Software applications for phenotype analysis and strain design of cellular systems

Constraint-based reconstruction and analysis (COBRA) is one of the most widely used modeling approaches for describing and simulating cellular systems in silico. It has been increasingly applied to analyze the cellular metabolisms of over 100 species and characterize their phenotypes and metabolic behaviors under various environmental and/or genetic perturbations. Such popularity of COBRA framework has resulted in the development of a myriad of software applications that allow researchers to implement it conveniently without knowledge on theoretical backgrounds. Here, we first surveyed all publicly available software applications and reported their features and capability to apply various COBRA methods within the generic workflow. In addition, we also demonstrated the practical utility of software tools in postulating strain design strategies via a case study of Escherichia coli for overproducing succinate.