Life of a Lab Rat

This little fellow has been missing since Friday afternoon. Last seen in the Eastern Avenue Lecture Theatre (Carslaw Building), he answers to the name of 'Pokemonk' and is our lab mascot.

Any information leading to the safe return of Pokemonk will be gratefully received.

Wednesday's post was born of frustration. You see, I had a nice script hacked together, but it just would not 'print' what I expected it to during my debugging. Which made me think I was doing something boneheaded. I implemented Paul's suggestion, and I was still not getting the expected output.

Then it struck me. If my code was good, the CSV itself (produced by Filemaker) must be knackered. And indeed, playing with CSV::text showed that perl was barfing on, and thus unable to parse, the very first line.

I left the problem alone yesterday, mainly because we had a group meeting with a visiting speaker and I had to put together a spiel for it, but also because it felt like my brain was oozing out of my ears.

So this morning, I went to talk to my cells, came back to my desk, sipped the coffee that the Black Queen had kindly bought for me, and constructed a very simple CSV file;


"r1c1","r1c2","r1c3","r1c4"
"r2c1","r2c2","r2c3","r2c4"


Then I showed it to my perl script (irrelevant bits stripped; yes I'm using 'strict'):

open (CSV, $probefile) || die "Can't open probefile! $!\n";

}
close CSV;
print join("\t", @probeSetIDs), "\n";
print join("\t", @chrs), "\n";
print join("\t", @starts), "\n";
print join("\t", @stops), "\n";


And BINGO! Four arrays, each with the appropriate column:


"r1c1" "r2c1"
"r1c2" "r2c2"
"r1c3" "r2c3"
"r1c4" "r2c4"


The conclusion is that Filemaker Pro can't make proper CSV files. There appears to be an invisible character in the first line. Oh hum. There are ways around this, I hope, but damn, it'd be nice to be able to trust something occasionally.

As they say,

"AHS, ASS".

The Black Knight's iron heart is warmed by the emails he receives. Sometimes however his seemingly limitless capacity for helping poor and needy is exhausted.

So maybe someone else would like to assist this honest-sounding gentleman?

Dear Respected,

With deep appreciation of your esteem contact I got from your company through web directory , I wish to introduce myself; I am Mr. Ahmed N. Al-Karbooli. Actually I will like to invest in your company. I will like to know the procedures of non-citizen investors. In investments, you have to look for a good company that the safety environmental condition of the foreign investor is guaranteed, actually after reading through your web-site, I decided to contact you.

I will be very much more delighted if you can give me details about your company, I am also looking forward to read your reply soon so as to detail you my background of my investment programme and how much fund that I am intending to invest and also the area that I would like to invest it after good negotiation.

Thanks very much for taking time to go through to my e-mail, I shall be glad to reserve this respect and opportunity for you, if you so desire, but do urge you to give the matter your immediate attention it deserves. Respond to my private email: alkarbooli_iq@yahoo.com.my

Regards

Mr. Ahmed N. Al-Karbooli.

One of the things that annoys me about bioinformaticians is their propensity to say "look, I've got a cool algorithm/fast computer/nifty widget/whatever; look what I can do with it!" instead of the rather more useful "Do you have any interesting biological problems I can work on, please?". I think this is because most bioinformaticians are computer geeks first, and biologists only third, if at all. What we really want is biologists who know how to wrangle code to good effect.

Which is a convoluted way of saying that if there's a small computational problem I need addressing then I'm more likely to have a go at it myself rather than muck around trying to get someone else interested. And this usually works, at least at the level of perl scripts and web pages.

Unfortunately, I have a need for a small perl script that is giving me a bit of a headache. You see, I have these microarrays, and I need to get at the chromosome sequence that corresponds to the probe signals that go up and down. I thought this would be easy: output a CSV file that contains columns of probeID, chromosome number, start location and stop location, and build URLs from that information.

But it's turning out to a bit more complicated than I thought it would be, and my rusty perl skills are feeling the strain. I can open the CSV, read it in to an array (actually an array of arrays; n rows of four fields) but then getting those n rows into four sub-arrays (one for each of probeID, chromosome number, start location and stop location) each of n elements is proving tricky. I'd rather not use the CSV::Text and what-have-you modules, because I want the code to be portable, but even if I did I still don't see how to do it.

Constructing the actual URLs (a 0 . . n loop with concatenation of scalars from the four sub-arrays) will be trivial, once I can get the four sub-arrays sorted.

Ideas?

So far, today, I am more or less successfully resisting the urge to greet everyone I meet with "Why, yo ho ho" in my best Leslie Phillips voice.

Instead, let's have a sing-song.

Fifteen cells in a dead man's flask
Yo ho ho and a bottle of DMEM
Myco and strep's done for the rest
Yo ho ho and a bottle of DMEM

That's quite enough, I think.

For everyone missing my 'Word of the Week' feature, here is something to keep you occupied.

The Phrontistery: Obscure Words and Vocabulary Resources.

I have a friend who works in the medical communications industry. He has an interesting pharmaceutical perspective on the Open Access debate, which is well worth a read.

About, oh two days and six hours ago, I got the guys at Uni IT to sort out my 'Captcha' thing for the comments.

You can tell, can't you?

I am uncomfortable with the distinction between 'scientists' and 'the public' when it comes to science communication. I maintain that 'scientists' are a subset of 'public', and that until we grasp that we're not going to get anywhere with increasing scientific literacy.

You see, there has been this movement of trying to increase the public's scientific understanding, approached as if scientists were Victorian missionaries forging into the Dark Continent to bring light and understanding. And this is completely wrong-headed. Not only does it immediately create an unequal and unhelpful authority/subject relationship but it ignores something fundamental about human nature.

Your average person, I think, views the pursuit of science and scientific thinking as something beyond their ken. It's something clever (and probably quite unusual) people are, and do. There's this feeling that Science is inaccessible to the 'ordinary public'. And as long as we keep talking about 'engaging with the public' or whatever we perpetuate that dichotomy.

But really, anyone can think scientifically. Anyone can do science. The youngest children do it — infinitely curious about the natural world and asking 'why' all the time, and indeed, formulating hypotheses and doing experiments 'what happens if I do this' — until that wonderful, insatiable curiosity is beaten out of them (at school? Who knows?). An informal scientific process is an integral part of our human nature, until we get older and see that years of training and bookwork and sitting around in white coats while a mad professor drones at us ad tedium is required.

So then we give up, and blindly accept the orgone salesmen and the crystals and the MMR-autism link and the homeopathy freaks and everything else because we are not good enough to know about these things.

Which is tragic.

Anyone can do science. Anyone can think scientifically. I am not saying that what I do for my day job is not hard. It is. It requires hard work, the grasping of difficult concepts, infinite patience and sheer bloody-mindedness. But the essentials, the seeking of answers to questions and the understanding of cause and effect, turning why into how; they're trivial.

And those of us who have not lost our childhood wonder at the natural world have a duty to go back into our communities and our families and say "Look! This is really cool! We can do this".

Blink, and you miss it. A few minutes ago I saw this from my office window:

Peter has been getting rather agitated about Open Access and a publishing industry response — which demonstrates that it really is all about the money for the publishers.

I was going to weigh in and be scathing and witty, but I have a headache and I see that Alethea has beaten me to it, by linking to a wonderfully surreal piss-take.

The most excellent and talented Jorge Cham, of PHD Comics, is talking at li'l ol' Sydney Uni next week.

Unfortunately I will not be going to the talk, because my spies tell me

They were being exclusive about it. The whole thing was addressed to postgraduate students only.

They didn't even bother to reply [to] me. Also, they said that the 300 seats in the lecture room had been reserved already.

So bah. Bah, bah and triple bah. And humbug, too.

Progress is not always beneficial.

Back in my school days, in chemistry classes we used to pipette various liquids by mouth, and think nothing of it. Mouth-pipetting is great; if you're reasonably competent you just grab a pipette, suck, hold pressure with tip of tongue, blow when necessary. No extra equipment required. Of course, this must have been bad for us because school children in their thousands were dying from pipette-transmitted diseases and from ingesting benzine or whatever we happened to be playing with that week.

Yeah.

So, I went to university and found that the Health & Safety cretins officers had decreed that mouth-pipetting was far too dangerous (read, "people might sue us"), as witnessed by the carnage in our classrooms, and that we must use these beasties in our practical classes:
.

These were great: The glass pipettes, when put into the appropriate hole, would easily break, thus enabling cack-handed students to shove jagged glass spears through the palms of their hands (which, unlike the pipette-transmitted diseases and drinking of benzine, I actually observed, first-hand as it were. Twice). Glass pipettes, of course, are far more environmentally-friendly (and cheaper) than the disposable plastic ones that do not break quite so readily, and universities spend too much on Administration (including Health and Safety. . .) to be able to afford a good supply of these fellas:
.

I'm saying this because I spent fifteen minutes this morning wandering around the lab looking for one of those bloody things so that I could use a single rainforest-killing ozone-depleting global-warming non-student skewering plastic pipette. Eventually I found one of these
and was gratified that, after *mumble* years I still remembered how to use one, onehanded. Yay. Go me.

In the old days, I'd have just sucked up the 2xTY and spat it out. Progress, you see?

Oh, and while doing the Google thing to find some pictures with which to illustrate this rambling nonsense, I came across a girl band who call themselves the Pipettes. This tickles me.

(Image credit: foche)