Repositories list

• robotools

  Public
  Pythonic in-silico liquid handling and creation of Tecan FreedomEVO worklists.

  Python

  •

  GNU Affero General Public License v3.0

  •4•16•2•0•Updated Mar 31, 2026Mar 31, 2026

• bletl

  Public
  Parsing and data analysis with BioLector microbioreactor data.

  growth-curvestimeseries-analysisgrowthrate+ 1

  growth-curvestimeseries-analysisgrowthratebiolector

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •2•8•7•2•Updated Mar 30, 2026Mar 30, 2026

• calibr8

  Public
  Toolbox for non-linear calibration modeling.

  calibrationpymcbayesian-inference+ 2

  calibrationpymcbayesian-inferencelikelihood-functionscalibration-curve

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •2•29•7•2•Updated Mar 30, 2026Mar 30, 2026

• estim8

  Public
  Parameter estimation of bioprocess models

  parameter-estimationfmi-standardbioprocess-modeling

  parameter-estimationfmi-standardbioprocess-modeling

  Python

  •

  GNU Affero General Public License v3.0

  •0•2•1•5•Updated Mar 30, 2026Mar 30, 2026

• peak-performance

  Public
  A Python toolbox for Bayesian inference of peak areas.

  metabolomicsmass-spectrometrybayesian-inference+ 2

  metabolomicsmass-spectrometrybayesian-inferencehplcliquid-chromatography

  Python

  •

  GNU Affero General Public License v3.0

  •0•7•0•4•Updated Mar 30, 2026Mar 30, 2026

• detl

  Public
  Python package for processing of DASware raw data exports.

  parsingfermentationbioreactor+ 5

  parsingfermentationbioreactorbioprocessbioprocessingbioreactorsdasgipdasware

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •5•8•3•1•Updated Mar 30, 2026Mar 30, 2026

• CRI-Python-Lib

  Public
  Library to use Python to interact with the iRC igus Robot Control via the CRI interface

  Python

  •

  MIT License

  •6•0•0•0•Updated Feb 19, 2026Feb 19, 2026

• murefi

  Public
  Package for multiple replicate fitting and Bayesian modeling.

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •1•4•1•2•Updated Jan 30, 2026Jan 30, 2026

• Supplement-to-Prigolovkin-et-al.-2025

  Public
  Supplementary code and data to Prigolovkin et al. (2025)

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Jan 14, 2026Jan 14, 2026

• Supplement-to-Stratmann-et-al.-Bioinformatics-2025

  Public
  Python

  •1•1•0•0•Updated Oct 31, 2025Oct 31, 2025

• acia-core

  Public
  Highly automated AI workflows for single-cell analysis in time-lapse microscopy

  automationaisingle-cell+ 2

  automationaisingle-cellmicroscopytime-lapse

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

• PyUAT

  Public
  Efficient open-source Python implementation of the Uncertainty-Aware Tracking

  Jupyter Notebook

  •

  MIT License

  •0•3•0•0•Updated Oct 1, 2025Oct 1, 2025

• acia-workflows

  Public
  Highly automated AI workflows for single-cell analysis in time-lapse microscopy

  workflowanalysisjupyter-notebook+ 2

  workflowanalysisjupyter-notebooksingle-celltime-lapse

  Jupyter Notebook

  •

  MIT License

  •0•6•0•0•Updated Oct 1, 2025Oct 1, 2025

• Supplement_to_Jadebeck_et_al._MaxEnt_2024

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jul 27, 2025Jul 27, 2025

• Supplement-to-Breuer-et-al.-2023a

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 30, 2025Apr 30, 2025

• Supplement-to-Witting-et-al.-2024

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Mar 11, 2025Mar 11, 2025

• Supplement-to-Kasahara-et-al.-2025

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Mar 7, 2025Mar 7, 2025

• calibr8-paper

  Public
  Data and code to the paper "Bayesian calibration, process modeling and uncertainty quantification in biotechnology".

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• petase-ts-paper

  Public
  Repository with data, code and plots for PETase secretion study with Thompson Sampling.

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• Supplement_to_Heinzel_et_al._MaxEnt_2024

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Jul 14, 2024Jul 14, 2024

• MooViE

  Public
  Visualization tool for exploring multi variate data with an input - output semantic

  C++

  •

  MIT License

  •0•0•0•0•Updated Apr 19, 2024Apr 19, 2024

• Supplement-to-Theorell-et-al.-Metabolic_Engineering-2024

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Apr 1, 2024Apr 1, 2024

• Supplement-to-Seiffarth-et-al.-ISBI-2024

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 18, 2024Mar 18, 2024

• Supplement-to-Steier-et-al.-2024

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 11, 2024Mar 11, 2024

• Supplement-to-Helleckes-Kuesters-et-al.-2023

  Public
  Repository with code for analysis of CatIBs with Bayesian process model and Thompson sampling

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 26, 2024Jan 26, 2024

• Supplement-to-Mitosch-et-al.-PLOS-2023

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jun 23, 2023Jun 23, 2023

• Supplement-to-Reiter-et-al.-2023a

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated May 28, 2023May 28, 2023

• Supplement-to-Kasahara-et-al.-2023a

  Public
  Jupyter Notebook

  •1•1•0•0•Updated Apr 3, 2023Apr 3, 2023

• Supplement-to_Borah-et-al.-MSB-2023

  Public
  Shell

  •0•1•0•0•Updated Jan 5, 2023Jan 5, 2023

• diginbio-car-paper

  Public
  Data and analysis for the DigInBio CAR application study

  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •0•2•2•0•Updated Sep 12, 2022Sep 12, 2022