{"id":5722,"date":"2020-03-01T08:25:35","date_gmt":"2020-03-01T08:25:35","guid":{"rendered":"http:\/\/41j.com\/blog\/?p=5722"},"modified":"2020-03-01T08:27:02","modified_gmt":"2020-03-01T08:27:02","slug":"issues-replicating-bioinformatics-papers","status":"publish","type":"post","link":"https:\/\/41j.com\/blog\/2020\/03\/issues-replicating-bioinformatics-papers\/","title":{"rendered":"Issues Replicating Bioinformatics Papers"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Data Issues<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>The paper does not specify which database was used (for example to obtain a set of sequences).<\/li><li>The paper does not specify which release\/on which date data was extracted from a database.<\/li><li>The database has been updated since publication. Old releases\/versions of the database are not available.<\/li><li>The database is no longer available.<\/li><li>The database is not publicly available.<\/li><li>An old revision of the database are available, but the data format is not documented. Parsers are not available.<\/li><li>A copy of data extracted from a public database is not provided with the publication.<\/li><li>The publication does not provide enough information to verify data extracted from databases (number of sequences etc.)<\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Software Issues<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>The publication does not specify which software was used.<\/li><li>The publication does not specify which version of software was used.<\/li><li>The publication uses online tools, which are no longer available or have been updated.<\/li><li>The publication uses offline tools which are no longer available.<\/li><li>The publication uses offline tools which are available, but have been updated and the version used in the publication is no longer available.<\/li><li>The software used was never publicly available.<\/li><li>Binaries for the software used are available, but required libraries are no longer available (of the required version).<\/li><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Data Issues The paper does not specify which database was used (for example to obtain a set of sequences). The paper does not specify which release\/on which date data was extracted from a database. The database has been updated since publication. Old releases\/versions of the database are not available. The database is no longer available. [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-5722","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/p1RRoU-1ui","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/5722","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/comments?post=5722"}],"version-history":[{"count":3,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/5722\/revisions"}],"predecessor-version":[{"id":5725,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/5722\/revisions\/5725"}],"wp:attachment":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/media?parent=5722"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/categories?post=5722"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/tags?post=5722"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}