso Bueno-Orovio, Pamela Burrage and... |
e916a4502c9285e970aac9a04d4196c5d91dd05d791c82c0de95c756c9dd7e81 | Text | 1,195 | 24 | # MVGCN-iSL
THis is the code for our work "Multi-view graph convolutional network for predicting cancer cell-specific synthetic lethality". Our model, MVGCN-iSL, comprises three parts. In the first, the GCN processes multiple biological networks independently as cell-specific and cell-independent input graphs to obtai... |
dedfe18161ad9578b14a5b17d57f1e601e9b06d8951eecb6b068b122a8cd98f0 | Text | 1,215 | 25 | # Bicuculline
[](https://github.com/ScreenNeuroPharm/Bicuculline/blob/master/LICENSE)
> The repository contains the data and the functions needed to reproduce the analysis reported in the article "Lack of epileptogenic effects of the creatine precursor guan... |
57c83512cdf20021e55bd652987af96f5f61167ea02672c23d912b343eb7e942 | Text | 1,233 | 33 | ## motif4node ver 1.0
Motif4node is a package that allows systematic, high-throughput, and quantitative evaluation of how small transcriptional regulatory circuit motifs, and their coupling, responsible for a particular structure of gene expression state distributions. Moitf4node utilizes an ensemble-based mathematica... |
219db13bab25e7f9b0c2419147929ff17105c757bb1c394f8d46541b29ca78cf | Text | 1,237 | 22 | # LiveBirthPrediction_Data_Code
Data and code needed to reproduce the findings of the live birth prediction study:
Liu, Hang, Zhuoran Zhang, Yifan Gu, Changsheng Dai, Guanqiao Shan, Haocong Song, Daniel Li, Wenyuan Chen, Ge Lin, and Yu Sun. "Development and evaluation of a live birth prediction model for evaluating hu... |
90000febd4774dc9e78f2cb58d5a90e39533b85af2ffb82657d75d59334d4c80 | Text | 1,240 | 13 | # MRSartifactRemoval
This repository contains code for the removal of artifact signals from a magnetic resonance (MR) spectrum. The modelled situation consists of two artifact lines and one line originating from the investigated compound. Other signals can be present and should be preserved as long as their frequency ... |
8339a6e44f3ba7e0e4051abf51f1d9f5167332c8828105de06f59c645ca978fe | Text | 1,241 | 16 | # Hypoperfusion precedes tau deposition in the entorhinal cortex: a retrospective evaluation of ADNI-2 data
Authors: Anish Kapadia, Krish Bilimoria, Prarthna Desai, James T. Grist, Fulvio Zaccagna
Data: Collected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database: adni.loni.usc.edu, a multicentre pr... |
b320d522905981a51345cbd92de93fc780e4bff61b8f4b1d95f5262172869155 | Text | 1,243 | 9 | # Kymoanalyzer
These macros were originally made by the group of Sandra Encalada at The Scripps Research Institute, here they are with little modifications to fit our experimental assumptions and the FIJI version currently in use (solving dependency on other plugins, etc.).
I have prepared a quick guide to remind myse... |
63edc9cb1f70aba900c1ea8d6538a9ed17dcff77383aba1328378c629d305073 | Text | 1,246 | 21 | # cgRNASP
cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.
We developed our residue-separation-based CG statistical potentials (cgRNASP) at several CG levels:
(i) three CG beads at P, C4’, and N9 atoms for purine (or N1 atom for pyrimidine);
(ii) two CG beads at ... |
d2abf9d967014c8ede05eaf90b1c6ca8909e9532c4bae218c19aefd96c53fe57 | Text | 1,251 | 13 | # MRSartifactRemoval
This repository contains code for the removal of artifact signals from a magnetic resonance (MR) spectrum. The modelled situation consists of two artifact lines and one line originating from the investigated compound. Other signals can be present and should be preserved as long as their frequency ... |
974e0426ad9e033bd24877efa81c83d19817c3f819af0d66561009e2d7e7bd39 | Text | 1,252 | 34 | # intervole_timer
Partner preference test scoring script
## Web app
**Use it in your browser: https://beerylab.github.io/intervole_timer/**
Version 2.0 is a web app with the same functionality as the original Perl script:
score the focal vole's location across the five arena zones while watching the
test video, then... |
f6954be5f1c13d90d5adfa51671c404aad8d77495ee5061363ecd496cd9f8902 | Text | 1,266 | 35 | # TCTX
tctx is a Python library containing the code for the manuscript:
**Sequential propagation and routing of activity in a cortical network**
Juan Luis Riquelme, Mike Hemberger, Gilles Laurent, Julijana Gjorgjieva
## Installation
Use the package manager [pip](https://pip.pypa.io/en/stable/) to install tctx.
``... |
0b2df7abf4730e98ad8fb4ab91265291f3b9c41de38529027e85bce42fe267d3 | Text | 1,269 | 34 | # Dose calculation via Transformers #
This repository contains the code to calculate the dose deposited by a mono-energetic beam of protons, for arbitrary patient geometries and beam energies.
* GNU General Public License 3.0
* Copyright: Oscar Pastor-Serrano, TU Delft
The 'main' branch contains the code for proton... |
f00efd84d06d4179561c5d305d611bfd5b16a7051bfe3176b2f489738c1631d5 | Text | 1,285 | 13 | This repository holds the data and source code for the following manuscript:
[Vallabh SM, Zou D, Pitstick R, O'Moore J, Peters J, Silvius D, Kriz J, Jackson WS, Carlson GA, Minikel EV, Cabin DE. **Therapeutic Trial of anle138b in Mouse Models of Genetic Prion Disease.** _J Virol._ 2023 Jan 18:e0167222. doi: 10.1128/jv... |
21e56ef3c6a2e77b2cb9163a42cd10fa4f3406992186d5d36ed4b2e43d6ab8af | Text | 1,314 | 20 | # FADE_Neuropsy
**FADE/SAME scores reflect dissociable neuropsychological and anatomical signatures of neurocognitive aging**
This code belongs to the paper "Single-value scores of memory-related brain activity reflect dissociable neuropsychological and anatomical signatures of neurocognitive aging" by Richter et al.... |
2a9e2b4d76234e6e3c0495339658f2142ebebe693372a13508e0b7cf25744eda | Text | 1,337 | 13 | # calciumImaging
This is an imageJ plugin that can be used to evaluate temporal peaks in calcium imaging videos. To install the plugin, download the
calciumImaging_.jar file and place it into the plugins folder of your ImageJ (or Fiji) installation. Restart ImageJ, and there should be a menu "CalciumImaging" availabl... |
d834f912f26532100189e19a5eea9d5ff05238b72461b1db501dc575928f536f | Text | 1,353 | 24 | # FlyPN_development
Analysis workflow for [Xie et al. 2021](https://elifesciences.org/articles/63450)
This repository contains Jupyter Notebooks that were used to analyze the scRNA-seq data of Drosophila Olfactory Projection Neurons (PN) at 4 different developmental stages.
# Configuration
### Enviroment
Analysis req... |
8f544fd13509951766b6f820994ba1ed30a843efaabef1909f573c45737d6b72 | Text | 1,366 | 46 | Graph Convolutional Networks in PyTorch
====
PyTorch implementation of Graph Convolutional Networks (GCNs) for semi-supervised classification [1].
For a high-level introduction to GCNs, see:
Thomas Kipf, [Graph Convolutional Networks](http://tkipf.github.io/graph-convolutional-networks/) (2016)
. The core modules in this project were derived/modified from: [Iten, T. Metger, H.Wilming, L. del Rio, and R. R... |
bb29cb12d2985697837ad5400f0a5758887998ad4b33db0485b0e9ce254c32a1 | Text | 1,378 | 62 | # About qMriMaps
Scripts related to the corresponding [publication](https://doi.org/10.1093/braincomms/fcad047):
```
Köstner, M, Rebsamen, M, Radojewski, P, Rummel, C, Jin, B, Meier, R, Ahmadli, U, Schindler, K and Wiest, R.
Large-scale transient peri-ictal perfusion magnetic resonance... |
f128b486112883c8f9ef283e12e11303368d49ab286a675b3bef05e44b6eb376 | Text | 1,384 | 54 | MATLAB Compiler
1. Prerequisites for Deployment
. Verify the MATLAB Compiler Runtime (MCR) is installed and ensure you
have installed version 8.0 (R2012b).
. If the MCR is not installed, do the following:
(1) enter
>>mcrinstaller
at MATLAB prompt. The MCRINSTALLER command displays t... |
1454c41ab670d7d8d5356a4b46ff9f8d7584aeb40d84622126b6d20752c950e9 | Text | 1,388 | 24 | # ASRT_rapid_consolidation
Created by the <strong>MEMO Team</strong> of <strong>Lyon Neuroscience Research Center (CRNL)</strong>, Université Claude Bernard Lyon 1 (PI: Dezso Nemeth)
<img src="static/logo_memo.png" height="100">
Experimental code for the rapid consolidation project. The implementation of the codes o... |
bec19014f10f469002e46f53175a1599b1be9b2d3fc9fe184129e6da1efd442b | Text | 1,391 | 52 | # Context-Aware Attentive Knowledge Tracing
KDD'2020: Context-Aware Attentive Knowledge Tracing (Pytorch implementation for AKT).
This is the code for the paper:
[Context-Aware Attentive Knowledge Tracing](https://arxiv.org/abs/2007.12324)
Aritra Ghosh, Neil Heffernan, Andrew S. Lan
To be presented at [KDD 2020](ht... |
6a794570d6af9eb3b0de007b9856c77693b472e69484b309302b4c1335b80bc3 | Text | 1,398 | 39 | # Double-head Transformer Neural Network for Molecular Property Prediction
This is a Pytorch implementation of Double-head Transformer Neural Network for Molecular Property Prediction (DHTNN)
**Figure 1** Overall DHTNN architectural diagr... |
f05bb4d0fdf28c113a988ff55f798e781cd8e6d26450a8dc1cd6efd60c4014d7 | Text | 1,402 | 34 | # AmpSeqR: an R package for amplicon deep sequencing data analysis
https://github.com/bahlolab/AmpSeqR
AmpseqR is an R package for analysis of amplicon deep sequencing (AmpSeq) data generated on the Illumina platform. The pipeline offers various useful functions including Data pre-processing, Amplicon sequence variant... |
d82f29b6deceaaf4be67585230944a346c3169aa13c65949d14fc5aedaac0efb | Text | 1,454 | 45 | # Motif-based Graph Self-Supervised Learning for Molecular Property Prediction
Official Pytorch implementation of NeurIPS'21 paper "Motif-based Graph Self-Supervised Learning for Molecular Property Prediction"
(https://arxiv.org/abs/2110.00987).
## Requirements
```
pytorch 1.8.1
torch-ge... |
dcb9c95368ae7794fb1fb9cc9a880d61425fe01f06080beb4857e5387fc26494 | Text | 1,455 | 44 | # M2TR: Multi-modal Multi-scale Transformers for DeepfakeDetection
## Introduction
This is the official pytorch implementation of [Multi-modal Multi-scale for Deepfake detection](https://arxiv.org/abs/2104.09770), which is accepted by ICMR 2022.
<p align="center">
<img width="75%" src="./imgs/network.png" />
</p>
... |
94719d4a988fccefd1dcd250c6059bf6d64f1bba25e2086d73d7d09731b87b7b | Text | 1,467 | 23 | # vestibularHairCellCalyxNQT
Welcome to the file repository for the research paper:
***"Nonquantal Transmission at the Vestibular Hair Cell-Calyx Synapse: KLV Currents Modulate Fast Electrical and Slow K+ Potentials"***
**Paper Status:** Published in PNAS: https://www.pnas.org/doi/10.1073/pnas.2207466120
An older pr... |
4aeeec6ffab8fdea5bda25adf033b0f59949d0e71d83c7bcf4fb2c0781966912 | Text | 1,480 | 32 |
# Characterization of regional differences in resting-state fMRI with a data-driven network model of brain dynamics
This repository contains the code used in the study by [Sip et al. (2023)](#references). The study explores building data-driven dynamical models of the brain activity captured with resting state fMRI... |
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