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.
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Updated
May 7, 2021 - Python
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.
Machine learning - breast cancer and ecoli - classification
Maximum Entropy (MaxEnt) parameter inference in biological networks.
Annotation for full-genome assembly of Escherichia coli str. K12, substr. MG1655
Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.
Meta-Bio-Cargo predict #Ru-Bi-CO-S protein
Using machine learning to predict E. coli phenotypes
Nanopore base caller based on original Chiron adding Dropout and SRU
Presentations and work done for University of Pittsburgh course, Synthetic Biology.
The Monorepo for all things Toronto Beaches
Collection of 1069 Escherichia coli virulence factors
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
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.
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