Software

Over the years, we developed several codes to analyze data and run model simulations. Code is available via GitHub profile at https://github.com/jonascremer, or send an email to Jonas.

Modeling growth of the human gut microbiota

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. We plan to make a commented version of the code available via GitHub soon. Until then, send an email to Jonas if you are interested in the code.

Collective movement by chemotaxis

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. Code and description available via GitHub at:https://github.com/jonascremer/chemotaxis_simulation .

Analyzing bacterial swimming behavior

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 cell. Code and description available via GitHub at:https://github.com/jonascremer/swimming_analysis.

Analyzing the collective migration of chemotactic bacteria

We used this Python script to analyze expansion and growth dynamics of fluorescently labeled cells expanding in soft-agar. Code is available via GitHub at:https://github.com/jonascremer/chemotaxis_imageanalysisexpansiondynamics