{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T02:19:46Z","timestamp":1719886786098},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":368,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a Python library providing all requested features to setup, run and monitor workflows.<\/jats:p>\n               <jats:p>Availability and implementation: Jflow is available under the GNU General Public License (GPL) at http:\/\/bioinfo.genotoul.fr\/jflow. The package is coming with full documentation, quick start and a running test portal.<\/jats:p>\n               <jats:p>Contact: \u00a0Jerome.Mariette@toulouse.inra.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv589","type":"journal-article","created":{"date-parts":[[2015,10,11]],"date-time":"2015-10-11T01:19:15Z","timestamp":1444526355000},"page":"456-458","source":"Crossref","is-referenced-by-count":3,"title":["Jflow: a workflow management system for web applications"],"prefix":"10.1093","volume":"32","author":[{"given":"J\u00e9r\u00f4me","family":"Mariette","sequence":"first","affiliation":[{"name":"1 Plate-forme Bio-informatique Genotoul, INRA, UR875 Mathmatiques et Informatique Appliques Toulouse, Castanet-Tolosan, France and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Escudi\u00e9","sequence":"additional","affiliation":[{"name":"1 Plate-forme Bio-informatique Genotoul, INRA, UR875 Mathmatiques et Informatique Appliques Toulouse, Castanet-Tolosan, France and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Bardou","sequence":"additional","affiliation":[{"name":"2 Plate-forme SIGENAE, INRA, GenPhyse, Castanet-Tolosan Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ibouniyamine","family":"Nabihoudine","sequence":"additional","affiliation":[{"name":"1 Plate-forme Bio-informatique Genotoul, INRA, UR875 Mathmatiques et Informatique Appliques Toulouse, Castanet-Tolosan, France and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C\u00e9line","family":"Noirot","sequence":"additional","affiliation":[{"name":"1 Plate-forme Bio-informatique Genotoul, INRA, UR875 Mathmatiques et Informatique Appliques Toulouse, Castanet-Tolosan, France and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-St\u00e9phane","family":"Trotard","sequence":"additional","affiliation":[{"name":"1 Plate-forme Bio-informatique Genotoul, INRA, UR875 Mathmatiques et Informatique Appliques Toulouse, Castanet-Tolosan, France and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine","family":"Gaspin","sequence":"additional","affiliation":[{"name":"1 Plate-forme Bio-informatique Genotoul, INRA, UR875 Mathmatiques et Informatique Appliques Toulouse, Castanet-Tolosan, France and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Klopp","sequence":"additional","affiliation":[{"name":"1 Plate-forme Bio-informatique Genotoul, INRA, UR875 Mathmatiques et Informatique Appliques Toulouse, Castanet-Tolosan, France and"},{"name":"2 Plate-forme SIGENAE, INRA, GenPhyse, Castanet-Tolosan Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,10]]},"reference":[{"key":"2023020110311981700_btv589-B1","article-title":"Makeflow: a portable abstraction for data intensive computing on clusters, clouds, and grids","volume":"20","author":"Albrecht","year":"2012","journal-title":"SWEET at ACM SIGMOD"},{"key":"2023020110311981700_btv589-B2","author":"Bui","year":"2012"},{"key":"2023020110311981700_btv589-B3","doi-asserted-by":"crossref","first-page":"2956","DOI":"10.1093\/bioinformatics\/btu385","article-title":"COSMOS: python library for massively parallel workflows","volume":"30","author":"Gafni","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020110311981700_btv589-B4","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biol."},{"key":"2023020110311981700_btv589-B5","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1093\/bioinformatics\/btq524","article-title":"Ruffus: a lightweight Python library for computational pipelines","volume":"26","author":"Goodstadt","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020110311981700_btv589-B6","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake\u2014a scalable bioinformatics workflow engine","volume":"28","author":"Koster","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020110311981700_btv589-B7","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1093\/bioinformatics\/btq430","article-title":"Cytoscape Web: an interactive web-based network browser","volume":"26","author":"Lopes","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020110311981700_btv589-B8","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1186\/1471-2164-13-462","article-title":"NG6: Integrated next generation sequencing storage and processing environment","volume":"13","author":"Mariette","year":"2012","journal-title":"BMC Genomics"},{"key":"2023020110311981700_btv589-B9","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0096821","article-title":"RNAbrowse: RNA-seq de novo assembly results browser","volume":"9","author":"Mariette","year":"2014","journal-title":"PLoS ONE"},{"key":"2023020110311981700_btv589-B10","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1186\/1471-2105-9-386","article-title":"The metagenomics RAST server a public resource for the automatic phylogenetic and functional analysis of metagenomes","volume":"9","author":"Meyer","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023020110311981700_btv589-B13","first-page":"3005","article-title":"Mobyle: a new full web bioinformatics framework","volume":"25","author":"N\u00e9ron","year":"2009"},{"key":"2023020110311981700_btv589-B11","first-page":"26","article-title":"Ergatis: a web interface and scalable software system for bioinformatics workflows","volume":"15","author":"Orvis","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020110311981700_btv589-B12","doi-asserted-by":"crossref","first-page":"3074","DOI":"10.1093\/bioinformatics\/btr519","article-title":"Metavir: a web server dedicated to virome analysis","volume":"21","author":"Roux","year":"2011","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/3\/456\/49016630\/bioinformatics_32_3_456.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/3\/456\/49016630\/bioinformatics_32_3_456.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T21:50:39Z","timestamp":1675288239000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/3\/456\/1744024"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,10,10]]},"references-count":13,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2016,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv589","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,2,1]]},"published":{"date-parts":[[2015,10,10]]}}}