{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T11:55:43Z","timestamp":1773143743172,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T00:00:00Z","timestamp":1724112000000},"content-version":"vor","delay-in-days":19,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Royal Society Te Apar\u0101ngi"},{"name":"Catalyst Leader Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Catalytic reaction networks serve as fundamental models for understanding biochemical systems. CatReNet is a novel software designed to facilitate interactive analysis of such networks. It offers fast and exact algorithms for computing various types of self-sustaining autocatalytic subnetworks, including so-called CAFs (constructively autocatalytic food-generated networks), RAFs (reflexively autocatalytic food-generated networks), and pseudo-RAFs. It provides dynamic visualizations to aid exploration and understanding.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>This open-source Java application runs on Linux, MacOS, and Windows. It is available at https:\/\/github.com\/husonlab\/catrenet under a GPL3 license.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae515","type":"journal-article","created":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T19:59:52Z","timestamp":1724183992000},"source":"Crossref","is-referenced-by-count":1,"title":["CatReNet: interactive analysis of (auto-) catalytic reaction networks"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2961-604X","authenticated-orcid":false,"given":"Daniel H","family":"Huson","sequence":"first","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , 72076 T\u00fcbingen, Germany"}]},{"given":"Joana C","family":"Xavier","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Imperial College , London SW7 2BX, United Kingdom"}]},{"given":"Mike A","family":"Steel","sequence":"additional","affiliation":[{"name":"Biomathematics Research Centre, University of Canterbury , Christchurch 8041, New Zealand"}]}],"member":"286","published-online":{"date-parts":[[2024,8,20]]},"reference":[{"key":"2024083002040351700_btae515-B1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1007\/s10818-020-09295-4","article-title":"On the emergence of ecological and economic niches","volume":"22","author":"Cazzolla Gatti","year":"2020","journal-title":"J Bioecon"},{"key":"2024083002040351700_btae515-B2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13015-015-0042-8","article-title":"Algorithms for detecting and analysing autocatalytic sets","volume":"10","author":"Hordijk","year":"2015","journal-title":"Algorithms Mol Biol"},{"key":"2024083002040351700_btae515-B3","doi-asserted-by":"crossref","first-page":"20230732","DOI":"10.1098\/rsif.2023.0732","article-title":"Self-generating autocatalytic networks: structural results, algorithms, and their relevance to early biochemistry","volume":"21","author":"Huson","year":"2024","journal-title":"J R Soc Interface"},{"key":"2024083002040351700_btae515-B4","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195079517.001.0001","volume-title":"The Origins of Order","author":"Kauffman","year":"1993"},{"key":"2024083002040351700_btae515-B5","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1038\/d41586-024-00544-4","article-title":"To unravel the origin of life, treat findings as pieces of a bigger puzzle","volume":"626","author":"Lane","year":"2024","journal-title":"Nature"},{"key":"2024083002040351700_btae515-B6","first-page":"20192377","article-title":"Autocatalytic chemical networks at the origin of metabolism","volume":"287","author":"Xavier","year":"2020","journal-title":"Proc Biol Sci"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae515\/58869646\/btae515.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/8\/btae515\/58967196\/btae515.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/8\/btae515\/58967196\/btae515.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,30]],"date-time":"2024-08-30T02:04:26Z","timestamp":1724983466000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae515\/7737469"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,8]]},"references-count":6,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,8,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae515","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,8]]},"published":{"date-parts":[[2024,8]]},"article-number":"btae515"}}