PyOMES: an open-source framework for biochemical process modelling

Abstract

PyOMES is a Python-based, Open-source Modelling Environment for (bio)chemical process Simulation that aims to simplify the modelling of dynamic (including steady state) processes. This is done in a generalied, modular way to facilitate modelling a broad range of biological, chemical, and biochemical systems under a single modelling framework. PyOMES has been built to be accessible to a broad range of users - ranging from those with little modelling experience, such as experimentalists and students, through to more experienced power-users. Here, an introduction is provided to the PyOMES software including a summary of the design, architecture and vision. Use cases are then provided to demonstrate applicability of PyOMES to a number of (bio)chemical process modelling scenarios. Comparisons of predictions against existing benchmark software (i.e. PHREEQC) demonstrate the robustness of the package. Finally, a summary is provided of future directions for the PyOMES package - highlighting its establishment as a unified modelling framework and its potential for community-driven improvement as future developments.