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README.md

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DOI

This repository contains the data, code and manuscript of Control of Parallelized Bioreactors II - Probabilistic Quantification of Carboxylic Acid Reductase Activity for Bioprocess Optimization (2022), N. von den Eichen, M. Osthege, M. Dölle, L. Bromig, W. Wiechert, M. Oldiges, D. Weuster-Botz.

Contents

  • /data contains the raw experimental data
  • /manuscript includes the manuscript TeX files and figures
  • /code contains Jupyter notebooks and Python modules for the data processing pipeline

Installation of the Environment

An environment.yml file is provided. You can create an environment for running the data analysis with

conda env create -f environment.yml

Running the analysis

Each step of the data analysis pipeline is a function in /code/pipeline.py.

We ran these steps in a parallelized setup on a cluster. The important part is to run the tasks in the order found in code/pipeline_run_all.py.