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) went, and – God, who could have possibly seen this coming? – Jordan and Peter split up. Had it really only been a month?
I 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 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.
And after a few pilots and bedding in, every day in the lab I did exactly the same thing. 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 – as gigabytes of data started pouring in – 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.
The 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 – hopefully less if I can get some decent automated image analysis up and running.
But 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 – not just low through-put, but no 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 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 – their answer, just a few hours around the corner.
It felt wonderful.
welcome home, Jenny.
in truth I did sometimes enter into an altered state of consciousness
I think every crystallography gets to that stage, round about 3 in the morning at Daresbury. Stephen?
In the interest of full disclosure, I should have mentioned that I do miss the five kinds of freshly baked Bretzel in the staff canteen.
Welcome back! I must admit that i read your tag as anal screens which is comical and disturbing in equal measure (to me, at least).
3.5 terabytes of data!! Wow. Do you not fancy a sabbatical from your sabbatical? I’ve been wondering how you arranged these trips. Do you know someone over there or is this something the lab does? You propose something and they invite you over to work for a month on your grant?
I think every crystallography gets to that stage, round about 3 in the morning at Daresbury. Stephen?
At 3.23 am. Precisely.
‘crystallographer’, of course.
Stephen, I found Beethoven helped. Especially on 9.6 when the walls closed in.
damage control: fiddle with spreadsheets to tweak the schedule to take into account yet another failure in microscope performance and – as gigabytes of data started pouring in – 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
Somehow that seems to contradict the image of efficiency you drew before…
The microscopes are all experimental — the researchers working together with the microscope manufacturers to do functions specific for the research question. I have no doubt that the collaboration is an efficient one, but it does mean that there are a lot of bugs and that the set-ups are always at the cutting edge. But they suggested I predict failures and build them into my schedule — I just didn’t believe it, at the beginning.
@Richard – ‘crystallographer’, of course.
No, no – I am crystallography.
And Spartacus.
well, I am the Law, so there.
I feel I ought to make some sort of I, Robot joke at this juncture.
Tell me, crystallography personified: what is it about the tasks that put you into a trance? I always pictured it as very mentally active.
well, I am the Law, so there.
Brag(g)’s law?
Jenny – there are 2 kinds of trance – one induced by hellish over-activity, the other due to hellish inactivity (induced by an unscheduled beam dump). The first is slightly better.
“The pervasive hum of the machinery – the air-conditioners, the bits and pops that direct the kilosun light into narrow beams and focus it at the crystal apex – blurs into the background after a while, like the engines on a long-haul flight. At least here I’ve got leg room, I can go and make a cup of tea, and the added bonus of being able to freeze my fingers off when I mount a fresh crystal in a couple of hours’ time. ”
— written about 03.23 at Daresbury, a few years back. Think it was beamline 14.2. Or was it 14.1?
I’ve been wondering how you arranged these trips. Do you know someone over there or is this something the lab does? You propose something and they invite you over to work for a month on your grant?
Ian, I was awarded an EMBO short-term fellowship for this work. It’s a scheme to promote collaborations between labs in Europe and it’s for 30, 60 or 90 days. My boss had an idea that we needed to do the work, so proposed it to the host lab, and then it was just a matter of finding the funding. I think if it’s a good idea and the labs are reputable, it’s fairly straightforward to propose a successful fellowship to EMBO. At least, the people I know who’ve tried have succeeded.
Jenny, did your tabby recognise you upon your return?
I say Bob, that’s rather an ungentlemanly question.
As it happens, Bob, it was supper time when I arrived, so I was able to renew the friendship via the tin-opener. He only gained about half a stone in my absence.
Welcome back!! It was really interesting to read what you did over there. It sounds like a good plan to have something “quick results to get” when getting back from tonnes and tonnes of data. Good luck with all of the analyzing!! And that there are a few of those “really, nahh… woow” results in there.
bq. I say Bob, that’s rather an ungentlemanly question.
Possibly so, but one must stay true to one’s core concerns. Especially when The Beast is sitting on you.
I can’t wait to see the movie. Not of the cat, of the cells. With Cate Blanchett.
I thought the book was better.
The book is always better.
Jenny – any chance of getting some rough footage out to share with us? We don’t need the full descriptions, but I would love to see some of the images.
Glad your trip was safe and productive.
Hi Craig
Is it possible to put videos into these comment boxes?
You can embed YouTube videos, and some other stuff, so it should be possible. I don’t know the technical details, though.
You could upload to YouTube and add the code for embedding to your comment.
Only just realizing how long it will take to make 20,000 films from 800,000 tifs- it’s not going to be trivial. Anyone got a cluster they can lend me?
I’ve got a bunch of grapes. It’s sort of a cluster.
800,000 images at 25 fps makes for a 9 hour film. Who do you think you are – Peter Jackson?
Yes, please, I want to see some, Jenny. Glowing actin, I mean, not grapes.
The book is always better.
I think I love you, Richard.
Do you think you could make it to my party (tomorrow), Amy?
Stephen, it’s actually lots of small ones with only 40 frames. Think of it as an indie Shorts festival.
Must be one or two in there where the cells do a bit of a pratfall. Those are the ones we want to see. Forget about the science!
Good idea, Stephen. In my spare time, I should put together a Jackie Chan-style collection of outtakes. Like when cytokinesis goes horribly wrong and the stunt-cell ends up getting rushed to Casualty.
Am I to understand that you were recently in Germany? What a pity that we missed the opportunity to have met, but perhaps you were too busy. I do hope the trip was worth it, and that you enjoyed your stay.
Crap. I missed a party? Was there cake?
Better than cake. There was tiramisu.
And ice cream. And barbecued bananas with honey.
homemade ice cream.
And in the interests of full disclosure, the bananas and honey were thanks entirely to Jenny.
bq. the bananas and honey were thanks entirely to Jenny.
fnar fnar.
…i’ll get me coat…
Brooks, I think you need a vacation.
A long one. Far away from internet access.