{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,17]],"date-time":"2026-05-17T02:26:29Z","timestamp":1778984789600,"version":"3.51.4"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T00:00:00Z","timestamp":1674086400000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009139","name":"German Center for Infection Research","doi-asserted-by":"publisher","award":["8020708703"],"award-info":[{"award-number":["8020708703"]}],"id":[{"id":"10.13039\/100009139","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections"},{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Baden-W\u00fcrttemberg Ministry of Science"},{"name":"Excellence Strategy of the German Federal and State Governments"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The human body harbours a plethora of microbes that play a fundamental role in the well-being of the host. Still, the contribution of many microorganisms to human health remains undiscovered. To understand the composition of their communities, the accurate genome-scale metabolic network models of participating microorganisms are integrated to construct a community that mimics the normal bacterial flora of humans. So far, tools for modelling the communities have transformed the community into various optimization problems and model compositions. Therefore, any knockout or modification of each submodel (each species) necessitates the up-to-date creation of the community to incorporate rebuildings. To solve this complexity, we refer to the context of SBML in a hierarchical model composition, wherein each species\u2019s genome-scale metabolic model is imported as a submodel in another model. Hence, the community is a model composed of submodels defined in separate files. We combine all these files upon parsing to a so-called \u2018flattened\u2019 model, i.e., a comprehensive and valid SBML file of the entire community that COBRApy can parse for further processing. The hierarchical model facilitates the analysis of the whole community irrespective of any changes in the individual submodels.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The module is freely available at https:\/\/github.com\/manuelgloeckler\/ncmw.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad040","type":"journal-article","created":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T12:01:32Z","timestamp":1674129692000},"source":"Crossref","is-referenced-by-count":3,"title":["Hierarchical modelling of microbial communities"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3707-9395","authenticated-orcid":false,"given":"Manuel","family":"Gl\u00f6ckler","sequence":"first","affiliation":[{"name":"Department of Computer Science, Eberhard Karl University T\u00fcbingen, Sand 14 , T\u00fcbingen 72076, Germany"},{"name":"Machine Learning in Science, Excellence Cluster \u2018Machine Learning\u2019, Eberhard Karl University of T\u00fcbingen, Maria-von-Linden-Str. 6 , T\u00fcbingen 72076, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1240-5553","authenticated-orcid":false,"given":"Andreas","family":"Dr\u00e4ger","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Eberhard Karl University T\u00fcbingen, Sand 14 , T\u00fcbingen 72076, Germany"},{"name":"Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI) , Sand 14 , T\u00fcbingen 72076, Germany"},{"name":"German Center for Infection Research (DZIF), Partner Site T\u00fcbingen , Wilhelmstr. 27 , T\u00fcbingen 72074, Germany"},{"name":"Cluster of Excellence \u2018Controlling Microbes to Fight Infections\u2019, Eberhard Karl University T\u00fcbingen , Auf der Morgenstelle 28 , T\u00fcbingen 72074, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2479-6851","authenticated-orcid":false,"given":"Reihaneh","family":"Mostolizadeh","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Eberhard Karl University T\u00fcbingen, Sand 14 , T\u00fcbingen 72076, Germany"},{"name":"Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI) , Sand 14 , T\u00fcbingen 72076, Germany"},{"name":"German Center for Infection Research (DZIF), Partner Site T\u00fcbingen , Wilhelmstr. 27 , T\u00fcbingen 72074, Germany"},{"name":"Cluster of Excellence \u2018Controlling Microbes to Fight Infections\u2019, Eberhard Karl University T\u00fcbingen , Auf der Morgenstelle 28 , T\u00fcbingen 72074, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,1,19]]},"reference":[{"key":"2023013106112673500_btad040-B1","doi-asserted-by":"crossref","DOI":"10.3389\/fbinf.2022.827024","article-title":"NCMW: a python package to analyze metabolic interactions in the nasal microbiome","volume":"2","author":"Gl\u00f6ckler","year":"2022","journal-title":"Front. Bioinf"},{"key":"2023013106112673500_btad040-B2","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1016\/S0006-3495(02)73903-9","article-title":"Dynamic flux balance analysis of diauxic growth in Escherichia coli","volume":"83","author":"Mahadevan","year":"2002","journal-title":"Biophys. J"},{"key":"2023013106112673500_btad040-B3","doi-asserted-by":"crossref","first-page":"925215","DOI":"10.3389\/fcimb.2022.925215","article-title":"Towards the human nasal microbiome: simulating D. pigrum and S. aureus","volume":"12","author":"Mostolizadeh","year":"2022","journal-title":"Front. Cell. Infect. Microbiol"},{"key":"2023013106112673500_btad040-B4","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1515\/jib-2015-268","article-title":"SBML level 3 package: hierarchical model composition, version 1 release 3","volume":"12","author":"Smith","year":"2015","journal-title":"J. Integr. 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