Blake A. Wilson's repositories
blakeaw.github.io
Personal website and blog.
blog-posts
Source code and notebooks for blog posts on blakeaw.github.io.
lammps-post
Python tools to parse, post-process, and analyze outputs from LAMMPS MD simulations.
change-extension
Bash script to change the extension of all files with a given extension.
52-hike-app
A streamlit web app or data dashboard for my 52 Hike Challenge log.
PySB-Models
A repository of mathematical models of biological systems that are encoded using PySB.
MYGO
Model of Yeast Glycolytic Oscillations in PySB
three-component-repressive-network-model
Generic three-component repressive network model from Mogilner et al. encoded in PySB.
pysb
Python framework for Systems Biology modeling
peptide-property-app
Used peptides.py to predict peptide properties from the amino acid sequence.
extracellular-models
Reaction-diffusion models to simulate the dynamics of fluorescent dyes and peptides in the brain extracellular space implemented using the extracellular simulator in NEURON.
atomic-molecular-nested-sampling
Nested Sampling implementations and case studies developed during my Ph.D. work.
PyBILT
Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
BashAdventure
A simple text based game for the terminal (written in bash)
NVT_MetropolisMonteCarlo_LJ_particles
Metropolis Monte Carlo simulations of Lennard-Jones particles in the canonical ensemble.
streamlit-pyvipr
streamlit components for PyViPR visualizations.
roi-plotter
A streamlit app to read cell ROI data from csv files and plot the fluorescence traces.
insurance-pro-rata-calculator
Compute the pro rata rate for adding trucks or vehicles to a commercial insurance policy.
pydream_it
Read PySB models and generate a script for PyDREAM calibration
summarize
TACC Institute summarize - Summarize a random list of numbers
swarm_it
Utility to help setup PSO runs for PySB models.
galibrate_performance_comparison
Jupyter notebook comparing the performance of GAlibrate's Cython, Numba, and pure-Python implementations of the core GA.
BioComparator
software toolset to compare biological-models
ObjectiveLearner
Get more out of objective function evaluations made during model calibrations.
conda-build_recipes
Conda build recipe files that I've used/written to build packages for my Anaconda cloud channel.
Gleipnir
A python toolkit for Nested Sampling, Gleipnir allows users to compute the Bayesian evidence and posterior parameter distributions of models.