{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T23:50:55Z","timestamp":1770421855328,"version":"3.49.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,17]],"date-time":"2023-01-17T00:00:00Z","timestamp":1673913600000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HG004483"],"award-info":[{"award-number":["HG004483"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM080203"],"award-info":[{"award-number":["GM080203"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a package that provides a Python interface to JBrowse 2\u2019s suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google\u2019s Colab notebooks, providing reproducible interactive views.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>JBrowse Jupyter is released under the Apache License and is available for download on PyPI. Source code and demos are available on GitHub at https:\/\/github.com\/GMOD\/jbrowse-jupyter.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad032","type":"journal-article","created":{"date-parts":[[2023,1,17]],"date-time":"2023-01-17T22:40:38Z","timestamp":1673995238000},"source":"Crossref","is-referenced-by-count":5,"title":["JBrowse Jupyter: a Python interface to JBrowse 2"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1947-9539","authenticated-orcid":false,"given":"Teresa","family":"De Jesus Martinez","sequence":"first","affiliation":[{"name":"Department of Bioengineering, Stanley Hall, University of California , Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2068-3366","authenticated-orcid":false,"given":"Elliot A","family":"Hershberg","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanley Hall, University of California , Berkeley, CA 94720, USA"}]},{"given":"Emma","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanley Hall, University of California , Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9781-5323","authenticated-orcid":false,"given":"Garrett J","family":"Stevens","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanley Hall, University of California , Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2629-7570","authenticated-orcid":false,"given":"Colin","family":"Diesh","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanley Hall, University of California , Berkeley, CA 94720, USA"}]},{"given":"Peter","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanley Hall, University of California , Berkeley, CA 94720, USA"}]},{"given":"Caroline","family":"Bridge","sequence":"additional","affiliation":[{"name":"Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510 , Toronto, ON M5G 0A3, Canada"}]},{"given":"Scott","family":"Cain","sequence":"additional","affiliation":[{"name":"Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510 , Toronto, ON M5G 0A3, Canada"}]},{"given":"Robin","family":"Haw","sequence":"additional","affiliation":[{"name":"Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510 , Toronto, ON M5G 0A3, Canada"}]},{"given":"Robert M","family":"Buels","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanley Hall, University of California , Berkeley, CA 94720, USA"}]},{"given":"Lincoln D","family":"Stein","sequence":"additional","affiliation":[{"name":"Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510 , Toronto, ON M5G 0A3, Canada"}]},{"given":"Ian H","family":"Holmes","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanley Hall, University of California , Berkeley, CA 94720, USA"}]}],"member":"286","published-online":{"date-parts":[[2023,1,17]]},"reference":[{"key":"2023013106112753200_btad032-B1","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1089\/cmb.2016.0213","article-title":"D3GB: an interactive genome browser for R, Python, and WordPress","volume":"24","author":"Barrios","year":"2017","journal-title":"J. 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Vis. Comput. 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