Bioreactor

Bioreactor is an upstream processing software tool developed by Ypso-Facto, aimed at scientists and engineers working on cell culture and bioprocess development in biologics. It is designed to support data management, analysis, and mechanistic modelling for upstream bioprocessing (USP) projects involving organisms such as CHO cells and E. coli.

The tool combines a structured data management interface with built-in data treatment functions and a mechanistic modelling framework, positioning itself as an alternative to Monod-like kinetics and purely data-driven approaches, which Ypso-Facto considers limited in predictive capability.

Interface and Navigation

• A structured arborescence provides fast and easy navigation through projects.
• Users can select preferred units at any point during their work.
• All data types — online, inline, atline, and offline — are organised in clearly labelled tables and stored with units.
• Process descriptions are stored alongside the corresponding experimental data.
• Charts can be fully customised and formatted using custom templates.
• Experiments can be compared directly within the interface.

Built-in Data Treatment Features

• Growth rate calculation
• Substrate uptake rate calculation
• Product formation rate calculation
• Additional data treatment functions beyond the above

Reporting

• Word reports can be generated by exporting detailed process descriptions accompanied by charts.

Mechanistic Modelling Framework

• The modelling approach is based on four key physico-chemical phenomena rather than empirical or purely data-driven methods.
• The four modelled phenomena are: transfer of substrates and products across the cell membrane; intracellular reactions; cell growth and cell division; and cell death.
• Each phenomenon is adapted to the specific organism of interest, such as CHO cells or E. coli.
• Organism-specific adaptations are supported; for example, product exit can be deactivated when modelling E. coli inclusion bodies.

Bioreactor is developed by Ypso-Facto, a company combining expertise in chemistry, biotechnology, and process engineering with experience in chemical, pharmaceutical, and biotech industries as well as academic research.