When I returned to the lab last year, I wasn’t just changing fields of expertise: I was encountering a whole new way of doing science. Instead of tinkering on one gene or pathway, I found myself thrown headlong into the world of high through-put genomic screens – a world that came bundled with a lot of technologies I had never before encountered. (A nice chap from Nature Protocols interviewed me about my experiences; if you’re interested, scroll down to the section called ‘My First Robot’.)
And your point is? User-friendly dialogue boxes are probably the least of a developer’s worries
All of this shiny kit, from aerodynamically automated microscope stages to zealously zippy liquid handling robots, is of course powered by software. When you buy a brand new piece of basic lab equipment – a PCR machine, say – from a reputable supplier, you know that its software interface is going to work precisely as advertised. You grow to trust the reliability of the machinery in your lab; your own manual endeavors may be imperfect, but at least the kit is not going to screw up your experiment. What you learn very quickly, however, is that new technology breeds new software, and new software is inherently buggy. Developers – who are more often than not colleagues, or coders hired by equipment companies to facilitate the needs of a few valued customers – don’t have the time to test every last ramification of their code or to make the experience corporate-smooth, so it is left to the user to work out the ways and means of these often surprisingly finicky beasts.
I had my first intensive experience with this at the EMBL in Heidelberg this past February, where I was learning how to do high-throughput timelapse videomicroscopy RNAi screens. The patient and skilled technician who was assigned to help me out was a dab hand at setting up these screens, but she employed an almost a superstitious approach to achieving this without perturbing the whole system, which had been designed by Leica engineers especially for their facility and was very much a work in progress. “You see, it doesn’t like it if you do things out of order, even though you are supposed to be able to,” she whispered, as if the software might overhear and take offense. Deviate even one iota from a scripted task, she warned, just one errant click on the desktop or a too-long pause between steps, and the software would produce a floridly incomprehensible dialogue box (usually involving 25-digit numerals) and crash out the entire system, microscope and all. I recall one day when the software resisted even the sizeable charms of the technician and we banged our heads against the wall for eight solid hours trying to persuade the system to do its job.
Closer to home, I am privileged to be able to work with a home-made database and associated programmes designed to help me store, compare and analyze all my phenotypic data. And it is marvelous. But it is a primitive affair, I must confess. The other day, while agonizing over a hierarchical clustering session, I encountered the oddest dialogue box I had ever seen (see image above). I had no idea what I did to cause it or what it meant, but I sent the screen grab to Richard and it seemed to cheer him up, so it must have been of some use.
You’ll be happy to know I’ve since worked out how to cluster my phenotypes, but the pressing question still remains: who the hell is Alok, and what did I say about his stub that caused so much offense?
Thank you, Jenny. I now remember why I left lab.
The software that runs a great deal of lab equipment is beyond abominable. New equipment is, more often than not, impeccable, but comes with the most crap software imaginable. I don’t understand how the money needed to develop the machine doesn’t stretch to writing the code that controls it.
I distinctly remember having to talk myself down from throwing an ancient Mac through a plate glass window – it was the only “computer” (more GameBoy than computer when it came to processor power) in our department which could run the 10 year old software controlling the 15 year old RT PCR machine. It generally and consistently refused to do anything that was asked of it. And there was nothing to be done about it. There was no newer version of the software to upload because the product was discontinued. No other software package available to run the RT machine. It was horrible.
Anna: deep breaths.
In.
Out.
I feel your pain: our lab’s FACS machine is running a 12-year-old copy of CellQuest on MacOS9. (Remember MacOS9? Funny little blue-and-grey smiley square-faced thing on startup. OS9, which can’t load any modern web pages.) All the old-timers tolerate it cheerfully: I think they are secretly pleased to have the arcane knowledge of its function (such as it is) and enjoy watching the young whipper-snappers flail around.
How dare you call Alok’s stub MRJ!
What really gets me is the word “somehow”.
It’s so…poetic. Whimsical. Do I detect a trace of poignancy about the randomness of life, the quirks of cause and effect that ensnare our lives?
My once-missus built a satellite and that required lots of engineers and software peeps and stuff. The thing is, budgets are tight and software engineers (good ones) are very expensive. So as soon as they had a semi-working system they fired all the programmers and let the rest of ’em troubleshoot, because in $$/manhr/day of wasted effort it was cheaper than re-hiring a software engineer.
Now you know. That’s why the software is usually shite :)
That is a recipe for disaster, Ian. Complete world destruction kind of disaster, especially when you’re talking satellites. Dumbest plan ever.
Ian, admit it. You really just wanted the excuse to say “My once-missus built a satellite”.
But seriously – that is the thing. Making a programme comfortable may seem a frill; but if you look at people-hours wasted by crashing and just general crap performance, it can also cost money.
Ian, that story seems odd somehow – if I can remember next time I have a spare life I’ll dig up the story about NASA software engineers. How they’re treated, etc. (like, you will go home at 1730) because when people’s lives (as well as billions of $CURRENCY) are at stake no bugs are allowed.
Jenny, word. But it’s not a very popular with most bioinformaticians; they have no time for making software actually usable. This is why I’m so taken with Mek & Tosj ; their programs are a joy to use.
Heck, I even try to make my perl scripts (and they’re inherently user unfriendly) give sensible progress and error messages, with a splash screen to say what they’re doing — even if I’m the only one who ever uses them. I live in fear of my boss saying “why are you wasting your time writing that?” but I think it’s important.
Now I know why I was a palaeontologist. When your most sophisticated piece of kit is a set of vernier calipers, you can’t really go wrong.
Jennifer – Just be grateful you didn’t get an error like the one here
Apparently not, Henry ( see comment by Stephen Turner 14:23, 13 November 2006).
Hilary, that is hilarious! If Alok starts calling me a ‘dumbass’, the gloves will come off, I can tell you: his diminutive stub will get the description it truly deserves.
Henry, don’t modern paleo people use all sorts of imaging techniques, like MRI? I can see that being rife with alarming dialogue boxes too.
Sigh. Yes, modern palaeo people do use all sorts of fancy imaging techniques such as CAT and smart 3-D graphics programs and the like. But I did my research >20 years ago when computers hadn’t been invented, much.
I’d love to see dialogue box messages composed by you, Henry. Bet you’d be good at those really scathing ones.
I’m not sure I could better the ones highlighted by Hilary.
How about incorporating the word ‘chthonic’?
Be careful what you wish for. I could arrange for you to have an effluvia.exe overflow error.
Good thing I’m on a Mac, then.
I sniff at your .exey threats.
The only time my Mac crashes is when I try to run Windows.
Blah.
>OS9, which can’t load any modern web pages
And on the machine that’s supposed to be running your FACS, that’s a bad thing how?
Old-timers tolerate old Macs because they are old enough to remember what the old alternatives were :-)
I wrote my Ph.D. thesis on a MacSE, but that doesn’t mean I wouldn’t rather have something that works a lot better. (It was so cute, though, that squat little rectangle…)
Sometimes when I’m doing FACS it’s quite handy to check protocols and published materials and methods, that’s all.
it doesn’t like it if you do things out of order, even though you are supposed to be able to
Sounds like our purchasing system then. Even supposedly robust commercial software can become flakey in the right hands.
Perhaps, Frank, it is a global conspiracy – the soft version of the uprising described in I, Robot. Those of you with cabins in the woods in Idaho, time to start stockpiling food, water and ammo now.
cough that sounds like someone who’s only seen the film…
Good thing I’m on a Mac, then.
Oh. I thought you had a computer.
I wrote my undergraduate projects on a spectrum 48K and Ph.D. on an Amstrad PCW. Happy days.
Ha ha. I often get that from Windows users.
“Oh, a pretty toy”.
Yeah, and you know what?
I’m happier than you are. And my teeth are correctly polarized.
A game of Jet Set Willy Henry? download
There’s a gazillion other ZX games here c/o World of Spectrum Happy days indeed
I’ve read everything Azimov ever wrote, actually. And as a child, I used to try to teach my dolls the Three Laws of Robotics — I think this worried my mother a bit.
Funny.
Jennifer, why don’t you ask Alok Saldanha about his stubs?
alok@genome.stanford.edu
Fantastic! He really is a person!
This gets better and better. Although now I am feeling a bit shy.
I think you mean ‘Asimov’ rather than ‘Azimov’
-it seems that he adopted the French spelling :) -though, curiously, Tolkien spelled him ‘Azimov’ and was a great admirer of his stories.I managed to find the error message haikus that I received by email many moons ago.
Oh, how true.
Yikes – sorry for the authorial typo. I am trying to stave off old age-associated neurodegeneration by pointedly not looking up things that I think I know before posting.
The first step is admitting you have a problem.
Cath, those are hilarious!
My favorite:
Everything is gone;
Your life’s work has been destroyed.
Squeeze trigger (yes/no)?
There’s a problem about this discussion that has been nagging me, just below the threshold of consciousness. It’s just surfaced – that the messages you see on the screen are called dialogue boxes when dialogue is the very thing that they do not invite. Rather, they are more-or-less
chthonicdelphic statements that defy interpretation, let alone an answer.A dialogue box would say something like
I’m sorry to have disturbed you, Dr Rohn, but the comms port spline buffer reports an address failure at 999.000.ABC#prime. Failure to immediately reset the xxx.ccc.98302.9 fragmentation girrafe to 0000.0000 will result in cerebral implosion in 899 seconds. Would you like a cup of coffee while you’re waiting?
Otherwise, I think they’re just monologue boxes whose function is to whisper sweet nothings to their own internal address registers. It’s a cry for help, really – software’s way of wanting to be loved.
Monologue boxes: that’s priceless, Henry.
I guess it’s no surprise all this software is so insecure, going about life with only a stub.
Fnarr fnarr fnarr.
You’ve been reading one of my novels again.
It’s been fnarr since the original post, to be honest.
Those error messages Hilary Spencer posted the link to made me LOL.
My favourite all-time is from Mac OS though…
“Sorry, a system error occurred.”
Complete with a little icon of a bomb, and a button that says “ok”, which, if you click on it, hangs the system.
This would have been MacOS circa 1993 I suspect – the experts (Richard Grant, are you listening?) can probably tell you which version.
My current favorite nonsensical monologue box is the one Firefox produces if you try to open a Word doc attached to an email.
First it says, “The file {filename.doc} is a Word document.”
Then it asks what programme I’d like to use to open it, and offers a browsing menu.
Well, duh.
For me it’s a toss-up between
Chaos reigns within.
Reflect, repent and reboot.
Order shall return.
and
A file that big?
It might be very useful.
But now it is gone.
Even though the latter is 4-7-5.
If you say ‘file’ out loud, it does seem to have two syllables.
At least in my Ohio accent.
Gawd, I turn my back for a few hours and look what I’ve missed!
Richard:Ian, that story seems odd somehow – if I can remember next time I have a spare life I’ll dig up the story about NASA software engineers. How they’re treated, etc. (like, you will go home at 1730) because when people’s lives (as well as billions of $CURRENCY) are at stake no bugs are allowed.
Huh… on this project (just a weasly half billion by launch), it was my ex and me who debugged the pin-outs. No one cared to care because they didn’t care about the science and the data so it was up to the hapless and underpaid sciencewonks to debug the stuff…after hours.
Thereby saving the free world from rogue, I Robotesque killer satellites who, just before shooting out their death rays, say: “Are you sure you want to be blown up now? [yes/no/cancel]”.
Not in mine, although my sister would have said fi-yul (and chi-yuld and sti-yul) until my parents (teachers both) made her stop.
It would have been simpler just to teach the satellites the 3 laws.
How can you say ‘file’ with one syllable? I can’t even imagine it.
We’re going to have to have a mary marry merry thing in London, aren’t we?
All the same to me!
Yeah, I once had to explain to a Canadian colleague that I was late home the night before because of the damn ferries, not the damn fairies. The men in white coats were almost called before she worked out what I was saying.
Hairy Mary will marry Harry at a very merry ceremony.
You don’t really pronounce Harry and Hairy differently, do you?
(For those of you who have no idea what we’re on about, Brits pronounce ‘Mary’, ‘merry’ and ’marry" three different ways, while Americans use the exact same sounds for all three.)
None of you have been to Norfolk recently, have you?
Monologue boxes – I like it, but monologue suggests a long soliloquy on the issue at hand. I think the haikus fit the bill better.
I do like Ian’s Rhett Butleresque version though.
Do elaborate, Henry.
(This is the same Norfolk that is pronounced Nor-easter-blowin-knee-ache, right?)
How about:
“Frankly my dear, you can go ahead and overwrite that new file with an old one. You’re a grown-up, you can do what you want; it’s all the same to me.”
And Henry, before Richard beats me to it:
“none” is singular.
How is ‘hairy’ anything like ‘Harry’?!
Take me to your leader.
@ Ian: Love the indifferent little Processing box- reminds me of one of my favorite McSweeney’s lists.
Kristi, a NN monologue box just told me “We’re sorry, but this page does not exist”.
Who’s we, though?
Cath:
Ooops! Let me try typing in that URL correctly. Not sure who “we” are, though. And I don’t know why NN should apologize for my poor typing skills-that’s the fault of the magnet education program in Texas public schools. I can interpret an EKG strip, but I can’t type.
McSweeneys
My leader, Jenny? Cheeky wench.
Error Messages, by rpg
Dreary monologue
boxes rain like autumn leaves:
haiku is easy.
No wit can thus be inferred,
To write in haiku is absurd!
A fine programmer will
With consummate skill—
Whoops! A Type 11 has occurred.
I can make Mary, marry, and merry sound different, but it’s too much work.
ROTFL. I have finally found a real occasion to use that acronym. Thanks, folks.
The Americans pronounce that Rot-full, and the Brits, Rhhail-Brittania-fling.
Richard, your poem brought tears to me eyes – especially the way the 6th and 8th lines failed to scan.
it’s post-modern irony.
Actually, we pronounce it roffle.
Oh dear, Heather: wiktionary thinks your slang is obsolete.
Now, about Norfolk …
Yes, dear? We are all ears.
Our eggplants are entirely zucchinied.
I have one thing to say to you.
‘Cilantro’.
Oh, coriander off.
Isn’t it thyme for your nap?
I rose merry but your puns – mint to be so clever – are too unsage.
Sorry. I’ve forgotten.
I was thinking that though ‘monologue box’ is nice, ‘diatribe box’ might be even more appropriate.
Cockspur hawthorne.
Ten points to anyone else who can explain that to me.
Jenny (and Heather)> It just goes to show that we learned the lingo before it got popular and everyday as it is now :)
And of course, that we might be obsolete in the eyes of some people . I guess today it is all about l33t sp34k?
I am minded for no particular reason of the Hungarian tourist who shot himself in a London hotel room after reading a theatre notice that read as follows:
NOEL COWARD’S ‘CAVALCADE’: PRONOUNCED SUCCESS
The classic “sad mac” error message:
Simple, but wonderfully tragicomic at the same time.
And Richard, here is your bomb:
Bloody hell, time differnce again…
How to pronounce “file” as one syllable. Easy. Move to Memphis and it become Faaaaaaaaaaal. “Did yuh moov thu faaal ovuhh?”
Heather, your bomb diatribe box nearly gave me a heart attack – brought back vivid flashbacks of writing up on the old MacSE. I was almost there again, the rifle fire, the thwap-thwap-thwap of helicopters in the background…
(oops, wrong flashback.)
Ta, Hilary. “Restart”, that’s the one.
Someone told me that if you keep clicking on it over and over, it actually does restart the computer. I have my doubts.
I will now spend the rest of the day trying to develop a punny sentence using the names of various herbs and spices, while trying to get “Rule Britannia” out of my head. Darned Nature Network.
Oh, and I prefer ROFPML in case anyone cares.
Now that truly conjures up an image, Richard.
Brooks> How to pronounce “file” as one syllable. Easy. Move to Memphis and it become Faaaaaaaaaaal. “Did yuh moov thu faaal ovuhh
you nailed it there :D
Tennessee English, another language for Word to sort out.
‘Cockspur hawthorne’ looks odd but is actually pronounced ‘look out, the Redcoats are coming’.
Oh, we’ve established that they’re no threat.
That’s what they want you to think…
and then they kill you with a word.
“Incentivise”
serious, but not fatal.
Normalcy? Burglerize? Conversate?
Totally! Like…so, totally D.E.D. ded!
Actually, if the Red Coats are the ones saying the word, we really need a British weapon of pithy destruction.
“Asda”
“Black pudding”
Uncle.
‘Black pudding’ isn’t a word. It’s two words (I counted them very carefully). In any case, in some parts of the world, black pudding counts as a weapon.
And in other news, Mrs Gee has returned from a day of
bullshit bingomeetings in London. Truly, in the quest for hog-whimperingly awful and unnecessarily neologistic English, one need look no further than management.