{"id":141912,"date":"2013-11-27T18:47:00","date_gmt":"2013-11-27T18:47:00","guid":{"rendered":"https:\/\/staging2.simonw59.sg-host.com\/quantifying-reproducibility-in-computational-biology-the-case-of-the-tuberculosis-drugome\/"},"modified":"2022-05-26T13:43:43","modified_gmt":"2022-05-26T13:43:43","slug":"quantifying-reproducibility-in-computational-biology-the-case-of-the-tuberculosis-drugome","status":"publish","type":"post","link":"https:\/\/force11.org\/post\/quantifying-reproducibility-in-computational-biology-the-case-of-the-tuberculosis-drugome\/","title":{"rendered":"Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome"},"content":{"rendered":"<div class=\"ct_body\">\n<p>Authors: Daniel Garijo<br \/>\n\tSarah Kinnings<br \/>\n\tLi Xie<br \/>\n\tLei Xie<br \/>\n\tYinliang Zhang<br \/>\n\tPhilip E. Bourne<br \/>\n\tYolanda Gil<\/p>\n<p><span style=\"font-family: arial, sans-serif;font-size: 13px;line-height: 18px\">How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to &ldquo;reproducibility maps&rdquo; that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one&rsquo;s own laboratory.<\/span><\/p>\n<p><span style=\"font-family: arial, sans-serif;font-size: 13px;line-height: 18px\">Journal: PLOS ONE 2013<\/span><\/p>\n<\/div>\n<p class=\"ct_meta\"><span class=\"ct_label\">Archive:<\/span>&nbsp;<a class=\"ct_archive\" target=\"_blank\" href=\"https:\/\/archive.force11.net\/node\/6389\" rel=\"noopener\">https:\/\/archive.force11.net\/node\/6389<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Authors: Daniel Garijo Sarah Kinnings Li Xie Lei Xie Yinliang Zhang Philip E. Bourne Yolanda Gil How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we &#8230; <a title=\"Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome\" class=\"read-more\" href=\"https:\/\/force11.org\/post\/quantifying-reproducibility-in-computational-biology-the-case-of-the-tuberculosis-drugome\/\" aria-label=\"More on Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome\">Read more<\/a><\/p>\n","protected":false},"author":205903,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"advgb_blocks_editor_width":"","advgb_blocks_columns_visual_guide":"","footnotes":""},"categories":[151],"tags":[],"force11":[],"blog_series":[],"working_group":[],"class_list":["post-141912","post","type-post","status-publish","format-standard","hentry","category-news"],"acf":[],"author_meta":{"display_name":"FORCE11 Admin","author_link":"\/members\/admin"},"featured_img":null,"coauthors":[],"tax_additional":{"categories":{"linked":["<a href=\"https:\/\/force11.org\/category\/news\/\" class=\"advgb-post-tax-term\">News<\/a>"],"unlinked":["<span class=\"advgb-post-tax-term\">News<\/span>"]}},"comment_count":"0","relative_dates":{"created":"Posted 12 years ago","modified":"Updated 4 years ago"},"absolute_dates":{"created":"Posted on 27 Nov 2013","modified":"Updated on 26 May 2022"},"absolute_dates_time":{"created":"Posted on 27 Nov 2013 18:47","modified":"Updated on 26 May 2022 13:43"},"featured_img_caption":"","series_order":"","_links":{"self":[{"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/posts\/141912","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/users\/205903"}],"replies":[{"embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/comments?post=141912"}],"version-history":[{"count":0,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/posts\/141912\/revisions"}],"wp:attachment":[{"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/media?parent=141912"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/categories?post=141912"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/tags?post=141912"},{"taxonomy":"force11","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/force11?post=141912"},{"taxonomy":"blog_series","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/blog_series?post=141912"},{"taxonomy":"working_group","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/working_group?post=141912"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}