MATLAB and Python Scripts by Gabriel Bronk: Selected Scripts from Journal Articles by Bronk and Educational Scripts for College/High School Lessons
Below, I list the scripts that I have posted to my GitHub. If you have any questions or would like to see scripts from my research that I have not posted, please email me at gbronk AT brandeis.edu
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IntroductionToModelingChromosomesWithFreelyJointedChain.m This MATLAB code simulates a random conformation of the arm of a chromosome in a yeast cell's nucleus. This script is intended for any researcher who wishes to learn how to model a chromosome in a simple manner. It is also useful for teaching college (or advanced high school) students how to create a simple Monte Carlo simulation.
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ModelingChromosomeWithFreelyJointedChainFastAlgorithm.m This MATLAB code simulates a random conformation of the arm of a chromosome in a yeast cell's nucleus, and it uses an algorithm I developed in order to reduce the computation time compared to doing a regular random walk chromosome simulation. This script is intended for any researcher who wishes to model a chromosome in a simple manner and wants to reduce the computation time. This FAST ALGORITHM is useful for simulating a freely-jointed chain chromosome that is confined to a certain region and/or attached to certain locations. I developed this algorithm for the paper "Chromosome-refolding model of mating-type switching in yeast" published in PNAS in 2016 by Avaroglu, Bronk, et al. The algorithm is described in the paper's Supplementary Information under the heading "Polymer Model Simulation Details."
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IntroductionToMachineLearningWithPython.py This Python code loads patient data (physiological measurements from the ICU) and uses it to predict whether patients will get sepsis. This code is inteded for teaching college or advanced high school students how to do machine learning (using the specific machine learning example of a generalized linear model).