{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:24Z","timestamp":1753875804766,"version":"3.41.2"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T00:00:00Z","timestamp":1744761600000},"content-version":"vor","delay-in-days":111,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Portuguese Foundation for Science and Technology","award":["UIDB\/04469\/2020","DFA\/BD\/08789\/2021"],"award-info":[{"award-number":["UIDB\/04469\/2020","DFA\/BD\/08789\/2021"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>In recent years, genome-scale metabolic models have become indispensable tools for studying complex metabolic processes occurring within living organisms. Understanding plants\u2019 metabolic behaviour under diel cycles (24-h day\u2013night 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code is freely available at https:\/\/github.com\/BioSystemsUM\/diel_models.git and can be installed using the command pip install diel_models.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioadv\/vbaf087","type":"journal-article","created":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T15:39:14Z","timestamp":1744817954000},"source":"Crossref","is-referenced-by-count":0,"title":["diel_models: a python package for systematic integration of day\u2013night cycles into plant genome-scale metabolic models"],"prefix":"10.1093","volume":"5","author":[{"given":"Luciana","family":"Martins","sequence":"first","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]}]},{"given":"Jo\u00e3o","family":"Capela","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]}]},{"given":"Emanuel","family":"Cunha","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]}]},{"given":"Marta","family":"Sampaio","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1765-7178","authenticated-orcid":false,"given":"Oscar","family":"Dias","sequence":"additional","affiliation":[{"name":"Centre of Biological Engineering, University of Minho , Braga 4710-057,","place":["Portugal"]},{"name":"LABBELS\u2014Associate Laboratory , Braga, 4710-057,","place":["Portugal"]}]}],"member":"286","published-online":{"date-parts":[[2025,4,16]]},"reference":[{"key":"2025061901530888400_vbaf087-B1","doi-asserted-by":"crossref","first-page":"e1000859","DOI":"10.1371\/journal.pcbi.1000859","article-title":"Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes","volume":"6","author":"Bordel","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"2025061901530888400_vbaf087-B2","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1111\/TPJ.12252","article-title":"A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions","volume":"75","author":"Cheung","year":"2013","journal-title":"Plant J"},{"key":"2025061901530888400_vbaf087-B3","doi-asserted-by":"publisher","first-page":"e1011499","DOI":"10.1371\/journal.pcbi.1011499","article-title":"The first multi-tissue 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