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

• Author(s): Martins, Luciana ; Capela, João ; Cunha, Emanuel Rodrigues ; Sampaio, Marta ; Dias, Oscar
• Date: 2025
• Persistent ID: https://hdl.handle.net/1822/95932
• Origin: RepositóriUM - Universidade do Minho
• Document Type: Journal article
• Language: English
• Contributor(s): Universidade do Minho

Description

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 daynight 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 (v3.8þ), 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.