The Biorefinery Simulation and Techno-Economic Analysis Modules; Life Cycle Assessment; Chemical Process Simulation Under Uncertainty

Mechanistic models in fermentation

Deep hybrid modeling of bioreactor cell culture data using Long Short-Term Memory (LSTM) networks combined with first principles equations

sbml2hyb is a tool for SBML compatible hybrid modelling of biological systems

Python package for processing of DASware raw data exports.

Material for standard text book model of batch cultivation where substrate measurement noise added and end of batch detected

Material for standard text book model of fedbatch cultivation. Updated.

Material for standard text book model of perfusion cultivation. Updated.

Code behind 'Data Driven Modelling and Optimisation for Sustainable Bio-Production' as well as a related simple kinetic model using odes

Material for model of aerated fedbatch cultivation of yeast. Updated.

Material for model of fedbatch cultivation of CHO cells. Updated.

Material for standard text book model of batch cultivation where model is calibrated using time series data for substrate and cell concentration. Updated.

Material for standard text book model of batch cultivation. Updated.

Material for model of batch cultivation of yeast and exploring constraint-based view of metabolism and growth.

Material for standard text book model of chemostat (continuous) cultivation. Updated.

R Scripts for quantification of microbial robustness from high-throughput screenings

Notebooks with examples to be presented at Modelica 15 in October 2023

Documentation

Clonalyzer is a Python-based tool designed to clean, process, and analyze kinetic data from CHO (Chinese Hamster Ovary) cell clones. It supports experiments involving multiple clones and replicates, enabling users to evaluate performance across various experimental conditions systematically.

BioReact is a Python tool for simulating the dynamics of a Continuous Stirred Tank Bioreactor (CSTR). It uses the Monod model and Runge-Kutta method, with customizable parameters and automated visualizations, ideal for biotechnology research.