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biofilm

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katrinleinweber /PhD-thesis

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

markdown latex makefile biology pandoc latexmk latex-document biochemistry make zotero phd-thesis electron-microscopy microscopy citer eds diatom biofilm markdown-template

UpdatedOct 20, 2021
Shell

Russel88 /RCon3D

3D Analysis of confocal images of microbial biofilms/communities

microbial-communities quantitative image-analysis 3d confocal-microscopy biofilm confocal-images microbial-biofilms

UpdatedJun 5, 2024
R

markowkes /Biofilm.jl

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

UpdatedFeb 26, 2025
Julia

jkglasbrenner /biofilm-simulation

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

cpp simulation cellular-automata biofilm modeling-and-simulation

UpdatedMay 6, 2019
C++

hancockinformatics /ABCindex

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

bioinformatics r shiny assay biofilm

UpdatedFeb 14, 2025
R

cohenoa /An-Open-Source-Computational-Tool-for-Measuring-Bacterial-Biofilm-Morphology-and-Growth-Kinetics

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”

open-source bioinformatics computational-biology bioinformatics-pipeline image-procesing biofilm image-processing-python

UpdatedOct 20, 2022
Python

pbravoc /vertical_growth_biofilms

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

timelapse topography interferometry biofilm

UpdatedMar 20, 2023
HTML

fatihguelec /Stochastic-Modeling-of-Biofilm-Formation-with-Bacterial-Quorum-Sensing

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

gillespie stochastic-models quorum-sensing biofilm tau-leaping biofilm-growth

UpdatedSep 20, 2024
MATLAB

raphaelrubrice /Biofilm-Simulator

Project aimed at programming an individual based model (cellular automaton approach) for modeling bacterial biofilms and interactions within them.

simulation cellular-automata bacteria biofilm

UpdatedMay 30, 2024
Python

akshayparopkari /discover_tfbs

Discover transcription factor (TF) binding specificities/sites (TFBS) using binding site motif sequence and structural information.

python bash machine-learning bioinformatics transcription-factors r pathogen biology scripting computational-biology binding-sites fungal biofilm candida-albicans

UpdatedJun 17, 2024
Python

NeuroBox3D /ProMeshScripts

Scripts for ProMesh

grid imagej generation promesh polygons txt biofilm

UpdatedMay 31, 2021
Lua

pommevilla /sbfp

machine-learning bioinformatics snakemake feature-selection xgboost population-structure salmonella kmer-counting biofilm

UpdatedNov 15, 2023
Python

Biofilm-Project /BAS

Biofilm Analyzing Software (BAS)

open-source biofilm biofilm-growth

UpdatedJul 2, 2024
Python

matteomasi /biofilter-model

1D reactive–transport model of botanical biofiltration of VOCs

simulation scientific-computing finite-elements pde fenics biofilm

UpdatedMay 9, 2022
Python

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