Toronto's open source beach app

This work aims to explore the differences between Python and Julia and to propose a detailed overview of the best-suited applications for each language. The repository includes mechanistic models in both Python and Julia.

An ensemble of plasmid classification tools

Presentations and work done for University of Pittsburgh course, Synthetic Biology.

This is a pipeline that can be used to generate a phylogenetic tree, including a heatmap showing carriage of specific genes, the assigned phylogroup of each strain, and the names of each strain. It should now be capable of working with any sort of strains - currently I'm working on making small improvements.

Determines the serotype and virulence in Escherichia coli isolates using NGS data (reads) through kmer alignment.

The Monorepo for all things Toronto Beaches

Collection of 1069 Escherichia coli virulence factors

Using machine learning to predict E. coli phenotypes

Nanopore base caller based on original Chiron adding Dropout and SRU

EcoliTyper: Unified MLST + Serotyping + Clermont typing for Escherichia coli A comprehensive bioinformatics tool that unifies three essential E. coli genotyping methods into a single, high-performance workflow. Perfect for clinical microbiology, outbreak investigations, and genomic research.

Maximum Entropy (MaxEnt) parameter inference in biological networks.

Annotation for full-genome assembly of Escherichia coli str. K12, substr. MG1655

Diffusion model of a system where sender strains produce AHL and has induced motility in the presence of arabinose. AHL diffuses and motility in receiver strains.

Ecoli related analysis for the SOFI platform.

Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.

Machine learning - breast cancer and ecoli - classification

📈 Visualize Anti Microbial Research (D3.js). 🎨 Design and development of an interactive 🖥 Website for the iGem IISER team sharing their Research on Culturing hybrid bacteria named Coli Kaze. 🦠

Bacterial motility patterns adapt smoothly in response to spatial confinement and disorder [Zhang H., Wetherington M.T., Ko H., FitzGerald C.E., Luzzatto L.V., Kovács I.A., Munro E.M., Nirody J.A.]