{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:50Z","timestamp":1740185090450,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,6,12]],"date-time":"2018-06-12T00:00:00Z","timestamp":1528761600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["DBI-1265383"],"award-info":[{"award-number":["DBI-1265383"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["IOS-1445025"],"award-info":[{"award-number":["IOS-1445025"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The rapid accumulation of both sequence and phenotype data generated by high-throughput methods has increased the need to store and analyze data on distributed storage and computing systems. Efficient data management across these heterogeneous systems requires a workflow management system to simplify the task of analysis through automation and make large-scale bioinformatics analyses accessible and reproducible.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed SciApps, a web-based platform for reproducible bioinformatics workflows. The platform is designed to automate the execution of modular Agave apps and support execution of workflows on local clusters or in a cloud. Two workflows, one for association and one for annotation, are provided as exemplar scientific use cases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/www.sciapps.org<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty439","type":"journal-article","created":{"date-parts":[[2018,5,25]],"date-time":"2018-05-25T11:22:15Z","timestamp":1527247335000},"page":"3917-3920","source":"Crossref","is-referenced-by-count":19,"title":["SciApps: a cloud-based platform for reproducible bioinformatics workflows"],"prefix":"10.1093","volume":"34","author":[{"given":"Liya","family":"Wang","sequence":"first","affiliation":[{"name":"Cold Spring Harbor Laboratories, Cold Spring Harbor, Ithaca, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenyuan","family":"Lu","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratories, Cold Spring Harbor, Ithaca, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Van Buren","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratories, Cold Spring Harbor, Ithaca, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Doreen","family":"Ware","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratories, Cold Spring Harbor, Ithaca, NY, USA"},{"name":"USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,6,12]]},"reference":[{"volume-title":"Common Workflow Language, v1.0. figshare","year":"2016","author":"Amstutz","key":"2023012712370838800_bty439-B1"},{"volume-title":"Web Application Framework for R","year":"2015","author":"Chang","key":"2023012712370838800_bty439-B2"},{"key":"2023012712370838800_bty439-B3","article-title":"Software-as-a-service: the iPlant Foundation API","volume-title":"5th IEEE Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS)","author":"Dooley","year":"2012"},{"key":"2023012712370838800_bty439-B4","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1101\/gr.4086505","article-title":"Galaxy: a platform for interactive large-scale genome analysis","volume":"15","author":"Giardine","year":"2005","journal-title":"Genome Res."},{"key":"2023012712370838800_bty439-B5","doi-asserted-by":"crossref","first-page":"34","DOI":"10.3389\/fpls.2011.00034","article-title":"The iPlant collaborative: cyberinfrastructure for plant biology","volume":"2","author":"Goff","year":"2011","journal-title":"Front Plant Sci."},{"key":"2023012712370838800_bty439-B6","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1186\/1471-2105-12-491","article-title":"MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects","volume":"12","author":"Holt","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012712370838800_bty439-B7","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1093\/bioinformatics\/btt113","article-title":"EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats","volume":"29","author":"Ison","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712370838800_bty439-B8","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1471-2105-5-59","article-title":"Gene finding in novel genomes","volume":"5","author":"Korf","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012712370838800_bty439-B9","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":"Kurtzer","year":"2017","journal-title":"PLoS One"},{"key":"2023012712370838800_bty439-B10","first-page":"1984","article-title":"Irods: data sharing technology integrating communities of practice","volume-title":"International Geoscience and Remote Sensing","author":"Moore","year":"2010"},{"key":"2023012712370838800_bty439-B11","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng0506-500","article-title":"GenePattern 2.0","volume":"38","author":"Reich","year":"2006","journal-title":"Nat. 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