{"id":2711,"date":"2015-02-19T13:42:08","date_gmt":"2015-02-19T13:42:08","guid":{"rendered":"https:\/\/blogs.nature.com\/scientificdata\/?p=2711"},"modified":"2015-02-19T13:59:09","modified_gmt":"2015-02-19T13:59:09","slug":"code-sharing-tips","status":"publish","type":"post","link":"https:\/\/blogs.nature.com\/scientificdata\/2015\/02\/19\/code-sharing-tips\/","title":{"rendered":"Code Sharing \u2013 read our tips and share your own"},"content":{"rendered":"<table width=\"100%\" border=\"0\" cellspacing=\"0\" cellpadding=\"0\">\n<tbody>\n<tr>\n<td valign=\"top\">This week we <a title=\"Ctrl, alt, share editorial\" href=\"https:\/\/www.nature.com\/articles\/sdata20154\" target=\"_blank\">announced an update to our journal policies on code sharing<\/a>. To encourage our authors to share their code, we also added a new <strong>code availability section<\/strong> to our <a title=\"Scientific Data article templates\" href=\"https:\/\/www.nature.com\/sdata\/for-authors\/submission-guidelines?proof=true#templates\" target=\"_blank\">article templates<\/a>. This new code availability section focuses mainly on articles that rely on custom code to generate or process data described in our articles. But, almost all modern research employs code or software at some stage. We feel that, ideally, it is best <strong>to describe all code or software used in a study<\/strong> in a way that supports reproducible research. What does this mean for our authors who would like to share their code alongside their data? What should be included in the code availability section? Here are some suggestions from our editorial team.<\/td>\n<td width=\"20\"><\/td>\n<td valign=\"top\" width=\"200\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2761 wpn-image\" title=\"rsz_1scidata_codesharing\" alt=\"rsz_1scidata_codesharing\" src=\"https:\/\/blogs.nature.com\/scientificdata\/files\/2015\/02\/rsz_1scidata_codesharing.png\" width=\"200\" height=\"200\" srcset=\"https:\/\/blogs.nature.com\/scientificdata\/files\/2015\/02\/rsz_1scidata_codesharing.png 200w, https:\/\/blogs.nature.com\/scientificdata\/files\/2015\/02\/rsz_1scidata_codesharing-150x150.png 150w\" sizes=\"auto, (max-width: 200px) 100vw, 200px\" \/><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><!--more--><\/p>\n<ul>\n<table width=\"100%\" border=\"0\" cellspacing=\"0\" cellpadding=\"0\">\n<tbody>\n<tr>\n<td valign=\"top\" width=\"35\" height=\"30\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2747 wpn-image\" title=\"rsz_1idea1\" alt=\"rsz_1idea1\" src=\"https:\/\/blogs.nature.com\/scientificdata\/files\/2015\/02\/rsz_1idea2.png\" width=\"20\" height=\"22\" \/><\/td>\n<td valign=\"top\">Provide the name of any <strong>commercial<\/strong> or <strong>third party software<\/strong> and include a URL for it.<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"35\" height=\"55\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2747 wpn-image\" title=\"rsz_1idea1\" alt=\"rsz_1idea1\" src=\"https:\/\/blogs.nature.com\/scientificdata\/files\/2015\/02\/rsz_1idea2.png\" width=\"20\" height=\"22\" \/><\/td>\n<td valign=\"top\">Include citations to <strong>relevant papers and DOIs<\/strong> for previously published code and software, i.e. cite what you used in your study.<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"35\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2747 wpn-image\" title=\"rsz_1idea1\" alt=\"rsz_1idea1\" src=\"https:\/\/blogs.nature.com\/scientificdata\/files\/2015\/02\/rsz_1idea2.png\" width=\"20\" height=\"22\" \/><\/td>\n<td valign=\"top\">Provide details of where your <strong>previously unpublished source code<\/strong> can be found.<\/p>\n<ul>\n<li>For short, simple pieces of code, including it in <strong>a supplemental file<\/strong> may be adequate.<\/li>\n<\/ul>\n<ul>\n<li>For more complex source code, consider using <strong>a control version repository<\/strong> (for example <a href=\"https:\/\/github.com\/\">GitHub<\/a>).<\/li>\n<\/ul>\n<ul>\n<li>To ensure preservation and to make your code truly citable, consider archiving the specific version of code used in your article <strong>to a DOI minting repository<\/strong> (such as <a href=\"https:\/\/figshare.com\/\">figshare<\/a>).<\/li>\n<\/ul>\n<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"35\" height=\"30\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2747 wpn-image\" title=\"rsz_1idea1\" alt=\"rsz_1idea1\" src=\"https:\/\/blogs.nature.com\/scientificdata\/files\/2015\/02\/rsz_1idea2.png\" width=\"20\" height=\"22\" \/><\/td>\n<td valign=\"top\">Include <strong>details of the license<\/strong> under which you are sharing your code.<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"35\" height=\"55\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2747 wpn-image\" title=\"rsz_1idea1\" alt=\"rsz_1idea1\" src=\"https:\/\/blogs.nature.com\/scientificdata\/files\/2015\/02\/rsz_1idea2.png\" width=\"20\" height=\"22\" \/><\/td>\n<td>For authors using a reproducible manuscript system like <a href=\"https:\/\/www.statistik.lmu.de\/~leisch\/Sweave\/\" target=\"_blank\">sweave<\/a> or <a href=\"https:\/\/yihui.name\/knitr\/\" target=\"_blank\">knitr<\/a>, provide the <strong>source code for your manuscript<\/strong> as a supplementary file.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/ul>\n<h1><\/h1>\n<p><strong>But we want to hear from you!<\/strong> What are your top tips for sharing code successfully? Let us know by leaving a comment below, or join the conversation on twitter with <a title=\"Scientific Data Twitter account\" href=\"https:\/\/twitter.com\/ScientificData\" target=\"_blank\">@scientificdata<\/a> using the hashtag <a title=\"#codesharetips on Twitter\" href=\"https:\/\/twitter.com\/search?f=realtime&amp;q=%23codesharetips&amp;src=typd\" target=\"_blank\">#codesharetips<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Scientific Data editors share their top tips for usefully sharing code within a publication, and invite readers to contribute their thoughts to the Twitter hashtag #codesharetips.&nbsp; <a href=\"https:\/\/blogs.nature.com\/scientificdata\/2015\/02\/19\/code-sharing-tips\" class=\"more-link\">Read more<\/a> <a href=\"https:\/\/blogs.nature.com\/scientificdata\/2015\/02\/19\/code-sharing-tips\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":70485,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5,8],"tags":[],"class_list":["post-2711","post","type-post","status-publish","format-standard","hentry","category-editor-posts-2","category-featured"],"_links":{"self":[{"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/posts\/2711","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/users\/70485"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/comments?post=2711"}],"version-history":[{"count":0,"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/posts\/2711\/revisions"}],"wp:attachment":[{"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/media?parent=2711"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/categories?post=2711"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.nature.com\/scientificdata\/wp-json\/wp\/v2\/tags?post=2711"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}