Journal Article

FZJ-2021-00120

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png pyFOOMB: Python framework for object oriented modeling of bioprocesses

Hemmerich, J.FZJ* ; Tenhaef, N.FZJ* ; Wiechert, W.FZJ* ; Noack, S. (Corresponding author)FZJ*

2021
Wiley-VCH Weinheim

This record in other databases:  

Please use a persistent id in citations: http://hdl.handle.net/2128/27337  doi:10.1002/elsc.202000088

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.

---

Contributing Institute(s):

1. Biotechnologie (IBG-1)

Research Program(s):

1. 2171 - Biological and environmental resources for sustainable use (POF4-217) (POF4-217)

Appears in the scientific report 2021

---

Database coverage:
; ; ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Ebsco Academic Search ; Essential Science Indicators ; IF < 5 ; JCR ; PubMed Central ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

---