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asu-dissertation-template

LaTeX Template for Typesetting Arizona State University Dissertations and Theses

azdna

azdna_env

Sets up an environment to run azDNA within vagrant/virtualbox

duplex_bead_model

Data extraction and example files for coarse-grained DNA/RNA folding model

gromacs_bench

Generate SLURM submit scripts to test a set of resource allocations for GROMACS simulations

kinetic_folder

Kinetic folding of RNA structures based on energy penalties for breaking base pairs

md_playground

Play with MC and MD simulations in iPython notebooks

metro-ui-css

Impressive component library for expressive web development! Build responsive projects on the web with the first front-end component library in Metro Style. And now there are even more opportunities every day!

oat_benchmark

Benchmarking for oxDNA Analysis Tools

oxdna

A new (unstable) version of the code to simulate the oxDNA/oxRNA models, now equipped with rudimentary Python bindings

oxdna-viewer

oxView: Visualization and editing tool for DNA/RNA nanotechnology and oxDNA/oxRNA configuration analysis

oxdna-viewerthree.js-instancing-demo

A demonstration of geometry instancing that reads oxDNA .dat files

oxdna-web

Environment for running oxdna.org webserver for oxDNA/oxRNA simulation submission and analysis

oxdna_performance

Performance benchmarks for oxDNA

oxpy_minimal

Minimal example of oxpy zombie processes

portfolio

Coding exmaples from my projects

resubmitters

Resubmit your MD simulations automatically

rl-rna

rollout_plotter

plotting scripts for outputs from the rollout/RNAfold algorithm

twitter_getter

Scrape Twitter for recent tweets on a topic