{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T13:39:26Z","timestamp":1762868366033,"version":"3.37.3"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"22-23","license":[{"start":{"date-parts":[[2020,12,26]],"date-time":"2020-12-26T00:00:00Z","timestamp":1608940800000},"content-version":"vor","delay-in-days":25,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020884","name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100020884","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Ministerio de Ciencia"},{"name":"Tecnolog\u00eda, Conocimiento e Innovaci\u00f3n, Chile","award":["PCHA-2014-21140377","1190074","1181089"],"award-info":[{"award-number":["PCHA-2014-21140377","1190074","1181089"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Cells are complex systems composed of hundreds of genes whose products interact to produce elaborated behaviors. To control such behaviors, cells rely on transcription factors to regulate gene expression, and gene regulatory networks (GRNs) are employed to describe and understand such behavior. However, GRNs are static models, and dynamic models are difficult to obtain due to their size, complexity, stochastic dynamics and interactions with other cell processes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed Atlas, a Python software that converts genome graphs and gene regulatory, interaction and metabolic networks into dynamic models. The software employs these biological networks to write rule-based models for the PySB framework. The underlying method is a divide-and-conquer strategy to obtain sub-models and combine them later into an ensemble model. To exemplify the utility of Atlas, we used networks of varying size and complexity of Escherichia coli and evaluated in silico modifications, such as gene knockouts and the insertion of promoters and terminators. Moreover, the methodology could be applied to the dynamic modeling of natural and synthetic networks of any bacteria.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Code, models and tutorials are available online (https:\/\/github.com\/networkbiolab\/atlas).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1040","type":"journal-article","created":{"date-parts":[[2020,12,12]],"date-time":"2020-12-12T12:40:19Z","timestamp":1607776819000},"page":"5473-5480","source":"Crossref","is-referenced-by-count":5,"title":["<i>Atlas<\/i>: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0075-4921","authenticated-orcid":false,"given":"Rodrigo","family":"Santib\u00e1\u00f1ez","sequence":"first","affiliation":[{"name":"Laboratorio de Biolog\u00eda de Redes, Centro de Gen\u00f3mica y Bioinform\u00e1tica, Universidad Mayor , Santiago 8580745, Chile"},{"name":"Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Cat\u00f3lica de Chile , Santiago 7820436, Chile"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4982-134X","authenticated-orcid":false,"given":"Daniel","family":"Garrido","sequence":"additional","affiliation":[{"name":"Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Cat\u00f3lica de Chile , Santiago 7820436, Chile"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6147-3325","authenticated-orcid":false,"given":"Alberto J M","family":"Martin","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda de Redes, Centro de Gen\u00f3mica y Bioinform\u00e1tica, Universidad Mayor , Santiago 8580745, Chile"}]}],"member":"286","published-online":{"date-parts":[[2020,12,26]]},"reference":[{"key":"2023062707304907100_btaa1040-B1","doi-asserted-by":"crossref","first-page":"e1002980","DOI":"10.1371\/journal.pcbi.1002980","article-title":"The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysognum","volume":"9","author":"Agren","year":"2013","journal-title":"PLoS Comput. 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