MicroBenthos is a modeling framework (in python) useful for studies of benthic microbial systems, such as microbial mats, marine sediments, etc. It enables in silico experiments in microbial ecophysiology and biogeochemistry through computational simulations of geochemical processes, microbial metabolism and mass transport physics.

• Free software: MIT license
• Documentation: https://microbenthos.readthedocs.io
• Source code: https://github.com/achennu/microbenthos

Simulation example

From youtube

Features

• Create microbenthic systems:

  Study dynamics of microbial and geochemical sedimentary processes by solving their partial differential equations. Easily include microbial populations, solar irradiance, anisotropic diffusion and more in your models.

• Scientist-friendly:

  Define constitutive chemical and biological processes simply as mathematical formulae. Data is saved in open archival format.

• Visualize on the go:

  Includes visualization of modelled parameters and results that can be viewed live, and exported to video. Progress information on simulation is also shown.

• Stateful simulations:

  Simulations can be interrupted and then resumed, allowing for interactive inspection and time-saving.

• No programming required:

  Systems and behavior can be defined through a structured text file.

• Extensible:

  New modalities of microbial systems can be created with simple programming around a defined structure.