semvec/pypi-packages huggingface dataset:
microbenthos 0.14
Modeling framework for microbenthic habitats useful for studies in biogeochemistry and marine microbial ecology.
License: MIT license
Keywords: microbenthos,biogeochemistry,marine biology,microbial ecology,simulation,modeling,microbial mats,sediments


.. image:: https://img.shields.io/pypi/v/microbenthos.svg
    :target: https://pypi.python.org/pypi/microbenthos

.. image:: https://travis-ci.org/achennu/microbenthos.svg?branch=master
    :target: https://travis-ci.org/achennu/microbenthos

.. image:: https://readthedocs.org/projects/microbenthos/badge/?version=latest
    :target: https://microbenthos.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

.. image:: http://joss.theoj.org/papers/5daae2e14258034d77cb694370cbae23/status.svg
    :target: http://joss.theoj.org/papers/5daae2e14258034d77cb694370cbae23
    :alt: Journal of Open Source Software

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3583388.svg
   :target: https://doi.org/10.5281/zenodo.1240939
   :alt: 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.

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

Simulation example
-------------------

From `youtube <https://www.youtube.com/watch?v=CnHjVJKXo0A>`_


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.