Optimal Allocation and the Flux Parity Model
Python code written by Griffin Chure, 2022
This repository houses all of our work related to our recent paper presenting the flux-parity model of ribosomal allocation. Custom software (growth.py) provides utilities for numerical integration of different allocation models with various features.
Collective movement by chemotaxis
Python code written by Jonas Cremer, 2019
This Python code can be used to numerically solve the Growth Expansion Model we recently formulated to describe the collective growth of chemotactic bacterial populations moving (and competing) along self-driven gradients.
Analyzing bacterial swimming behavior
Python code written by Jonas Cremer, 2019
We used this Python based script to track swimming bacterial cells and to get a statistics of their swimming behavior, including the fraction of non-motile cells.
Analyzing the collective migration of chemotactic bacteria
Python code written by Jonas Cremer, 2019
We used this Python script to analyze expansion and growth dynamics of fluorescently labeled cells expanding in soft-agar.
Modeling growth of the human gut microbiota
Python code written by Jonas Cremer, 2019
Towards a mechanistic understanding of the human gut microbiota and its composition, we developed a spatiotemporal model of bacterial growth within the human large intestine, considering key factors like nutrient availability, flow conditions and pH. Send an email to Jonas if you are interested in the code.