Automated Approaches for the Development of Genome‐Scale Metabolic Network Models

Genome-scale metabolic network models (GSMs) are powerful tools for gaining a deeper understanding of cellular metabolism through in silico modeling and simulation. While GSMs were initially constructed manually, many automated network reconstruction approaches have been developed over the past decade resulting in the creation of more than 250,000 GSMs. Here, we explore the process of GSM construction from both a manual and automated perspective and describe 20 different tools for GSM construction and analysis. Additionally, we highlight key examples of how large-scale GSM collections have been used to solve scientific problems in biological and biomedical research, microbiome studies, and personalized medicine, while discussing existing challenges and the future of GSM construction.