This repository contains codes developed in 2022 to simulate the biofilm formation with the proposed stochastic model based on quorum sensing and chemical reactions.

This package models the dynamics of a biofilm using the Julia programming language.

A web app to calculate Anti-Biofilm Combination Index (ABCI)

Biofilm Analyzing Software (BAS)

3D Analysis of confocal images of microbial biofilms/communities

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.

This is all the code utilized in the analysis for "Vertical growth dynamics of biofilms".

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”

1D reactive–transport model of botanical biofiltration of VOCs

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

Scripts for ProMesh

2D biofilm simulation based on the implementation outlined in Introduction to Computational Science by Angela and George Shiflet.