{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T08:57:41Z","timestamp":1776416261985,"version":"3.51.2"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,18]],"date-time":"2022-02-18T00:00:00Z","timestamp":1645142400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"CAS Mellon Fund at American University"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["1U01EB024501-01"],"award-info":[{"award-number":["1U01EB024501-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["NSF CBET-1750183"],"award-info":[{"award-number":["NSF CBET-1750183"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["NIH 1R01AI135128-01"],"award-info":[{"award-number":["NIH 1R01AI135128-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["NIH 1R01GM127909-01"],"award-info":[{"award-number":["NIH 1R01GM127909-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We introduce SteadyCellPhenotype, a browser-based interface for the analysis of ternary biological networks. It includes tools for deterministically finding all steady states of a network, as well as the simulation and visualization of trajectories with publication quality graphics. Simulations allow us to approximate the size of the basin for attractors and deterministic simulations of trajectories nearby specified points allow us to explore the behavior of the system in that neighborhood.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/knappa\/steadycellphenotype MIT License.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac097","type":"journal-article","created":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T23:54:55Z","timestamp":1644882895000},"page":"2369-2370","source":"Crossref","is-referenced-by-count":4,"title":["<i>SteadyCellPhenotype<\/i>\n                    : a web-based tool for the modeling of biological networks with ternary logic"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5719-6003","authenticated-orcid":false,"given":"Adam C","family":"Knapp","sequence":"first","affiliation":[{"name":"Department of Medicine, University of Florida , Gainesville, FL 32611, USA"},{"name":"Department of Mathematics and Statistics, American University , Washington, DC 20016, USA"}]},{"given":"Luis","family":"Sordo Vieira","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Florida , Gainesville, FL 32611, USA"}]},{"given":"Reinhard","family":"Laubenbacher","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Florida , Gainesville, FL 32611, USA"}]},{"given":"Julia","family":"Chifman","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, American University , Washington, DC 20016, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,2,18]]},"reference":[{"key":"2023020109025021000_btac097-B1","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D3: data-driven documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans. Visual. Comput. Graph"},{"key":"2023020109025021000_btac097-B2","doi-asserted-by":"crossref","first-page":"e1005352","DOI":"10.1371\/journal.pcbi.1005352","article-title":"Activated oncogenic pathway modifies iron network in breast epithelial cells: a dynamic modeling perspective","volume":"13","author":"Chifman","year":"2017","journal-title":"PLoS Comput. Biol"},{"key":"2023020109025021000_btac097-B3","doi-asserted-by":"crossref","first-page":"2923","DOI":"10.1105\/tpc.104.021725","article-title":"A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles[W]","volume":"16","author":"Espinosa-Soto","year":"2004","journal-title":"Plant Cell"},{"key":"2023020109025021000_btac097-B4","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy","volume":"585","author":"Harris","year":"2020","journal-title":"Nature"},{"key":"2023020109025021000_btac097-B5","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/0022-5193(69)90015-0","article-title":"Metabolic stability and epigenesis in randomly constructed genetic nets","volume":"22","author":"Kauffman","year":"1969","journal-title":"J. Theor. Biol"},{"key":"2023020109025021000_btac097-B6","doi-asserted-by":"crossref","DOI":"10.1145\/2833157.2833162","article-title":"Numba: A LLVM-based python JIT compiler","author":"Lam","year":"2015"},{"key":"2023020109025021000_btac097-B7","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1093\/bioinformatics\/btq124","article-title":"BoolNet\u2014an R package for generation, reconstruction and analysis of Boolean networks","volume":"26","author":"M\u00fcssel","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020109025021000_btac097-B8","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.biosystems.2009.04.008","article-title":"Logical modelling of regulatory networks with ginsim 2.3","volume":"97","author":"Naldi","year":"2009","journal-title":"Biosystems"},{"key":"2023020109025021000_btac097-B9","doi-asserted-by":"crossref","first-page":"4042","DOI":"10.1158\/0008-5472.CAN-15-0602","article-title":"A modeling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis","volume":"75","author":"Remy","year":"2015","journal-title":"Cancer Res"},{"key":"2023020109025021000_btac097-B10","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.jbiotec.2017.05.001","article-title":"Use of CellNetAnalyzer in biotechnology and metabolic engineering","volume":"261","author":"von Kamp","year":"2017","journal-title":"J. Biotechnol"},{"key":"2023020109025021000_btac097-B11","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1093\/bioinformatics\/btp617","article-title":"SimBoolNet\u2014a Cytoscape plugin for dynamic simulation of signaling networks","volume":"26","author":"Zheng","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac097\/42628821\/btac097.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/8\/2369\/49009339\/btac097.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/8\/2369\/49009339\/btac097.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T15:52:11Z","timestamp":1675266731000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/8\/2369\/6531958"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,2,18]]},"references-count":11,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2022,4,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac097","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.08.10.454961","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,4,15]]},"published":{"date-parts":[[2022,2,18]]}}}