Skip to content

Latest commit

 

History

History
executable file
·
92 lines (56 loc) · 5.32 KB

README.md

File metadata and controls

executable file
·
92 lines (56 loc) · 5.32 KB
Raw

DEMENTpy

A trait- and individual-based spatially explicit soil microbial systems modelling framework

GitHub repo size GitHub contributors GitHub stars GitHub forks

This model is spatially and mechanistically explicit in simulating a microbial system comprising a large number of hypothetical microbial taxa in terrestial environments. As indicated by the 'py' in its name, DEMENTpy is developed and programmed in Python, based on its predecesor DEMENT developed by Steven Allison (promgrammed in R).

Vision

DEMENTpy, initiated with in mind practicing Real Open Science, is devoted to 100% OPEN SOURCE and longterm maintanence and development, which, however, will not be limited to ourselves but sincerely seek inputs from the communities that could be as broad as microbial ecology, systems biology, theoretical ecology, etc. Just because of community inputs, please read closely our statement on policies and rules of making contributions to DEMENTpy or applying it to your own research.

Structure and Process

This model is built upon its predecessor--DEMENT, an R-based framework initially developed by Steven Allison back in 2012. Except for the programming language change, a series of changes have been made with an overarching goal of making it more readily accessible to the research and teaching communities as broad as microbial ecology, theoretical ecology, and ecosystem ecology, as well as biology. This model simulates processes ranging from degradation of substrates through microbial processes encompassing uptake, metabolism, mortality, reproduction, and dispersal in a spatially explicit, mechanistically explicit fashion. For more detailed information about DEMENTpy, we refer readers/users temporarily to an Appendix of the 1st manuscript applying this model. An actual documentation is under conceiving.

Run DEMENTpy

Get the code:

git clone https://github.com/bioatmosphere/DEMENTpy

Directory structure:

  • src/: all source code

  • input/: data required to drive the model

  • output/: folder where the output object in .pickle will be residing

  • SPA/: Scripts of Processing and Analyzing (SPA) outputs

Run DEMENTpy:

  • Configure Environment
    • Python >= 3.7
    • Numpy >= 1.16.4
    • Pandas >= 0.24.2

A simple example of bash script, dementpy.sh, for running jobs on HPC is provided.

Contribution

The space for contribution is HUGE and OPEN! For instance:

  • New processes/algorithms are more than welcome.
  • Programming improvement is absolutely needed.
  • Any bugs are possible.
  • ...

Feel free to reach out, or directly fork, change, and create pull requests, or create new branches to contribute.

License

MIT LICENSE

References

  1. Wang, B., & Steven D. Allison. (2022) Climate-driven legacies in simulated microbial communities alter litter decomposition rates. Frontiers in Ecology and Evolution 10,841824

  2. Wang, B., & Steven D. Allison. (2021) Drought Legacies Mediated by Trait Tradeoffs in Soil Microbiomes. Ecosphere 12, e03562

  3. Wang, B., & Allison, S. D. (2019).Emergent properties of organic matter decomposition by soil enzymes. Soil Biology and Biochemistry, 136, 107522

  4. Allison, S. D., & Goulden, M. L. (2017). Consequences of drought tolerance traits for microbial decomposition in the DEMENT model. Soil Biology and Biochemistry, 107, 104-113.

  5. Allison, S. D. (2012). A trait‐based approach for modelling microbial litter decomposition. Ecology Letters, 15, 1058-1070.