Inferred biomass biogeochemical model of Mystic Lake.
by Scott W Olesen, Sarah P Preheim, and Eric J Alm
Mystic is a Matlab program (with supporting Python scripts) that runs a conceptual, quantitative simulation of the biogeochemistry of Mystic Lake, a polluted, dimictic lake outside Boston. The model was designed to predict the overall vertical spatial distribution of major chemical species and microbial metabolisms in the lake.

Sarah P. Preheim, Scott W. Olesen, Sarah J. Spencer, Arne Materna, Charuleka Varadharajan, Matthew Blackburn, Jonathan Friedman, Jorge Rodrguez, Harold Hemond and Eric J. Alm. Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem. Nature Microbiology (2016) doi:10.1038/nmicrobiol.2016.130

The source for the model run in the paper:
Mystic (zipped source)
Mystic (Alm Lab github page)