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MicroBenthos

MicroBenthos: a modeling framework for microbial benthic ecology - Published in JOSS (2018)

https://github.com/achennu/microbenthos

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
  • Host: GitHub
  • Owner: achennu
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 620 KB
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 4
Created almost 8 years ago · Last pushed about 5 years ago
Metadata Files
Readme Contributing License Authors

README.rst 

.. 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 `_


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.

Owner

  • Login: achennu
  • Kind: user

JOSS Publication

MicroBenthos: a modeling framework for microbial benthic ecology
Published
May 04, 2018
DOI
Volume 3, Issue 25, Page 674
Authors
Arjun Chennu ORCID
Max Planck Institute for Marine Microbiology
Editor
Lindsey Heagy ORCID
Tags
marine biology biogeochemistry microbial ecology microbial mats sediments modeling simulation microbenthic habitat
View PDF Review Thread Software Archive

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 199
  • Total Committers: 2
  • Avg Commits per committer: 99.5
  • Development Distribution Score (DDS): 0.226
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Arjun Chennu a****u@g****m 154
Arjun Chennu a****u@m****e 45
Committer Domains (Top 20 + Academic)
mpi-bremen.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 3
  • Average time to close issues: 9 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 4.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • leouieda (3)
  • lheagy (1)
Pull Request Authors
  • leouieda (1)
  • achennu (1)
  • pyup-bot (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 27 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 6
  • Total maintainers: 1
pypi.org: microbenthos

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

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 27 Last month
Rankings
Dependent packages count: 10.1%
Average: 19.4%
Dependent repos count: 21.6%
Downloads: 26.4%
Maintainers (1)
achennu
Last synced: 6 months ago

Dependencies

.github/workflows/python-publish.yml actions
  • actions/checkout master composite
  • actions/setup-python master composite
requirements_docs.txt pypi
  • sphinx *
  • sphinx-autodoc-typehints *
  • sphinx_rtd_theme *
  • sphinxcontrib-programoutput *