{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:39:47Z","timestamp":1772138387548,"version":"3.50.1"},"reference-count":62,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,10,28]],"date-time":"2017-10-28T00:00:00Z","timestamp":1509148800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54-HL127624"],"award-info":[{"award-number":["U54-HL127624"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and methods<\/jats:title>\n                    <jats:p>We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols, and as ubiquitous.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jamia\/ocx120","type":"journal-article","created":{"date-parts":[[2017,9,28]],"date-time":"2017-09-28T07:10:08Z","timestamp":1506582608000},"page":"4-12","source":"Crossref","is-referenced-by-count":23,"title":["Reproducible Bioconductor workflows using browser-based interactive notebooks and containers"],"prefix":"10.1093","volume":"25","author":[{"given":"Reem","family":"Almugbel","sequence":"first","affiliation":[{"name":"Institute of Technology, University of Washington, Tacoma, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling-Hong","family":"Hung","sequence":"additional","affiliation":[{"name":"Institute of Technology, University of Washington, Tacoma, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiaming","family":"Hu","sequence":"additional","affiliation":[{"name":"Institute of Technology, University of Washington, Tacoma, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abeer","family":"Almutairy","sequence":"additional","affiliation":[{"name":"Institute of Technology, University of Washington, Tacoma, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole","family":"Ortogero","sequence":"additional","affiliation":[{"name":"Department of Clinical Investigation, Madigan Army Medical Center, Tacoma, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yashaswi","family":"Tamta","sequence":"additional","affiliation":[{"name":"Institute of Technology, University of Washington, Tacoma, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ka Yee","family":"Yeung","sequence":"additional","affiliation":[{"name":"Institute of Technology, University of Washington, Tacoma, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,10,28]]},"reference":[{"key":"2020110612451012500_ocx120-B1","author":"Peter"},{"issue":"6","key":"2020110612451012500_ocx120-B2","doi-asserted-by":"crossref","first-page":"e1002165","DOI":"10.1371\/journal.pbio.1002165","article-title":"The economics of reproducibility in preclinical research","volume":"13","author":"Freedman","year":"2015","journal-title":"PLoS Biol."},{"key":"2020110612451012500_ocx120-B3","article-title":"Software solutions for reproducible RNA-seq workflows","author":"Meiss","year":"2017","journal-title":"bioRxiv."},{"issue":"10","key":"2020110612451012500_ocx120-B4","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2020110612451012500_ocx120-B5","article-title":"Rapid and efficient analysis of 20,000 RNA-seq samples with Toil","author":"Vivian","year":"2016","journal-title":"bioRxiv."},{"key":"2020110612451012500_ocx120-B6","article-title":"JupyterHub: deploying Jupyter notebooks for students and researchers","author":"Ragan-Kelley","year":"2016","journal-title":"."},{"key":"2020110612451012500_ocx120-B7"},{"issue":"6","key":"2020110612451012500_ocx120-B8","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1073\/pnas.1421412111","article-title":"Opinion: Reproducible research can still be wrong: adopting a prevention approach","volume":"112","author":"Leek","year":"2015","journal-title":"Proc Natl Acad Sci USA."},{"key":"2020110612451012500_ocx120-B9","volume-title":"Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools","author":"Buffalo","year":"2015"},{"issue":"4","key":"2020110612451012500_ocx120-B10","doi-asserted-by":"crossref","first-page":"e0152686","DOI":"10.1371\/journal.pone.0152686","article-title":"GUIdock: using docker containers with a common graphics user interface to address the reproducibility of research","volume":"11","author":"Hung","year":"2016","journal-title":"PLoS One."},{"issue":"1","key":"2020110612451012500_ocx120-B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1198\/106186007X178663","article-title":"Statistical analyses and reproducible research","volume":"16","author":"Gentleman","year":"2007","journal-title":"J Comput Graphical Stats."},{"key":"2020110612451012500_ocx120-B12"},{"issue":"1","key":"2020110612451012500_ocx120-B13","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1145\/2723872.2723882","article-title":"An introduction to Docker for reproducible research","volume":"49","author":"Boettiger","year":"2015","journal-title":"ACM SIGOPS Operating Systems Review, Special Issue on Repeatability and Sharing of Experimental Artifacts."},{"key":"2020110612451012500_ocx120-B14","doi-asserted-by":"crossref","first-page":"53","DOI":"10.4103\/2153-3539.197197","article-title":"Use of application containers and workflows for genomic data analysis","volume":"7","author":"Schulz","year":"2016","journal-title":"J Pathol Inform."},{"issue":"4","key":"2020110612451012500_ocx120-B15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giw013","article-title":"GUIdock-VNC: Using a graphical desktop sharing system to provide a browser-based interface for containerized software","volume":"6","author":"Mittal","year":"2017","journal-title":"Gigascience."},{"key":"2020110612451012500_ocx120-B16","article-title":"Building containerized workflows for RNA-seq data using the BioDepot-workflow-Builder (BwB)","author":"Hung","year":"2017","journal-title":"bioRxiv."},{"key":"2020110612451012500_ocx120-B17","first-page":"87","article-title":"Jupyter Notebooks \u2013 a publishing format for reproducible computational workflows","volume-title":"Positioning and Power in Academic Publishing: Players, Agents and Agendas","author":"Kluyver","year":"2016"},{"issue":"3","key":"2020110612451012500_ocx120-B18","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1109\/MCSE.2007.53","article-title":"IPython: A System for Interactive Scientific Computing","volume":"9","author":"Perez","year":"2007","journal-title":"Computing Sci Eng."},{"key":"2020110612451012500_ocx120-B19"},{"key":"2020110612451012500_ocx120-B20"},{"key":"2020110612451012500_ocx120-B21"},{"key":"2020110612451012500_ocx120-B22"},{"key":"2020110612451012500_ocx120-B23"},{"key":"2020110612451012500_ocx120-B24"},{"key":"2020110612451012500_ocx120-B25"},{"key":"2020110612451012500_ocx120-B26","doi-asserted-by":"crossref","first-page":"e12559","DOI":"10.7554\/eLife.12559","article-title":"Neural coding in barrel cortex during whisker-guided locomotion","volume":"4","author":"Sofroniew","year":"2015","journal-title":"eLife."},{"issue":"24","key":"2020110612451012500_ocx120-B27","doi-asserted-by":"crossref","first-page":"241103","DOI":"10.1103\/PhysRevLett.116.241103","article-title":"GW151226: observation of gravitational waves from a 22-solar-mass binary black hole coalescence","volume":"116","author":"Collaboration","year":"2016","journal-title":"Phys Rev Lett."},{"key":"2020110612451012500_ocx120-B28"},{"key":"2020110612451012500_ocx120-B29"},{"issue":"5","key":"2020110612451012500_ocx120-B30","doi-asserted-by":"crossref","first-page":"491","DOI":"10.2217\/17455057.4.5.491","article-title":"Predicting outcomes in pregnancies of unknown location","volume":"4","author":"Kirk","year":"2008","journal-title":"Women's Health."},{"issue":"2","key":"2020110612451012500_ocx120-B31","first-page":"158","article-title":"Expectant management of early pregnancies of unknown location: a prospective evaluation of methods to predict spontaneous resolution of pregnancy","volume":"108","author":"Banerjee","year":"2001","journal-title":"BJOG."},{"issue":"6","key":"2020110612451012500_ocx120-B32","first-page":"73","article-title":"Surveillance for ectopic pregnancy: United States, 1970\u20131989","volume":"42","author":"Goldner","year":"1993","journal-title":"MMWR. CDC surveillance summaries"},{"issue":"2","key":"2020110612451012500_ocx120-B33","doi-asserted-by":"crossref","first-page":"104","DOI":"10.5152\/jtgga.2013.74317","article-title":"Pregnancy of unknown location","volume":"14","author":"Boyraz","year":"2013","journal-title":"J Turkish German Gynecol Assoc."},{"issue":"11","key":"2020110612451012500_ocx120-B34","doi-asserted-by":"crossref","first-page":"3220","DOI":"10.1093\/humrep\/13.11.3220","article-title":"The accuracy of single serum progesterone measurement in the diagnosis of ectopic pregnancy: a meta-analysis","volume":"13","author":"Mol","year":"1998","journal-title":"Human Reproduction."},{"issue":"6","key":"2020110612451012500_ocx120-B35","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1016\/S0015-0282(16)56749-1","article-title":"The discriminatory human chorionic gonadotropin zone for endovaginal sonography: a prospective, randomized study","volume":"61","author":"Kadar","year":"1994","journal-title":"Fertility Sterility."},{"issue":"3","key":"2020110612451012500_ocx120-B36","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1097\/01.AOG.0000198635.25135.e7","article-title":"Human chorionic gonadotropin profile for women with ectopic pregnancy","volume":"107","author":"Silva","year":"2006","journal-title":"Obstetrics Gynecol."},{"issue":"2","key":"2020110612451012500_ocx120-B37","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1002\/uog.2838","article-title":"Pregnancies of unknown location: consensus statement","volume":"28","author":"Condous","year":"2006","journal-title":"Ultrasound Obstet Gynecol."},{"issue":"8","key":"2020110612451012500_ocx120-B38","doi-asserted-by":"crossref","first-page":"e23595","DOI":"10.1371\/journal.pone.0023595","article-title":"Ectopic pregnancy as a model to identify endometrial genes and signaling pathways important in decidualization and regulated by local trophoblast","volume":"6","author":"Duncan","year":"2011","journal-title":"PLoS One."},{"key":"2020110612451012500_ocx120-B39"},{"key":"2020110612451012500_ocx120-B40"},{"key":"2020110612451012500_ocx120-B41"},{"key":"2020110612451012500_ocx120-B42"},{"issue":"9","key":"2020110612451012500_ocx120-B43","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Significance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"Tusher","year":"2001","journal-title":"Proc Natl Acad Sci USA."},{"key":"2020110612451012500_ocx120-B44","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1027","article-title":"Linear models and empirical Bayes methods for assessing differential expression in microarray experiments","volume":"3","author":"Smyth","year":"2004","journal-title":"Stat Appl Genet Mol Biol."},{"issue":"43","key":"2020110612451012500_ocx120-B45","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci USA."},{"key":"2020110612451012500_ocx120-B46","article-title":"A review of connectivity map and computational approaches in pharmacogenomics","author":"Musa","journal-title":"Brief Bioinform."},{"issue":"9","key":"2020110612451012500_ocx120-B47","doi-asserted-by":"crossref","first-page":"e1004498","DOI":"10.1371\/journal.pcbi.1004498","article-title":"Predicting anticancer drug responses using a dual-layer integrated cell line-drug network model","volume":"11","author":"Zhang","year":"2015","journal-title":"PLoS Comput Biol."},{"issue":"7391","key":"2020110612451012500_ocx120-B48","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature."},{"key":"2020110612451012500_ocx120-B49"},{"key":"2020110612451012500_ocx120-B50","author":"Hung"},{"issue":"3","key":"2020110612451012500_ocx120-B51","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/nbt.3080","article-title":"A comprehensive transcriptional portrait of human cancer cell lines","volume":"33","author":"Klijn","year":"2015","journal-title":"Nat Biotechnol."},{"issue":"10","key":"2020110612451012500_ocx120-B52","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1093\/bioinformatics\/17.10.977","article-title":"Model-based clustering and data transformations for gene expression data","volume":"17","author":"Yeung","year":"2001","journal-title":"Bioinformatics."},{"key":"2020110612451012500_ocx120-B53","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.12688\/f1000research.7035.1","article-title":"RNA-Seq workflow: gene-level exploratory analysis and differential expression","volume":"4","author":"Love","year":"2015","journal-title":"F1000Research."},{"issue":"6","key":"2020110612451012500_ocx120-B54","doi-asserted-by":"crossref","first-page":"e99625","DOI":"10.1371\/journal.pone.0099625","article-title":"RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells","volume":"9","author":"Himes","year":"2014","journal-title":"PLoS One."},{"issue":"10","key":"2020110612451012500_ocx120-B55","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"issue":"9","key":"2020110612451012500_ocx120-B56","doi-asserted-by":"crossref","first-page":"4666","DOI":"10.1021\/ac303478g","article-title":"Mass spectrometry based method to increase throughput for kinome analyses using ATP probes","volume":"85","author":"McAllister","year":"2013","journal-title":"Analytical Chem."},{"issue":"5","key":"2020110612451012500_ocx120-B57","doi-asserted-by":"crossref","first-page":"1780","DOI":"10.1172\/JCI76094","article-title":"Targeting cancer with kinase inhibitors","volume":"125","author":"Gross","year":"2015","journal-title":"J Clin Invest."},{"key":"2020110612451012500_ocx120-B58"},{"key":"2020110612451012500_ocx120-B59","first-page":"342","article-title":"Large-scale integration of small molecule\u2013induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action","volume":"5","author":"Vidovic","year":"2014","journal-title":"Front Genet."},{"key":"2020110612451012500_ocx120-B60"},{"key":"2020110612451012500_ocx120-B61"},{"key":"2020110612451012500_ocx120-B62"}],"container-title":["Journal of the American Medical Informatics Association"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/25\/1\/4\/34149720\/ocx120.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/25\/1\/4\/34149720\/ocx120.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,25]],"date-time":"2025-06-25T18:46:45Z","timestamp":1750877205000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jamia\/article\/25\/1\/4\/4571788"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,28]]},"references-count":62,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,10,28]]},"published-print":{"date-parts":[[2018,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jamia\/ocx120","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/144816","asserted-by":"object"}]},"ISSN":["1067-5027","1527-974X"],"issn-type":[{"value":"1067-5027","type":"print"},{"value":"1527-974X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,1]]},"published":{"date-parts":[[2017,10,28]]}}}