{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T10:14:16Z","timestamp":1725617656263},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or <jats:italic>pipelines<\/jats:italic>. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1) a web based, graphical user interface (<jats:italic>GUI<\/jats:italic>) that enables a pipeline operator to manage the system; 2) the <jats:italic>Scheduler<\/jats:italic>, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3) the <jats:italic>Executor<\/jats:italic>, which searches for scheduled jobs and executes these on a compute cluster.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-96","type":"journal-article","created":{"date-parts":[[2008,2,12]],"date-time":"2008-02-12T19:12:17Z","timestamp":1202843537000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["High-throughput bioinformatics with the Cyrille2 pipeline system"],"prefix":"10.1186","volume":"9","author":[{"given":"Mark WEJ","family":"Fiers","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ate","family":"van der Burgt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erwin","family":"Datema","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joost CW","family":"de Groot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roeland CHJ","family":"van Ham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,2,12]]},"reference":[{"key":"2081_CR1","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/6.2.178","volume":"6","author":"PBT Neerincx","year":"2005","unstructured":"Neerincx PBT, Leunissen JAM: Evolution of web services in bioinformatics. Brief Bioinform 2005, 6: 178\u2013188. 10.1093\/bib\/6.2.178","journal-title":"Brief Bioinform"},{"key":"2081_CR2","doi-asserted-by":"publisher","first-page":"D447","DOI":"10.1093\/nar\/gki138","volume":"33","author":"T Hubbard","year":"2005","unstructured":"Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E: Ensembl 2005. Nucleic Acids Res 2005, 33: D447\u201353. 10.1093\/nar\/gki138","journal-title":"Nucleic Acids Res"},{"key":"2081_CR3","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/1471-2105-5-40","volume":"5","author":"SP Shah","year":"2004","unstructured":"Shah SP, He DYM, Sawkins JN, Druce JC, Quon G, Lett D, Zheng GXY, Xu T, Ouellette BFF: Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 2004, 5: 40. 10.1186\/1471-2105-5-40","journal-title":"BMC Bioinformatics"},{"key":"2081_CR4","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/1471-2105-6-87","volume":"6","author":"A Garcia Castro","year":"2005","unstructured":"Garcia Castro A, Thoraval S, Garcia LJ, Ragan MA: Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. BMC Bioinformatics 2005, 6: 87. 10.1186\/1471-2105-6-87","journal-title":"BMC Bioinformatics"},{"key":"2081_CR5","doi-asserted-by":"publisher","first-page":"3045","DOI":"10.1093\/bioinformatics\/bth361","volume":"20","author":"T Oinn","year":"2004","unstructured":"Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P: Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004, 20: 3045\u20133054. 10.1093\/bioinformatics\/bth361","journal-title":"Bioinformatics"},{"key":"2081_CR6","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/1471-2105-6-69","volume":"6","author":"F Tang","year":"2005","unstructured":"Tang F, Chua CL, Ho L, Lim YP, Issac P, Krishnan A: Wildfire: distributed, grid-enabled workflow construction and execution. BMC Bioinformatics 2005, 6: 69. 10.1186\/1471-2105-6-69","journal-title":"BMC Bioinformatics"},{"key":"2081_CR7","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1093\/bioinformatics\/bti740","volume":"22","author":"I Navas-Delgado","year":"2006","unstructured":"Navas-Delgado I, Rojano-Mu\u00f1oz MDM, Ram\u00edrez S, P\u00e9rez AJ, Andr\u00e9s Le\u00f3n E, Aldana-Montes JF, Trelles O: Intelligent client for integrating bioinformatics services. Bioinformatics 2006, 22: 106\u2013111. 10.1093\/bioinformatics\/bti740","journal-title":"Bioinformatics"},{"issue":"3","key":"2081_CR8","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1007\/s10723-005-9007-3","volume":"3","author":"I Taylor","year":"2005","unstructured":"Taylor I, Shields M, Wang I, Harrison A: Visual Grid Workflow in Triana. Journal of Grid Computing 2005, 3(3):153\u2013169. 10.1007\/s10723-005-9007-3","journal-title":"Journal of Grid Computing"},{"key":"2081_CR9","first-page":"423","volume-title":"Proceedings of the 16th International Conference on Scientific and Statistical Database Management (SSDBM'04): 21-23 June 2004; Santorini Island, Greece","author":"I Altintas","year":"2004","unstructured":"Altintas I, Berkley C, Jaeger E, Jones M, Lud\u00e4scher B, Mock S: Kepler: An Extensible System for Design and Execution of Scientific Workflows. In Proceedings of the 16th International Conference on Scientific and Statistical Database Management (SSDBM'04): 21\u201323 June 2004; Santorini Island, Greece. IEEE Computer Society; 2004:423\u2013424."},{"key":"2081_CR10","doi-asserted-by":"publisher","first-page":"RESEARCH0082","DOI":"10.1186\/gb-2002-3-12-research0082","volume":"3","author":"SE Lewis","year":"2002","unstructured":"Lewis SE, Searle SMJ, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME: Apollo: a sequence annotation editor. Genome Biol 2002, 3: RESEARCH0082. 10.1186\/gb-2002-3-12-research0082","journal-title":"Genome Biol"},{"key":"2081_CR11","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1093\/bib\/3.4.331","volume":"3","author":"MD Wilkinson","year":"2002","unstructured":"Wilkinson MD, Links M: Biomoby: an open source biological web services proposal. Brief Bioinform 2002, 3: 331\u2013341. 10.1093\/bib\/3.4.331","journal-title":"Brief Bioinform"},{"key":"2081_CR12","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1101\/gr.403602","volume":"12","author":"LD Stein","year":"2002","unstructured":"Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S: The generic genome browser: a building block for a model organism system database. Genome Res 2002, 12: 1599\u20131610. 10.1101\/gr.403602","journal-title":"Genome Res"},{"key":"2081_CR13","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1101\/gr.1859804","volume":"14","author":"SC Potter","year":"2004","unstructured":"Potter SC, Clarke L, Curwen V, Keenan S, Mongin E, Searle SMJ, Stabenau A, Storey R, Clamp M: The ensembl analysis pipeline. Genome Res 2004, 14: 934\u2013941. 10.1101\/gr.1859804","journal-title":"Genome Res"},{"key":"2081_CR14","first-page":"933","volume-title":"Breeding For Success: Diversity In Action. Proceedings Of The 13Th Australasian Plant Breeding Conference","author":"J Jacobs","year":"2006","unstructured":"Jacobs J, Conner A, Bachem C, van Ham R, Visser R: The potato genome sequence consortium. In Breeding For Success: Diversity In Action. Proceedings Of The 13Th Australasian Plant Breeding Conference Edited by: Mercer C. 2006, 933\u2013936."},{"key":"2081_CR15","doi-asserted-by":"publisher","first-page":"1310","DOI":"10.1104\/pp.105.060707","volume":"138","author":"LA Mueller","year":"2005","unstructured":"Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst EV, Keyder ER, Menda N, Zamir D, Tanksley SD: The sol genomics network: a comparative resource for solanaceae biology and beyond. Plant Physiol 2005, 138: 1310\u20131317. 10.1104\/pp.105.060707","journal-title":"Plant Physiol"},{"key":"2081_CR16","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1186\/1471-2105-6-198","volume":"6","author":"P Gouret","year":"2005","unstructured":"Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, Danchin EGJ: Figenix: intelligent automation of genomic annotation: expertise integration in a new software platform. BMC Bioinformatics 2005, 6: 198. 10.1186\/1471-2105-6-198","journal-title":"BMC Bioinformatics"},{"key":"2081_CR17","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1101\/gr.1857204","volume":"14","author":"A Stabenau","year":"2004","unstructured":"Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E: The ensembl core software libraries. Genome Res 2004, 14: 929\u2013933. 10.1101\/gr.1857204","journal-title":"Genome Res"},{"key":"2081_CR18","unstructured":"Web Services Business Process Execution Language Version 2.0[http:\/\/docs.oasis-open.org\/wsbpel\/2.0\/wsbpel-v2.0.pdf]"},{"key":"2081_CR19","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215: 403\u2013410.","journal-title":"J Mol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-96.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:20:03Z","timestamp":1630466403000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-96"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,2,12]]},"references-count":19,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2081"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-96","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,2,12]]},"assertion":[{"value":"14 July 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 February 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 February 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"96"}}