Pinned

1. simple_biofx_tutorial simple_biofx_tutorial Public

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

   Nextflow

2. VoronoiAnalysis VoronoiAnalysis Public

   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 partia…

   Python 8 1

3. Stochastic-Notch-Patterns Stochastic-Notch-Patterns Public

   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…

   Jupyter Notebook

4. EMT_MR EMT_MR Public

   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

   Jupyter Notebook

5. RACIPEwb_stemness RACIPEwb_stemness Public

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

   PostScript

6. qmcpack_input_generator qmcpack_input_generator Public

   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.

   Python