Tuesday, April 04, 2006

Computational work is starting to look really good

[More whining]
After fighting his way past the lair of contaminated reagents, getting stuck for a week in the swamp of non-growing cells and narrowly winning a long battle with yeastie beasties that refused to eat perfectly good DNA placed in front of them [despite repeated imprecations along the lines of "There are starving cells in the fridge next door ! Eat your DNA !"] , our hapless protagonist now finds himself facing yet another foe: the Plasmid That Is Not What You Think It Is.

Ok, that's enough talking about myself in the third person.

I obtained said plasmid [basically, a bit of DNA] from somebody in another lab and was counting on it to do great things for me, in terms of reducing the amount of work I had to do. Unfortunately, it turns out that there's a large-ish mismatch between what the plasmid is supposed to do [and the DNA sequence it's supposed to contain] and what it actually does. I initially became suspicious when some cells with that plasmid that shouldn't have grown [because I screwed up the experimental procedure] grew like crazy. And my suspicion was further heightened when I looked at the supposed DNA sequence and found it sorely at odds with what it was supposed to be. Further digging revealed that the person I got it from wasn't entirely sure how it had really been constructed and was a bit fuzzy on certain fairly basic aspects of how plasmids work. Not reassuring.

So at this point, I think the safest thing to do is not waste any more time trying to figure out what it actually is, but rather just make my own from scratch. There go another few weeks. *Sigh*

What makes it all worse is that I have to present a poster in ~3.5 weeks at the annual CSBi retreat and I think that pretty much the only thing I'll be able to put on that poster is a fancy-sounding abstract and some high-level ideas that trail off into "... but I don't actually have any results."

At this rate, I may have to acknowledge defeat sooner rather than later and go back to being a keyboard jockey.


Blogger Son1 said...

Funny, I'm reading your post, and thinking: life in the lab doesn't sound too bad. I'm banging my head against some kind of intermittent bug which I'm pretty sure is a race condition in my code somewhere. But I'm not sure where.

3:53 PM  
Blogger Alex said...

Ok, so finding race conditions [and intermittent bugs in general] is a pain in the posterior. But at least you can see the source code, know that that's what's running, manipulate it easily, single-step through the code etc. I'd give half my kingdom, such as it is, for a "cell debugger". Hell, I'd settle for dead simple printf() functionality ...

4:06 PM  
Blogger Lawrence David said...

i totally agree - the handful of months i lived in a wet lab, i kept thinking how insane it was to try and debug an experiment. at least when programming, you know that if something doesn't work, there are two possible problems: 1) implementation or 2) algorithm. problems with the former give you something like compiler errors; problems with the second give weird nonsense that make you tear your hair out. but at least you have an idea of which mistake causes what kind of error output.

in the wet lab, screwing up either the implementation (like pipetting) or the theory (wrong protocol) often gives you the same result: nothing. the screw-up search space is just frickin' huge.

11:29 PM  
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3:45 AM  

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