ErikPoppleton
Staring into the RNA structure void... Current @HITS-MBM, Formerly @sulcgroup
Heidelberg University/MPI for Polymer Research
Pinned Repositories
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
kinetic_folder
Kinetic folding of RNA structures based on energy penalties for breaking base pairs
oxDNA_performance
Performance benchmarks for oxDNA
resubmitters
Resubmit your MD simulations automatically
rollout_plotter
plotting scripts for outputs from the rollout/RNAfold algorithm
oxDNA
A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
oxdna-viewer
oxView: Visualization and editing tool for DNA/RNA nanotechnology and oxDNA/oxRNA configuration analysis
ErikPoppleton's Repositories
ErikPoppleton/oxDNA_performance
Performance benchmarks for oxDNA
ErikPoppleton/rollout_plotter
plotting scripts for outputs from the rollout/RNAfold algorithm
ErikPoppleton/duplex_bead_model
Data extraction and example files for coarse-grained DNA/RNA folding model
ErikPoppleton/kinetic_folder
Kinetic folding of RNA structures based on energy penalties for breaking base pairs
ErikPoppleton/resubmitters
Resubmit your MD simulations automatically
ErikPoppleton/ASU-Dissertation-Template
LaTeX Template for Typesetting Arizona State University Dissertations and Theses
ErikPoppleton/azDNA
ErikPoppleton/azDNA_env
Sets up an environment to run azDNA within vagrant/virtualbox
ErikPoppleton/gromacs_bench
Generate SLURM submit scripts to test a set of resource allocations for GROMACS simulations
ErikPoppleton/oat_benchmark
Benchmarking for oxDNA Analysis Tools
ErikPoppleton/oxDNA
A new (unstable) version of the code to simulate the oxDNA/oxRNA models, now equipped with rudimentary Python bindings
ErikPoppleton/oxdna-viewer
oxView: Visualization and editing tool for DNA/RNA nanotechnology and oxDNA/oxRNA configuration analysis
ErikPoppleton/oxDNA-viewerTHREE.js-instancing-demo
A demonstration of geometry instancing that reads oxDNA .dat files
ErikPoppleton/oxdna-web
Environment for running oxdna.org webserver for oxDNA/oxRNA simulation submission and analysis
ErikPoppleton/MD_playground
Play with MC and MD simulations in iPython notebooks
ErikPoppleton/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!
ErikPoppleton/oat_workshop24
Workshop on oxDNA Analysis Tools given at the oxDNA Developers Conference 2024
ErikPoppleton/oxpy_minimal
Minimal example of oxpy zombie processes
ErikPoppleton/portfolio
Coding exmaples from my projects
ErikPoppleton/RL-RNA