Skip to main content

Modeling framework for microbenthic habitats useful for studies in biogeochemistry and marine microbial ecology.

Project description Documentation Status Journal of Open Source Software Zenodo software archive

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.

Simulation example

From youtube


  • 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.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for microbenthos, version 0.14
Filename, size File type Python version Upload date Hashes
Filename, size microbenthos-0.14-py2.py3-none-any.whl (88.1 kB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size microbenthos-0.14.tar.gz (570.4 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page