TY  - JOUR
AU  - Osthege, Michael
AU  - Tenhaef, Niklas
AU  - Zyla, Rebecca
AU  - Müller, Carolin
AU  - Hemmerich, Johannes
AU  - Wiechert, Wolfgang
AU  - Noack, Stephan
AU  - Oldiges, Marco
TI  - bletl ‐ A Python package for integrating BioLector microcultivation devices in the Design‐Build‐Test‐Learn cycle
JO  - Engineering in life sciences
VL  - 22
IS  - 3-4
SN  - 1618-0240
CY  - Weinheim
PB  - Wiley-VCH
M1  - FZJ-2022-01544
SP  - 242-259
PY  - 2022
AB  - Microbioreactor (MBR) devices have emerged as powerful cultivation tools for tasks of microbial phenotyping and bioprocess characterization and provide a wealth of online process data in a highly parallelized manner. Such datasets are difficult to interpret in short time by manual workflows. In this study, we present the Python package bletl and show how it enables robust data analyses and the application of machine learning techniques without tedious data parsing and preprocessing. bletl reads raw result files from BioLector I, II and Pro devices to make all the contained information available to Python-based data analysis workflows. Together with standard tooling from the Python scientific computing ecosystem, interactive visualizations and spline-based derivative calculations can be performed. Additionally, we present a new method for unbiased quantification of time-variable specific growth rate 𝜇⃗ 𝑡 based on unsupervised switchpoint detection with Student-t distributed random walks. With an adequate calibration model, this method enables practitioners to quantify time-variable growth rate with Bayesian uncertainty quantification and automatically detect switch-points that indicate relevant metabolic changes. Finally, we show how time series feature extraction enables the application of machine learning methods to MBR data, resulting in unsupervised phenotype characterization. As an example, Neighbor Embedding (t-SNE) is performed to visualize datasets comprising a variety of growth/DO/pH phenotypes
LB  - PUB:(DE-HGF)16
UR  - <Go to ISI:>//WOS:000762233800001
DO  - DOI:10.1002/elsc.202100108
UR  - https://juser.fz-juelich.de/record/906596
ER  -