CarveAdornCurate: a versatile cloud-based platform for constructing multiscale metabolic models.

Abstract

Multiscale modeling is a promising approach for understanding cellular behaviors. However, existing multiscale modeling tools require meticulously curated genome-scale metabolic models (GEMs) as inputs, limiting the broad applications of multiscale models due to complex and time-consuming construction processes. To this end, we developed a novel workflow named CarveAdornCurate (CAC) for de novo multiscale modeling. The Carve module generates an ensemble of GEMs with strong genetic evidence, which is then upgraded to multiscale models using Adorn module. The Curate module was designed to find features important to the generated models. These three modules are integrated into a cloud-based platform to promote broad accessibility. As proof of concept, we constructed CAC-based multiscale models for Corynebacterium glutamicum and Yarrowia lipolytica, demonstrating their potential in guiding metabolic engineering. Overall, CAC is demonstrated to be an efficient and user-friendly tool for constructing multiscale models. It is available online at www.carveadorncurate.com/.