{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T08:43:41Z","timestamp":1778575421026,"version":"3.51.4"},"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T00:00:00Z","timestamp":1668038400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"CIFRE doctoral grant","award":["2018\/1475"],"award-info":[{"award-number":["2018\/1475"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1010622","type":"journal-article","created":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T18:24:07Z","timestamp":1668104647000},"page":"e1010622","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Ten simple rules for developing visualization tools in genomics"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2734-4327","authenticated-orcid":true,"given":"Eloi","family":"Durant","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0284-1885","authenticated-orcid":true,"given":"Mathieu","family":"Rouard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric W.","family":"Ganko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cedric","family":"Muller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alan M.","family":"Cleary","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew D.","family":"Farmer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthieu","family":"Conte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8522-7583","authenticated-orcid":true,"given":"Francois","family":"Sabot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2022,11,10]]},"reference":[{"key":"pcbi.1010622.ref001","first-page":"233","article-title":"\u201cFlatten the Curve!\u201d But Which Curve?","volume":"XXXV","author":"\u00c9. Brian","year":"2020","journal-title":"Hist Mes."},{"key":"pcbi.1010622.ref002","author":"M. Krzywinski","year":"2022","journal-title":"A pandemic of bad charts"},{"key":"pcbi.1010622.ref003","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"J Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"pcbi.1010622.ref004","article-title":"Grand Challenges in Bioinformatics Data Visualization.","volume":"1","author":"SI O\u2019Donoghue","year":"2021","journal-title":"Front Bioinform"},{"key":"pcbi.1010622.ref005","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"R Buels","year":"2016","journal-title":"Genome Biol"},{"key":"pcbi.1010622.ref006","doi-asserted-by":"crossref","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","article-title":"Ensembl 2022.","volume":"50","author":"F Cunningham","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1010622.ref007","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.","volume":"14","author":"H Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Brief Bioinform"},{"key":"pcbi.1010622.ref008","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/s13742-015-0077-2","article-title":"Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.","volume":"4","author":"GA Pavlopoulos","year":"2015","journal-title":"GigaScience."},{"key":"pcbi.1010622.ref009","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1111\/cgf.13727","article-title":"Tasks, Techniques, and Tools for Genomic Data Visualization","volume":"38","author":"S Nusrat","year":"2019","journal-title":"Computer Graphics Forum"},{"key":"pcbi.1010622.ref010","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/s10038-019-0687-0","article-title":"Visualization tools for human structural variations identified by whole-genome sequencing","volume":"65","author":"TT Yokoyama","year":"2020","journal-title":"J Hum Genet"},{"key":"pcbi.1010622.ref011","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s13059-017-1161-y","article-title":"Software tools for visualizing Hi-C data","volume":"18","author":"GG Yard\u0131mc\u0131","year":"2017","journal-title":"Genome Biol"},{"key":"pcbi.1010622.ref012","first-page":"giy121","article-title":"MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks.","volume":"7","author":"Y Peng","year":"2018","journal-title":"GigaScience."},{"key":"pcbi.1010622.ref013","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome Res"},{"key":"pcbi.1010622.ref014","doi-asserted-by":"crossref","first-page":"2431","DOI":"10.1109\/TVCG.2012.213","article-title":"Design Study Methodology: Reflections from the Trenches and the Stacks","volume":"18","author":"M Sedlmair","year":"2012","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"pcbi.1010622.ref015","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pbio.1002195","article-title":"Big Data: Astronomical or Genomical?","volume":"13","author":"ZD Stephens","year":"2015","journal-title":"PLoS Biol"},{"key":"pcbi.1010622.ref016","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: Visualization of Intersecting Sets.","volume":"20","author":"A Lex","year":"2014","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"pcbi.1010622.ref017","article-title":"Graphs Beyond the Hairball.","author":"R. Kosara","year":"2012","journal-title":"In: eagereyes [Internet]."},{"key":"pcbi.1010622.ref018","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1109\/TVCG.2019.2934538","article-title":"Data Changes Everything: Challenges and Opportunities in Data Visualization Design Handoff","volume":"26","author":"J Walny","year":"2020","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"pcbi.1010622.ref019","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s12859-020-3373-5","article-title":"BigTop: a three-dimensional virtual reality tool for GWAS visualization","volume":"21","author":"ST Westreich","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1010622.ref020","first-page":"100149","article-title":"Delta.AR: An augmented reality-based visualization platform for 3D genome","volume":"2","author":"B Tang","year":"2021","journal-title":"Innovation (N Y)."},{"key":"pcbi.1010622.ref021","first-page":"1","article-title":"The Immersive Graph Genome Explorer: Navigating Genomics in Immersive Virtual Reality.","author":"M Kuznetsov","year":"2021","journal-title":"2021 IEEE 9th International Conference on Serious Games and Applications for Health (SeGAH)."},{"key":"pcbi.1010622.ref022","doi-asserted-by":"crossref","first-page":"e1010310","DOI":"10.1371\/journal.pcbi.1010310","article-title":"Graphia: A platform for the graph-based visualisation and analysis of high dimensional data.","volume":"18","author":"TC Freeman","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010622.ref023","doi-asserted-by":"crossref","DOI":"10.1201\/b17511","volume-title":"Visualization analysis and design","author":"T. Munzner","year":"2014"},{"key":"pcbi.1010622.ref024","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1177\/15291006211051956","article-title":"The Science of Visual Data Communication: What Works.","volume":"22","author":"SL Franconeri","year":"2021","journal-title":"Psychol Sci Public Interest"},{"key":"pcbi.1010622.ref025","volume-title":"Fundamentals of Data Visualization","author":"CO Wilke","year":"2019"},{"key":"pcbi.1010622.ref026","doi-asserted-by":"crossref","first-page":"e1008259","DOI":"10.1371\/journal.pcbi.1008259","article-title":"Ten simple rules to colorize biological data visualization.","volume":"16","author":"G Hattab","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010622.ref027","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/cgf.14298","article-title":"Accessible Visualization: Design Space, Opportunities, and Challenges.","volume":"40","author":"NW Kim","year":"2021","journal-title":"Comput Graph Forum"},{"key":"pcbi.1010622.ref028","first-page":"71","article-title":"World blindness and visual impairment: despite many successes, the problem is growing.","volume":"30","author":"P Ackland","year":"2017","journal-title":"Community Eye Health"},{"key":"pcbi.1010622.ref029","article-title":"The 15 Rules Every UX Designer Should Know | Adobe XD Ideas.","author":"N Babich","year":"2020","journal-title":"In: Ideas [Internet]."},{"key":"pcbi.1010622.ref030","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1080\/00031305.1973.10478966","article-title":"Graphs in statistical analysis.","volume":"27","author":"FJ Anscombe","year":"1973","journal-title":"Am Stat"},{"key":"pcbi.1010622.ref031","first-page":"1290","volume-title":"Same Stats, Different Graphs: Generating Datasets with Varied Appearance and Identical Statistics through Simulated Annealing. Proceedings of the 2017 CHI Conference on Human Factors in Computing Systems.","author":"J Matejka","year":"2017"},{"key":"pcbi.1010622.ref032","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/S0734-189X(85)80004-9","article-title":"Preattentive processing in vision","volume":"31","author":"A. Treisman","year":"1985","journal-title":"Comput Vis Graph Image Process"},{"key":"pcbi.1010622.ref033","doi-asserted-by":"crossref","DOI":"10.1109\/VIS49827.2021.9623273","article-title":"Jurassic Mark: Inattentional Blindness for a Datasaurus Reveals that Visualizations are Explored, not Seen.","author":"T Boger","year":"2021","journal-title":"2021 IEEE Visualization Conference (VIS)."},{"key":"pcbi.1010622.ref034","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1109\/VL.1996.545307","article-title":"The eyes have it: a task by data type taxonomy for information visualizations.","author":"B. Shneiderman","year":"1996","journal-title":"Proceedings 1996 IEEE Symposium on Visual Languages."},{"key":"pcbi.1010622.ref035","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1093\/bioinformatics\/btr056","article-title":"Gobe: an interactive, web-based tool for comparative genomic visualization","volume":"27","author":"BS Pedersen","year":"2011","journal-title":"Bioinformatics"},{"key":"pcbi.1010622.ref036","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.gene.2016.11.025","article-title":"PanGeT: Pan-genomics tool.","volume":"600","author":"I Yuvaraj","year":"2017","journal-title":"Gene"},{"key":"pcbi.1010622.ref037","article-title":"GenomeSpy: grammar-based interactive genome visualization.","volume":"9","author":"K Lavikka","year":"2020","journal-title":"F1000Res."},{"key":"pcbi.1010622.ref038","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1109\/TVCG.2021.3114876","article-title":"Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization","volume":"28","author":"S LYi","year":"2022","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"pcbi.1010622.ref039","article-title":"Web Site Delays: How Tolerant are Users?","volume":"5","author":"DF Galletta","year":"2004","journal-title":"J Assoc Inf Syst."},{"key":"pcbi.1010622.ref040","doi-asserted-by":"crossref","first-page":"e3000333","DOI":"10.1371\/journal.pbio.3000333","article-title":"Challenges and recommendations to improve the installability and archival stability of omics computational tools","volume":"17","author":"S Mangul","year":"2019","journal-title":"PLoS Biol"},{"key":"pcbi.1010622.ref041","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.csbj.2015.10.004","article-title":"A Review on Genomics APIs.","volume":"14","author":"R Swaminathan","year":"2016","journal-title":"Comput Struct Biotechnol J"},{"key":"pcbi.1010622.ref042","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1145\/2723872.2723882","article-title":"An introduction to Docker for reproducible research.","volume":"49","author":"C. Boettiger","year":"2015","journal-title":"SIGOPS Oper Syst Rev"},{"key":"pcbi.1010622.ref043","doi-asserted-by":"crossref","first-page":"e0177459","DOI":"10.1371\/journal.pone.0177459","article-title":"Singularity: Scientific containers for mobility of compute.","volume":"12","author":"GM Kurtzer","year":"2017","journal-title":"PLoS ONE"},{"key":"pcbi.1010622.ref044","unstructured":"Anaconda Software Distribution. Anaconda Documentation. Anaconda; 2020. Available from: https:\/\/docs.anaconda.com\/."},{"key":"pcbi.1010622.ref045","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"B Gr\u00fcning","year":"2018","journal-title":"Nat Methods"},{"key":"pcbi.1010622.ref046","article-title":"Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases","author":"M Staton","year":"2021","journal-title":"Brief Bioinformatics"},{"key":"pcbi.1010622.ref047","doi-asserted-by":"crossref","first-page":"3914","DOI":"10.1093\/bioinformatics\/btab459","article-title":"JBrowseR: an R interface to the JBrowse 2 genome browser","volume":"37","author":"EA Hershberg","year":"2021","journal-title":"Bioinformatics"},{"key":"pcbi.1010622.ref048","first-page":"2022","article-title":"JBrowse Jupyter: A Python interface to JBrowse 2.","author":"TDJ Martinez","year":"2022","journal-title":"bioRxiv"},{"key":"pcbi.1010622.ref049","first-page":"btac327","article-title":"Assessing and assuring interoperability of a genomics file format","author":"YN Niu","year":"2022","journal-title":"Bioinformatics"},{"key":"pcbi.1010622.ref050","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/s13059-019-1626-2","article-title":"Where is genomics going next?","volume":"20","author":"B. Cheifet","year":"2019","journal-title":"Genome Biol"},{"key":"pcbi.1010622.ref051","unstructured":"Diesh C. awesome-genome-visualization. [cited 2022 May 6]. Available from: https:\/\/cmdcolin.github.io\/awesome-genome-visualization."},{"key":"pcbi.1010622.ref052","doi-asserted-by":"crossref","first-page":"37","DOI":"10.3233\/DS-190026","article-title":"Towards FAIR principles for research software.","volume":"3","author":"A-L Lamprecht","year":"2020","journal-title":"Data Sci."},{"key":"pcbi.1010622.ref053","doi-asserted-by":"crossref","first-page":"100222","DOI":"10.1016\/j.patter.2021.100222","article-title":"Taking a fresh look at FAIR for research software.","volume":"2","author":"DS Katz","year":"2021","journal-title":"Patterns"},{"key":"pcbi.1010622.ref054","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1038\/s41556-018-0253-6","article-title":"Social media for scientists","volume":"20","year":"2018","journal-title":"Nat Cell Biol"},{"key":"pcbi.1010622.ref055","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/978-3-540-70956-5_2","volume-title":"Evaluating Information Visualizations","author":"S. Carpendale","year":"2008"},{"key":"pcbi.1010622.ref056","first-page":"1","volume-title":"The four-level nested model revisited: blocks and guidelines. Proceedings of the 2012 BELIV Workshop: Beyond Time and Errors\u2014Novel Evaluation Methods for Visualization","author":"M Meyer","year":"2012"},{"key":"pcbi.1010622.ref057","author":"J Zong","year":"2022","journal-title":"Rich Screen Reader Experiences for Accessible Data Visualization"},{"key":"pcbi.1010622.ref058","doi-asserted-by":"crossref","DOI":"10.1111\/cgf.14522","volume-title":"How accessible is my visualization? Evaluating visualization accessibility with Chartability. Chartability","author":"F Elavsky","year":"2022"},{"key":"pcbi.1010622.ref059","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1109\/TVCG.2020.3030335","article-title":"Visual Reasoning Strategies for Effect Size Judgments and Decisions","volume":"27","author":"A Kale","year":"2021","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"pcbi.1010622.ref060","doi-asserted-by":"crossref","DOI":"10.3389\/fbinf.2022.793819","article-title":"Uncertainty Visualization: Concepts, Methods, and Applications in Biological Data Visualization.","volume":"2","author":"D. Weiskopf","year":"2022","journal-title":"Front Bioinform."},{"key":"pcbi.1010622.ref061","article-title":"Data visualization: A view of every Points of View column.","author":"D. Evanko","year":"2013","journal-title":"Protoc Methods Community."}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010622","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T22:45:23Z","timestamp":1728341123000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010622"}},"subtitle":[],"editor":[{"given":"Scott","family":"Markel","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,11,10]]},"references-count":61,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010622","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,10]]}}}