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

3D Analysis of confocal images of microbial biofilms/communities

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

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

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".

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.

Scripts for ProMesh

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

1D reactive–transport model of botanical biofiltration of VOCs

Biofilm Analyzing Software (BAS)