{"created":"2023-05-15T16:39:47.762658+00:00","id":13823,"links":{},"metadata":{"_buckets":{"deposit":"471e01f4-c25d-4575-af47-1fa8abf82314"},"_deposit":{"created_by":2,"id":"13823","owners":[2],"pid":{"revision_id":0,"type":"depid","value":"13823"},"status":"published"},"_oai":{"id":"oai:nagasaki-u.repo.nii.ac.jp:00013823","sets":["10:11"]},"author_link":["49594","49595","49596","49593","49592"],"item_2_biblio_info_6":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2011-09-08","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"1","bibliographicPageStart":"331","bibliographicVolumeNumber":"4","bibliographic_titles":[{"bibliographic_title":"BMC Research Notes"}]}]},"item_2_description_4":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"ABSTRACT:  BACKGROUND: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. FINDINGS: We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. CONCLUSIONS: Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles may facilitate sharing workflows among the scientific community. Workflows for GATK and Dindel are available at http://github.com/misshie/Workflows.","subitem_description_type":"Abstract"}]},"item_2_description_63":{"attribute_name":"引用","attribute_value_mlt":[{"subitem_description":"BMC Research Notes, 4, 331; 2011","subitem_description_type":"Other"}]},"item_2_publisher_33":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"BioMed Central Ltd."}]},"item_2_relation_11":{"attribute_name":"PubMed番号","attribute_value_mlt":[{"subitem_relation_type":"isIdenticalTo","subitem_relation_type_id":{"subitem_relation_type_id_text":"21899774","subitem_relation_type_select":"PMID"}}]},"item_2_relation_12":{"attribute_name":"DOI","attribute_value_mlt":[{"subitem_relation_type":"isIdenticalTo","subitem_relation_type_id":{"subitem_relation_type_id_text":"10.1186/1756-0500-4-331","subitem_relation_type_select":"DOI"}}]},"item_2_rights_13":{"attribute_name":"権利","attribute_value_mlt":[{"subitem_rights":"© 2011 Mishima et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited."}]},"item_2_source_id_7":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"17560500","subitem_source_identifier_type":"ISSN"}]},"item_2_version_type_16":{"attribute_name":"著者版フラグ","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_970fb48d4fbd8a85","subitem_version_type":"VoR"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Mishima, Hiroyuki"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Sasaki, Kensaku"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Tanaka, Masahiro"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Tatebe, Osamu"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Yoshiura, Koh-Ichiro"}],"nameIdentifiers":[{}]}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2020-12-22"}],"displaytype":"detail","filename":"BMCRN4_331.pdf","filesize":[{"value":"341.6 kB"}],"format":"application/pdf","licensetype":"license_note","mimetype":"application/pdf","url":{"label":"BMCRN4_331.pdf","url":"https://nagasaki-u.repo.nii.ac.jp/record/13823/files/BMCRN4_331.pdf"},"version_id":"90ca291a-11b8-4656-acdf-109460466f5a"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourcetype":"journal article","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_title":"Agile parallel bioinformatics workflow management using Pwrake.","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Agile parallel bioinformatics workflow management using Pwrake."}]},"item_type_id":"2","owner":"2","path":["11"],"pubdate":{"attribute_name":"公開日","attribute_value":"2011-10-03"},"publish_date":"2011-10-03","publish_status":"0","recid":"13823","relation_version_is_last":true,"title":["Agile parallel bioinformatics workflow management using Pwrake."],"weko_creator_id":"2","weko_shared_id":-1},"updated":"2023-05-16T00:31:09.211511+00:00"}