{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T10:54:02Z","timestamp":1767178442475,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010635","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T00:00:00Z","timestamp":1669593600000}}],"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,14]],"date-time":"2022-11-14T00:00:00Z","timestamp":1668384000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004410","name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ftirma Kurumu","doi-asserted-by":"publisher","award":["118E131"],"award-info":[{"award-number":["118E131"]}],"id":[{"id":"10.13039\/501100004410","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Visualization is a key recurring requirement for effective analysis of relational data. Biology is no exception. It is imperative to annotate and render biological models in standard, widely accepted formats. Finding graph-theoretical properties of pathways as well as identifying certain paths or subgraphs of interest in a pathway are also essential for effective analysis of pathway data. Given the size of available biological pathway data nowadays, automatic layout is crucial in understanding the graphical representations of such data. Even though there are many available software tools that support graphical display of biological pathways in various formats, there is none available as a service for on-demand or batch processing of biological pathways for automatic layout, customized rendering and mining paths or subgraphs of interest. In addition, there are many tools with fine rendering capabilities lacking decent automatic layout support.<\/jats:p>\n                  <jats:p>\n                    To fill this void, we developed a web service named SyBLaRS (\n                    <jats:underline>Sy<\/jats:underline>\n                    stems\n                    <jats:underline>B<\/jats:underline>\n                    iology\n                    <jats:underline>La<\/jats:underline>\n                    yout and\n                    <jats:underline>R<\/jats:underline>\n                    endering\n                    <jats:underline>S<\/jats:underline>\n                    ervice) for automatic layout of biological data in various standard formats as well as construction of customized images in both raster image and scalable vector formats of these maps. Some of the supported standards are more generic such as GraphML and JSON, whereas others are specialized to biology such as SBGNML (The Systems Biology Graphical Notation Markup Language) and SBML (The Systems Biology Markup Language). In addition, SyBLaRS supports calculation and highlighting of a number of well-known graph-theoretical properties as well as some novel graph algorithms turning a specified set of objects of interest to a minimal pathway of interest.\n                  <\/jats:p>\n                  <jats:p>We demonstrate that SyBLaRS can be used both as an offline layout and rendering service to construct customized and annotated pictures of pathway models and as an online service to provide layout and rendering capabilities for systems biology software tools.<\/jats:p>\n                  <jats:p>\n                    SyBLaRS is open source and publicly available on\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/iVis-at-Bilkent\/syblars\" xlink:type=\"simple\">GitHub<\/jats:ext-link>\n                    and freely distributed under the MIT license. In addition, a sample deployment is available\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/syblars.cs.bilkent.edu.tr\/\" xlink:type=\"simple\">here<\/jats:ext-link>\n                    for public consumption.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1010635","type":"journal-article","created":{"date-parts":[[2022,11,14]],"date-time":"2022-11-14T13:30:55Z","timestamp":1668432655000},"page":"e1010635","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8319-7758","authenticated-orcid":true,"given":"Hasan","family":"Balci","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7153-0784","authenticated-orcid":true,"given":"Ugur","family":"Dogrusoz","sequence":"additional","affiliation":[]},{"given":"Yusuf Ziya","family":"Ozgul","sequence":"additional","affiliation":[]},{"given":"Perman","family":"Atayev","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,11,14]]},"reference":[{"key":"pcbi.1010635.ref001","doi-asserted-by":"crossref","first-page":"20200016","DOI":"10.1515\/jib-2020-0016","article-title":"Systems biology graphical notation markup language (SBGNML) version 0.3","volume":"17","author":"FT Bergmann","year":"2020","journal-title":"Journal of Integrative Bioinformatics"},{"key":"pcbi.1010635.ref002","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"M Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"pcbi.1010635.ref003","first-page":"D489","article-title":"Pathway Commons 2019 Update: integration, analysis and exploration of pathway data","volume":"48","author":"I Rodchenkov","year":"2020","journal-title":"Nucleic Acids Research"},{"key":"pcbi.1010635.ref004","doi-asserted-by":"crossref","first-page":"D661","DOI":"10.1093\/nar\/gkx1064","article-title":"WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research","volume":"46","author":"DN Slenter","year":"2018","journal-title":"Nucleic Acids Research"},{"key":"pcbi.1010635.ref005","doi-asserted-by":"crossref","first-page":"D691","DOI":"10.1093\/nar\/gkq1018","article-title":"Reactome: a database of reactions, pathways and biological processes","volume":"39","author":"D Croft","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"pcbi.1010635.ref006","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1145\/1924421.1924439","article-title":"Design principles for visual communication","volume":"54","author":"M Agrawala","year":"2011","journal-title":"Communications of the ACM"},{"key":"pcbi.1010635.ref007","unstructured":"Klauske LK. Effizientes Bearbeiten von Simulink Modellen mit Hilfe eines spezifisch angepassten Layoutalgorithmus. Technische Universit\u00e4t Berlin; 2012."},{"key":"pcbi.1010635.ref008","doi-asserted-by":"crossref","first-page":"1475","DOI":"10.1093\/bioinformatics\/btaa850","article-title":"Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps","volume":"37","author":"H Balci","year":"2020","journal-title":"Bioinformatics"},{"issue":"5","key":"pcbi.1010635.ref009","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":"A Funahashi","year":"2003","journal-title":"Biosilico"},{"key":"pcbi.1010635.ref010","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1093\/bioinformatics\/btq407","article-title":"Editing, validating and translating of SBGN maps","volume":"26","author":"T Czauderna","year":"2010","journal-title":"Bioinformatics"},{"key":"pcbi.1010635.ref011","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1186\/1471-2164-15-642","article-title":"Integrating biological pathways and genomic profiles with ChiBE 2","volume":"15","author":"Babur \u00d6zg\u00fcn","year":"2014","journal-title":"BMC genomics"},{"issue":"D1","key":"pcbi.1010635.ref012","first-page":"D407","article-title":"BioModels \u2014 15 years of sharing computational models in life science","volume":"48","author":"RS Malik-Sheriff","year":"2020","journal-title":"Nucleic Acids Research"},{"key":"pcbi.1010635.ref013","doi-asserted-by":"crossref","first-page":"W150","DOI":"10.1093\/nar\/gkq352","article-title":"VISIBIOweb: visualization and layout services for BioPAX pathway models","volume":"38","author":"A Dilek","year":"2010","journal-title":"Nucleic Acids Research"},{"issue":"9","key":"pcbi.1010635.ref014","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","article-title":"The BioPAX community standard for pathway data sharing","volume":"28","author":"E Demir","year":"2010","journal-title":"Nature Biotechnology"},{"key":"pcbi.1010635.ref015","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1093\/bioinformatics\/btv557","article-title":"Cytoscape.js: a graph theory library for visualisation and analysis","volume":"32","author":"M Franz","year":"2016","journal-title":"Bioinformatics"},{"key":"pcbi.1010635.ref016","article-title":"fCoSE: a fast compound graph layout algorithm with constraint support","author":"H Balci","year":"2021","journal-title":"IEEE Transactions on Visualization and Computer Graphics"},{"key":"pcbi.1010635.ref017","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1109\/TVCG.2012.178","article-title":"CiSE: A Circular Spring Embedder Layout Algorithm","volume":"19","author":"U Dogrusoz","year":"2013","journal-title":"IEEE Transactions on Visualization and Computer Graphics"},{"key":"pcbi.1010635.ref018","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-349-03521-2","volume-title":"Graph Theory with Applications","author":"JA Bondy","year":"1976"},{"key":"pcbi.1010635.ref019","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-10-376","article-title":"Algorithms for Effective Querying of Compound Graph-Based Pathway Databases","volume":"10","author":"U Dogrusoz","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"pcbi.1010635.ref020","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1093\/bioinformatics\/btv557","article-title":"Cytoscape. js: a graph theory library for visualisation and analysis","volume":"32","author":"M Franz","year":"2016","journal-title":"Bioinformatics"},{"key":"pcbi.1010635.ref021","doi-asserted-by":"crossref","first-page":"35","DOI":"10.2307\/3033543","article-title":"A set of measures of centrality based upon betweenness","volume":"40","author":"L Freeman","year":"1977","journal-title":"Sociometry"},{"issue":"1","key":"pcbi.1010635.ref022","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/BF01386390","article-title":"A note on two problems in connexion with graphs","volume":"1","author":"EW Dijkstra","year":"1959","journal-title":"Numerische mathematik"},{"key":"pcbi.1010635.ref023","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1126\/science.1141478","article-title":"MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling","volume":"316","author":"J Engelman","year":"2007","journal-title":"Science"},{"key":"pcbi.1010635.ref024","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature07385","article-title":"Comprehensive genomic characterization defines human glioblastoma genes and core pathways","volume":"455","author":"The Cancer Genome Atlas Research Network","year":"2008","journal-title":"Nature"},{"key":"pcbi.1010635.ref025","unstructured":"PathwayCommons. PathwayCommons\/cytoscape-sbgn-stylesheet: View Biological Networks via Cytoscape.js and sbgn-ml;. Available from: https:\/\/github.com\/PathwayCommons\/cytoscape-sbgn-stylesheet."},{"key":"pcbi.1010635.ref026","unstructured":"PathwayCommons. PathwayCommons\/sbgnml-to-cytoscape: An npm module that converts xml based SBGN files to JSON for Cytoscape.js;. Available from: https:\/\/github.com\/PathwayCommons\/sbgnml-to-cytoscape."},{"key":"pcbi.1010635.ref027","doi-asserted-by":"crossref","first-page":"104150","DOI":"10.1016\/j.biosystems.2020.104150","article-title":"libsbmljs\u2014Enabling web-based SBML tools","volume":"195","author":"JK Medley","year":"2020","journal-title":"Biosystems"},{"key":"pcbi.1010635.ref028","first-page":"501","volume-title":"Graph Drawing","author":"U Brandes","year":"2001"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1010635","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T00:00:00Z","timestamp":1669593600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010635","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,11]],"date-time":"2023-03-11T20:34:43Z","timestamp":1678566883000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010635"}},"subtitle":[],"editor":[{"given":"Pedro","family":"Mendes","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,11,14]]},"references-count":28,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010635","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,14]]}}}