diel_models: a python package for systematic integration of day-night cycles into plant genome-scale metabolic models.

Abstract

Summary: In recent years, genome-scale metabolic models have become indispensable tools for studying complex metabolic processes occurring within living organisms. Understanding plants' metabolic behaviour under diel cycles (24-h day-night cycles) is essential to explain their adaptive strategies to different light conditions. However, integrating these cycles in plant GEMs is complex, laborious, time-consuming, and not systematized. Here, we present diel_models, a novel python package that enables the systematization and accurate construction of diel models based on non-diel plant GEMs, tailored for generic and multi-tissue models. diel_models is a lightweight, modular package with minimal dependencies and broad Python compatibility (v3.8+), making it easy to use, integrate into reconstruction pipelines, and extend with community-driven enhancements. It is also supported on all operating systems, including Windows, MacOS, and Linux, ensuring cross-platform compatibility for a wide range of users.

Availability and implementation: The code is freely available at https://github.com/BioSystemsUM/diel_models.git and can be installed using the command pip install diel_models.