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

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.