pyFOOMB: Python framework for object oriented modeling of bioprocesses

Abstract

Quantitative characterization of biotechnological production processes requires the determination of different key performance indicators (KPIs) such as titer, rate and yield. Classically, these KPIs can be derived by combining black-box bioprocess modeling with non-linear regression for model parameter estimation. The presented pyFOOMB package enables a guided and flexible implementation of bioprocess models in the form of ordinary differential equation systems (ODEs). By building on Python as powerful and multi-purpose programing language, ODEs can be formulated in an object-oriented manner, which facilitates their modular design, reusability, and extensibility. Once the model is implemented, seamless integration and analysis of the experimental data is supported by various Python packages that are already available. In particular, for the iterative workflow of experimental data generation and subsequent model parameter estimation we employed the concept of replicate model instances, which are linked by common sets of parameters with global or local properties. For the description of multi-stage processes, discontinuities in the right-hand sides of the differential equations are supported via event handling using the freely available assimulo package. Optimization problems can be solved by making use of a parallelized version of the generalized island approach provided by the pygmo package. Furthermore, pyFOOMB in combination with Jupyter notebooks also supports education in bioprocess engineering and the applied learning of Python as scientific programing language. Finally, the applicability and strengths of pyFOOMB will be demonstrated by a comprehensive collection of notebook examples.