[NOTE: still under active development !!!; if interested, feel free to reach out to me via any media]
This model is spatially and mechanistically explicit in simulating microbial systems comprised of a large number of 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 which is R-based.
Vision
DEMENTpy is devoted to longterm maintanence and development with continuous updates not only from ourselves but also, hopefully, from the communities that can 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 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. Here is the underlying conceptual structure DEMENTpy:
Running DEMENTpy
File structure
./src: all source code
./input: data required to drive the model
./output: folder where the output object in .pickle will be residing
dementpy.sh: bash script for submitting job to HPC.
Contributing Guide
Please follow these rules if you want to contribute to this open source model:
License