1,976 Works

Python Implementation of Quality Threshold Clustering for Molecular Dynamics

Ryan Melvin & Freddie Salsbury
A python implementation of Heyer, 1999's Quality Threshold clustering algorithm specialized for molecular dynamics trajectories.

Perfect Revivals on Spin Chains

Alastair Kay
A mathematica workbook reproducing all the calculations presented in "Tailoring Spin Chain Dynamics for Fractional Revivals", arXiv%3A1609.01397.

PopSc in Python and R

Shi-Yi Chen &
PopSc is a bioinformatic toolkit for calculating 45 basic statistics in%0Amolecular population genetics, which could be categorized into three classes,%0Aincluding (i) genetic diversity of DNA sequences, (ii) statistical tests for neutral evolution, and (iii) measures of genetic differentiation among%0Apopulations. The project web of PopSc is at http%3A//chenshiyi.com/popsc.html.

hello_world (fe16338fc78f73ae4caa11673497f84e97df3961)

Jan Lietava
hello_world (Version fe16338fc78f73ae4caa11673497f84e97df3961)

Test upload

Jan Lietava
hello_world (Version fe16338fc78f73ae4caa11673497f84e97df3961)



Alastair Kay

pyRDM test upload

Jan Lietava
hello_world (Version fe16338fc78f73ae4caa11673497f84e97df3961)

Python codes for solving modes of anisotropic waveguides with arbitrary permittivity and permeability

These are python codes which can be used to solve transverse modes of waveguides with arbitrary permittivity and permeability.

Forest Structure gap-filling code

Adam Moreno
Code used to create pan-European forest structure data set. Gap-filling and clustering algorithm

05 NIS 2002-2011 Hospital Volume and Mortality

Jordan Kempker
Jordan A. Kempker, MD, MSc August 4, 2016 NIS 2002-2011 Hospital-Level Variables This Code will create the below hospital-level variables for the entire dataset and then merge these statistics back into each observation. hosp_vol Number of Annual Hospital Discharges hospmort Annual Hospital In-Hospital Mortality Rate Average Annual Hospital Elixhauser Score Of note, this code was first tested on a random 5% sample stratified by year before applying to entire dataset. Below, is the pared down...


Mohammad Elnesr
A software to visually discover the effects and contributions between interrelated features through artificial neural networks
This software is free for reuse but please drop a message to the corresponding author regarding your experience with this software, and how you would like it to be developed, suggest additional features, or report bugs to drnesr@gmail.com
For scientific research please add citation to this software as (DOI will be added soon, untill added, so cite this GIT repository as...

Random Codes

Alice Alonso
Diverse codes in Matlab. No wheel re-invented here, but it might help users save 15 minutes here and there.
- trendSign.m: Performs simple linear regression between X and Y using least square fit and tests the null hypothesis of non-significant slope at the alpha significance level.- cmpTrends.m: Compares the significance of the difference between two trends from two independent datasets.

planck keymap

Thomas Cook
keymap for the planck

BifLib (v1.0)

Martin O'Reilly
Library for generating BIFs (Basic Image Features) from images.

BifLib Matlab BIF library

Martin O'Reilly
A MATLAB library for efficiently generating Basic Image Features (BIFs) from images.

xml file for starBEAST analysis

xml file for starBEAST (*BEAST) analysis using BEAST 1.8.2


Tae-Hoon Chung
R library for gene signature index calculation for myeloma data.


Mads Hansen
R code to accompany the article "Postoperative Predictors of Speech Reception in Cochlear Implant Users" by Mads Hansen, Bjørn Petersen, Therese Ovesen, and Klaus B. Bærentsen.


Christine Ewers-Saucedo
*BEAST XML script used to reconstruct phylogeny of shame-faced crabs in Ewers-Saucedo et al.: EVOLUTION OF MALE COPULATORY ORGANS IN SHAME-FACED CRABS (DECAPODA: EUBRACHYURA: CALAPPIDAE DE HAAN, 1833)


Xing Tang
ChIP-exo data analysis pipeline for mouse

Wood et al Ecol Appl 2016 Code

Stephen Wood
Code for analysis of the dataset https://dx.doi.org/10.6084/m9.figshare.3083554.v1

COMBINE-compliant implementation of the Mycoplasma genitalium whole-cell model

Jonathan Karr
The goal of this project was to recode the Mycoplasma genitalium whole-cell model into COMBINE-compliant standards to faciliate interpretation, reuse, and extension of the model, as well as to help researchers build additional whole-cell models.This project was a part of the 2015 Whole-Cell Modeling Summer School which aimed to teach students about whole-cell modeling and systems biology standards.This repository includes recoded versions of all of the submodels of the Mycoplasma genitalium model.

Registration Year

  • 2016

Resource Types

  • Software