{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,13]],"date-time":"2025-09-13T15:38:21Z","timestamp":1757777901208},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1271,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner.<\/jats:p>\n               <jats:p>Results: We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats.<\/jats:p>\n               <jats:p>Availability: The biographer tool can be used at and downloaded from the web page http:\/\/biographer.biologie.hu-berlin.de\/. The different software packages, including a server-indepenent version as well as a web server for Windows and Linux based systems, are available at http:\/\/code.google.com\/p\/biographer\/ under the open-source license LGPL.<\/jats:p>\n               <jats:p>Contact: \u00a0edda.klipp@biologie.hu-berlin.de or handorf@physik.hu-berlin.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt159","type":"journal-article","created":{"date-parts":[[2013,4,11]],"date-time":"2013-04-11T02:41:33Z","timestamp":1365648093000},"page":"1467-1468","source":"Crossref","is-referenced-by-count":14,"title":["Biographer: web-based editing and rendering of SBGN compliant biochemical networks"],"prefix":"10.1093","volume":"29","author":[{"given":"Falko","family":"Krause","sequence":"first","affiliation":[{"name":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marvin","family":"Schulz","sequence":"additional","affiliation":[{"name":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ben","family":"Ripkens","sequence":"additional","affiliation":[{"name":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Max","family":"Fl\u00f6ttmann","sequence":"additional","affiliation":[{"name":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcus","family":"Krantz","sequence":"additional","affiliation":[{"name":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edda","family":"Klipp","sequence":"additional","affiliation":[{"name":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Handorf","sequence":"additional","affiliation":[{"name":"1 Theoretical Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115 Berlin, Germany and 2Codecentric AG, 40591 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,4,10]]},"reference":[{"key":"2023062610154549700_btt159-B1","doi-asserted-by":"crossref","first-page":"D504","DOI":"10.1093\/nar\/gkj126","article-title":"Pathguide: a pathway resource list","volume":"34","author":"Bader","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023062610154549700_btt159-B2","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1093\/bioinformatics\/btq407","article-title":"Editing, validating and translating of SBGN maps","volume":"26","author":"Czauderna","year":"2010","journal-title":"Bioinformatics"},{"key":"2023062610154549700_btt159-B3","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S1478-5382(03)02370-9","article-title":"CellDesigner: a process diagram editor for gene-regulatory and biochemical networks","volume":"1","author":"Funahashi","year":"2003","journal-title":"Biosilico"},{"key":"2023062610154549700_btt159-B4","doi-asserted-by":"crossref","first-page":"D428","DOI":"10.1093\/nar\/gki072","article-title":"Reactome: a knowledgebase of biological pathways","volume":"33","author":"Joshi-Tope","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023062610154549700_btt159-B5","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1093\/bioinformatics\/btp642","article-title":"Annotation and merging of SBML models with semanticSBML","volume":"26","author":"Krause","year":"2010","journal-title":"Bioinformatics"},{"key":"2023062610154549700_btt159-B6","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2202-7-S1-S11","article-title":"Model storage, exchange and integration","volume":"7","author":"Le Nov\u00e8re","year":"2006","journal-title":"BMC Neurosci."},{"key":"2023062610154549700_btt159-B7","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1038\/nbt1156","article-title":"Minimum information requested in the annotation of biochemical models (MIRIAM)","volume":"23","author":"Le Nov\u00e8re","year":"2005","journal-title":"Nat. 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