{"id":6220,"date":"2016-08-24T15:24:55","date_gmt":"2016-08-24T14:24:55","guid":{"rendered":"http:\/\/www.walkingrandomly.com\/?p=6220"},"modified":"2016-08-31T08:03:21","modified_gmt":"2016-08-31T07:03:21","slug":"software-problems-in-research-1-excel-turns-genes-into-dates","status":"publish","type":"post","link":"https:\/\/walkingrandomly.com\/?p=6220","title":{"rendered":"Software problems in research #1: Excel turns genes into dates!"},"content":{"rendered":"

I sometimes give a talk called Is Your Research Software correct<\/strong> (github repo<\/a>, slide deck<\/a>) where I attempt to give a (hopefully) entertaining overview of some of the basic issues in modern research software practice and what can be done to make the world a little better.<\/p>\n

One section of this talk is a look at some case studies where software errors caused problems in research. Ideally, I try to concentrate on\u00a0simple errors\u00a0<\/strong>that led to profound scientific screw-ups. I want the audience to think ‘Damn! *I* could have made that mistake in my code<\/em>‘.<\/p>\n

Curating this talk has turned me into an interested collector of such stories.\u00a0This is not an exercise in naming and shaming (after all, the odds are that its only a matter of time before I, or one of my collaborators, makes it into the list — why set myself up for a beating?). Instead, it is an exercise in observing the problems that other people have had and using them to enhance our own working practices.<\/p>\n

Thus begins a new recurring WalkingRandomly feature.<\/p>\n

Excel corrupts genetics data<\/strong><\/p>\n

Today’s entry comes courtesy of a recent paper by Mark Ziemann, Yotam Eren and Assam El-OstaEmail – ‘Gene name errors are widespread in the scientific literature<\/a>‘\u00a0<\/em><\/strong>where they demonstrate that the supplementary data files for hundreds of papers in genetics<\/strong>\u00a0have been corrupted by Microsoft Excel<\/strong> which has helpfully turned gene symbols into dates and floating point numbers.<\/p>\n

The paper gives advice to reviewers on how to spot this particular error and the authors have also published the code used for the analysis<\/a>. I’ve not run it myself so can only attest to its existence, not it’s accuracy.<\/p>\n

I’ve not dealt with genetic data directly myself so ask you — what would you have used instead of Excel? (my gut tells me R or Python but I have no details to offer).<\/p>\n

Do you have a story to contribute?<\/strong><\/p>\n

If you are interested in contributing a story where a software glitch caused problems in research, please contact me<\/a> to discuss details.<\/p>\n

Update (31st August 2016)<\/strong><\/p>\n

One of the authors of the paper, Mark Ziemann, has written a follow up of the Excel work on his blog:\u00a0http:\/\/genomespot.blogspot.co.uk\/2016\/08\/my-personal-thoughts-on-gene-name-errors.html<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

I sometimes give a talk called Is Your Research Software correct (github repo, slide deck) where I attempt to give a (hopefully) entertaining overview of some of the basic issues in modern research software practice and what can be done to make the world a little better. One section of this talk is a look […]<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":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":[7,80],"tags":[85],"class_list":["post-6220","post","type-post","status-publish","format-standard","hentry","category-programming","category-rse","tag-software-problems-in-research"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/p3swhs-1Ck","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=\/wp\/v2\/posts\/6220","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=6220"}],"version-history":[{"count":6,"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=\/wp\/v2\/posts\/6220\/revisions"}],"predecessor-version":[{"id":6228,"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=\/wp\/v2\/posts\/6220\/revisions\/6228"}],"wp:attachment":[{"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=6220"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=6220"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/walkingrandomly.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=6220"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}