PROSO Toolbox: a unified protein-constrained genome-scale modelling framework for strain designing and optimization

TL;DR

PROSO Toolbox is a user-friendly software suite that automates the construction and analysis of protein-constrained genome-scale models for microbial strain design and metabolic analysis.

Contribution

It introduces a unified, accessible toolbox capable of automatically building PC-models from various reconstructions and applying algorithms for strain design and metabolism analysis.

Findings

Automates PC-model construction from high-quality reconstructions

Enables computational strain design and simulation

Facilitates metabolism analysis from gene expression data

Abstract

The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality genome-scale metabolic reconstruction as the input. The toolbox can construct a PC-model automatically, apply various algorithms for computational strain design and simulation, and help unveil metabolism from gene expression data through a state-of-the-art OVERLAY workflow. It also has detailed tutorials and documentation for maximum accessibility to researchers from diverse backgrounds. PROSO Toolbox, tutorials, and documentation are freely available online: https://github.com/QCSB/PROSO-Toolbox.