| Repository | Description | Stats |
|---|---|---|
| WHAM | Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-consistent iteration approaches. |   |
| postmetad | Python package for post-processing PLUMED metadynamics and OPES simulations. |   |
| stringmethod | Python implementation of the string method to compute the minimum energy path between two points on any 2-dimensional energy landscape. |   |
| pyves | Python package to perform variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables, using OpenMM + PyTorch. |   |
| INDUSAnalysis | Python package to analyze molecular simulation data generated using GROMACS-INDUS. |   |
| bootstrapping_tutorial | Jupyter notebook tutorial on bootstrapping (and other related methods) for resampling and calculating uncertainties from correlated timeseries data. |   |
| gcmc | C++ code for Markov Chain Monte Carlo simulations in the grand canonical ensemble. |   |
| Repository | Description | Stats |
|---|---|---|
| paperfetcher | Python package to automate handsearching and citation searching for systematic reviews. |    |
| paperfetcher-web-app | Streamlit web-app for paperfetcher. |   |
| paperfetcheR-Notebooks | R-Notebooks demonstrating how to use paperfetcher in R. |   |
| paperfetcheR-starter | R scripts to help you quickly get started with handsearching and citation searching using paperfetcher. |   |
| Repository | Description | Stats |
|---|---|---|
| gemini_penn | Unofficial fork of the Gemini beamerposter theme with the University of Pennsylvania logo, colors, and fonts. |   |
| GameOfLife | Conway's Game of Life on a rectangular 2D grid with OpenMP parallelization. |   |
| multiagent_timetable_scheduling | Netlogo implementation of a multi-agent based algorithm for solving a simplified version of the University Timetabling Problem, using Simulated Annealing. |   |
| keras_sklearn_models | tf2/keras deep learning models on image data and sklearn machine learning models on tabular data. |   |
| torch_models | Deep learning models in PyTorch. |   |