This paper is under review which means review has begun. You can track the progress of this review on GitHub over here »
Modeling framework for microbenthic habitats useful for studies in biogeochemistry and marine microbial ecology. The MicroBenthos package, written in python, provides abstractions and simple interfaces to define, compose and simulate benthic microbial habitats. The user needs only to specify the constitutive relationships as mathematical formulae, which are symbolically cast (using sympy) into a set of partial differential equations and then solved (using fipy) to study the evolution of the model entities.
The files for the JOSS paper are in the folder "joss": https://github.com/achennu/microbenthos/tree/master/joss