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database_for_qm_results

A database for A database for retrieving and adding results generated via quantum package (including the input files).

emt_mr

Data generation and analysis of the coupled decision-making of the EMT and metabolism networks. This work is available as a preprint at https://www.biorxiv.org/content/10.1101/2022.08.02.502548v1

madgal.github.io

qmcpack_input_generator

Takes a file from quantum package that is ready for conversion (i.e. save_for_qmcpack has been used) and generates the *wfs.xml, *ptcl.xml, DMC folder, and Optimization folder.

quantum_package

Set of quantum chemistry programs and libraries

racipewb_stemness

The code for RACIPEwb framework to analyze a nine component stemness gene regulatory network

simple_biofx_tutorial

This repo contains a simple pipeline as an example of my approach to bioinformatics

stochastic-notch-patterns

Here you'll find the code for generating and analyzing Notch-Delta mediated pattern formation. Our results can be found in "Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway" https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010306

voronoianalysis

Python code that can be used to analyze molecular dynamics simulations of proteins/polymers solvated in water. The first and second hydration shells are calculated, the molecular volume, the partial molar volume, and the number of waters associated with each side chain are calculated. This is specifically for PNIPAM but can be modified fairly easily to suit other polymers/protiens. The MDAnalysis library is used for parsing trajectories. Voronio polygons are created using the pyvoro wrapper of Voro++.