{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,11,25]],"date-time":"2022-11-25T10:18:02Z","timestamp":1669371482708},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,9,21]],"date-time":"2012-09-21T00:00:00Z","timestamp":1348185600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,12]]},"DOI":"10.1186\/1471-2105-13-240","type":"journal-article","created":{"date-parts":[[2012,9,21]],"date-time":"2012-09-21T04:14:16Z","timestamp":1348200856000},"source":"Crossref","is-referenced-by-count":3,"title":["The Ruby UCSC API: accessing the UCSC genome database using Ruby"],"prefix":"10.1186","volume":"13","author":[{"given":"Hiroyuki","family":"Mishima","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Aerts","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Toshiaki","family":"Katayama","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raoul J P","family":"Bonnal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koh-ichiro","family":"Yoshiura","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,9,21]]},"reference":[{"key":"5565_CR1","doi-asserted-by":"publisher","first-page":"D876","DOI":"10.1093\/nar\/gkq963","volume":"39","author":"PA Fujita","year":"2010","unstructured":"Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ: The UCSC Genome Browser database: update 2011. Nucleic Acids Res 2010, 39: D876-D882.","journal-title":"Nucleic Acids Res"},{"key":"5565_CR2","unstructured":"UCSC Genome Browser. \n                    http:\/\/genome.ucsc.edu\/"},{"key":"5565_CR3","unstructured":"Kent W: Kent source tree. \n                    http:\/\/hgdownload.cse.ucsc.edu\/admin\/jksrc.zip"},{"key":"5565_CR4","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1371\/journal.pcbi.0030001","volume":"3","author":"P Schattner","year":"2007","unstructured":"Schattner P: Automated Querying of Genome Databases. PLoS Comput Biol 2007, 3: e1. 10.1371\/journal.pcbi.0030001","journal-title":"PLoS Comput Biol"},{"key":"5565_CR5","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-2-7","volume":"2","author":"R Dowell","year":"2001","unstructured":"Dowell R, Jokerst R, Day A, Eddy S, Stein L: The distributed annotation system. BMC Bioinforma 2001, 2: 7. 10.1186\/1471-2105-2-7","journal-title":"BMC Bioinforma"},{"key":"5565_CR6","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1101\/gr.229102. Article published online before print in May 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res 2002, 12: 996\u20131006.","journal-title":"Genome Res"},{"key":"5565_CR7","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1186\/1471-2105-10-221","volume":"10","author":"J Aerts","year":"2009","unstructured":"Aerts J, Law A: An introduction to scripting in Ruby for biologists. BMC Bioinforma 2009, 10: 221. 10.1186\/1471-2105-10-221","journal-title":"BMC Bioinforma"},{"key":"5565_CR8","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1186\/1756-0500-4-331","volume":"4","author":"H Mishima","year":"2011","unstructured":"Mishima H, Sasaki K, Tanaka M, Tatebe O, Yoshiura K: Agile parallel bioinformatics workflow management using Pwrake. BMC Research Notes 2011, 4: 331\u2013338. 10.1186\/1756-0500-4-331","journal-title":"BMC Research Notes"},{"key":"5565_CR9","doi-asserted-by":"publisher","first-page":"2617","DOI":"10.1093\/bioinformatics\/btq475","volume":"26","author":"N Goto","year":"2010","unstructured":"Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T: BioRuby: Bioinformatics software for the Ruby programming language. Bioinformatics 2010, 26: 2617\u20132619. 10.1093\/bioinformatics\/btq475","journal-title":"Bioinformatics"},{"key":"5565_CR10","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.1093\/bioinformatics\/btr050","volume":"27","author":"F Strozzi","year":"2011","unstructured":"Strozzi F, Aerts J: A Ruby API to query the Ensembl database for genomic features. Bioinformatics 2011, 27: 1013\u20131014. 10.1093\/bioinformatics\/btr050","journal-title":"Bioinformatics"},{"key":"5565_CR11","unstructured":"Hansson DH, the Rails core team: Ruby on Rails. \n                    http:\/\/rubyonrails.org\/"},{"key":"5565_CR12","unstructured":"Prins P: biogems.info. \n                    http:\/\/www.biogems.info\/"},{"key":"5565_CR13","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1093\/bioinformatics\/bts080","volume":"28","author":"RJP Bonnal","year":"2012","unstructured":"Bonnal RJP, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P: Biogem: an effective tool based approach for scaling up open source software development in bioinformatics. Bioinformatics 2012, 28: 1035\u20131037. 10.1093\/bioinformatics\/bts080","journal-title":"Bioinformatics"},{"key":"5565_CR14","unstructured":"UCSC Bioinformatics Group: all.joiner. \n                    http:\/\/genome-source.cse.ucsc.edu\/gitweb\/?p=kent.git;a=blob_plain;f=src\/hg\/makeDb\/schema\/all.joiner;hb=HEAD"},{"key":"5565_CR15","unstructured":"UCSC Bioinformatics Group: The joiner file. \n                    http:\/\/genome-source.cse.ucsc.edu\/gitweb\/?p=kent.git;a=blob;f=src\/hg\/makeDb\/schema\/joiner.doc;hb=HEAD"},{"key":"5565_CR16","doi-asserted-by":"publisher","first-page":"e1001046","DOI":"10.1371\/journal.pbio.1001046","volume":"9","author":"The ENCODE Project Consortium","year":"2011","unstructured":"The ENCODE Project Consortium: A user\u2019s guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 2011, 9: e1001046. 10.1371\/journal.pbio.1001046","journal-title":"PLoS Biol"},{"key":"5565_CR17","doi-asserted-by":"publisher","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","volume":"26","author":"WJ Kent","year":"2010","unstructured":"Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D: BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics 2010, 26: 2204\u20132207. 10.1093\/bioinformatics\/btq351","journal-title":"Bioinformatics"},{"key":"5565_CR18","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup: The sequence alignment\/map format and SAMtools. Bioinformatics 2009, 25: 2078\u20132079. 10.1093\/bioinformatics\/btp352","journal-title":"Bioinformatics"},{"key":"5565_CR19","unstructured":"Picard. \n                    http:\/\/picard.sourceforge.net\/"},{"key":"5565_CR20","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1751-0473-7-6","volume":"7","author":"RH Ramirez-Gonzalez","year":"2012","unstructured":"Ramirez-Gonzalez RH, Bonnal R, Caccamo M, MacLean D: Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments. Source Code for Biology and Medicine 2012, 7: 6. 10.1186\/1751-0473-7-6","journal-title":"Source Code for Biology and Medicine"},{"key":"5565_CR21","unstructured":"Engstr\u00f6m P: Genoman. \n                    http:\/\/www.ebi.ac.uk\/~engstrom\/genoman\/"},{"key":"5565_CR22","unstructured":"Pedersen B: Cruzdb. \n                    https:\/\/github.com\/brentp\/cruzdb"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-240.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-240\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-240.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T06:13:31Z","timestamp":1548224011000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-240"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,9,21]]},"references-count":22,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5565"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-240","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,9,21]]},"article-number":"240"}}