PhysioFit: a software to quantify cell growth parameters and extracellular fluxes

Area of Science:

• Systems and synthetic biology
• Computational biology
• Biotechnology

Background:

• Quantifying growth parameters and extracellular fluxes is crucial for systems and synthetic biology.
• Current tools for flux estimation are limited in interoperability and growth model flexibility.
• A need exists for accessible and adaptable software for non-computational biologists.

Purpose of the Study:

• To present PhysioFit, an open-source software for calculating extracellular fluxes.
• To provide a flexible and interoperable tool that supports various growth models.
• To enable accurate estimation of growth parameters for metabolic systems.

Main Methods:

• Development of PhysioFit as an open-source Python library.
• Implementation of common growth models with the capability for user-defined models.
• Provision of a graphical user interface (GUI) and a command-line interface (CLI).

Main Results:

• PhysioFit enables calculation of extracellular fluxes and other growth parameters.
• The software is designed for interoperability and supports any growth model.
• It offers both user-friendly GUI and streamlined CLI options for diverse user needs.

Conclusions:

• PhysioFit enhances the analysis of metabolic systems by providing a flexible and accessible flux calculation tool.
• The open-source nature and interoperability of PhysioFit promote wider adoption and integration in biological research.
• It empowers biologists to quantify key parameters for systems and synthetic biology applications.