Experimental tech-demo for PhD thesis in Scientific Markdown; official:
In this module, you will learn how to use a Docker container to analyze amplicon sequencing metagenomics data with common tools such as qiime2 and PICRUSt2
3D Analysis of confocal images of microbial biofilms/communities
2D biofilm simulation based on the implementation outlined in Introduction to Computational Science by Angela and George Shiflet.
This package models the dynamics of a biofilm using the Julia programming language.
A web app to calculate Anti-Biofilm Combination Index (ABCI)
Code to accompany the paper: ”An Open-Source Computational Tool for Measuring Bacterial Biofilm Morphology and Growth Kinetics upon One-Sided Exposure to an Anti-Microbial Source”
This is all the code utilized in the analysis for "Vertical growth dynamics of biofilms".
This repository contains codes developed in 2022 to simulate the biofilm formation with the proposed stochastic model based on quorum sensing and chemical reactions.
Project aimed at programming an individual based model (cellular automaton approach) for modeling bacterial biofilms and interactions within them.
Discover transcription factor (TF) binding specificities/sites (TFBS) using binding site motif sequence and structural information.
1D reactive–transport model of botanical biofiltration of VOCs
An aggregate-level simulation tool for Pseudomonas aeruginosa that captures both aggregate and cell-level behavior. My contributions are combined with contributions of Michael J Sweeney and Sarah Sundius.
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