{"id":718,"date":"2009-05-18T19:10:32","date_gmt":"2009-05-18T19:10:32","guid":{"rendered":"http:\/\/occamstypewriter.org\/mindthegap\/2009\/05\/18\/in_which_i_fail_to_repeat_myself\/"},"modified":"2009-05-18T19:10:32","modified_gmt":"2009-05-18T19:10:32","slug":"in_which_i_fail_to_repeat_myself","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/mindthegap\/2009\/05\/18\/in_which_i_fail_to_repeat_myself\/","title":{"rendered":"In which I fail to repeat myself"},"content":{"rendered":"

I am back in London after nearly a month away in Germany, and it is an incredible relief to be home. In my absence, the UK Parliament imploded<\/a>, my seed potatoes sprouted into healthy plants, swine flu<\/a> came and (possibly) went, and \u2013 God, who could have possibly seen this coming? \u2013 Jordan and Peter split up<\/a>. Had it really only been a month?<\/p>\n

\nI never thought I would be so happy to be back in my own messy, chaotic lab. After all, the equipment in the German institute was shiner, cleaner and more reliable; everything was organized just so to a remarkable degree of efficiency. The stainless steel surfaces gleamed, the robots purred, the Speed-vac thrummed, everything was put back exactly where I had left it the previous time: pipettors and haemocytometer in the first drawer, Petri dishes and tubes in the second drawer, calculator in the bottom drawer, tissue culture medium in a neat row in the refrigerator. The shuttle arrived at the hotel every morning at 8:15 sharp, and I was usually on the 19:20 back home if all went well (except the one night, near midnight, when I braved the Wilde Schweinen<\/em> and took the shortcut through the woods with a torch). A regimented meal from the hotel restaurant (rotating amongst about eight dishes and three wines) and in bed by ten: even the weekends had their routine, with the run through the forest to the labs and back, all at the appointed time to keep the schedule true.<\/p>\n

\nAnd after a few pilots and bedding in, every day in the lab I did exactly the same thing<\/em>. High through-put protocols make robots out of humans: process 96-well mother plates; rearray onto chips; seed cells onto chips; split cells to the desired confluency for the next day’s seeding; image the chips that were seeded previously; set up the thousands of files to compress overnight: a vast staggered pipeline that would tolerate no breaks. As one of the technicians told me, this sort of routine should be conducted with the serenity and thoughtfulness of a Japanese Tea Ceremony, and in truth I did sometimes enter into an altered state of consciousness. In little snatches of time between lab activities, it was project management and damage control: fiddle with spreadsheets to tweak the schedule to take into account yet another failure in microscope performance and \u2013 as gigabytes of data started pouring in \u2013 battle with slow servers to try to get a snapshot impression of whether a run was of sufficient quality to call it a true replicate, or whether I had to schedule in a replacement run.<\/p>\n

\nThe goal was three replicate timelapse imaging series of eight chips, each containing 384 siRNA spots. In theory this could have been completed in eight days; in practice I managed 2.5 replicates about an hour before I had to catch my flight home. Don’t get me wrong: what I have is amazing: nearly 20,000 movies of cells expressing fluorescent actin and DNA probes growing on a slide over a 24-hour period in the absence of one gene product out of a set of almost 600 key genes of interest. And, dear reader, they are beautiful. Picking a film almost at random for my farewell talk at the institute, I discovered something fascinating that had been wholly unapparent in my snapshot fixed screen with the same RNA and similar cells. And that was just scratching the surface of the nearly 3.5 terabytes of data I generated. It will take months, if not years, to get to the bottom of it all \u2013 hopefully less if I can get some decent automated image analysis up and running.<\/p>\n

\nBut that’s not what I wanted to talk about today. Today, I wanted to talk about how it felt to be back in my own lab, on my own time, wholly and utterly \u2013 not just low through-put, but no<\/em> through-put. Having some sense of what the sabbatical would be like, before I left, as a special treat on my return, I’d set up a little experiment. A bespoke<\/em> experiment, if you will, complete with one variable of interest, one hypothesis and designed to be informative no matter what the outcome. One of the post-docs obligingly fixed the transfection for me in my absence, and I returned to a multiwell plate full of just twenty glass slides, patiently waiting to be stained and lovingly viewed \u2013 their answer, just a few hours around the corner.<\/p>\n

\nIt felt wonderful.<\/p>\n","protected":false},"excerpt":{"rendered":"

I am back in London after nearly a month away in Germany, and it is an incredible relief to be home. In my absence, the UK Parliament imploded, my seed potatoes sprouted into healthy plants, swine flu came and (possibly) … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-718","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts\/718","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/comments?post=718"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts\/718\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/media?parent=718"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/categories?post=718"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/tags?post=718"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}