Ashley’s Blog
All my views are belong to me
Hi!
People often ask me what I do. The moment I open my mouth and say bioinformatics, this look of dread and regret for approaching me seeps out of their eyes and they make some excuse about having to take a closer look at the watercooler. So im just going to say i’m an alien researcher taking pictures of the savannah and give them the QR code to my blog instead. They’ll understand. I hope … Anyways, if you’re here and aren’t rolling your eyes, read on.
Aliens taking pictures
Imagine you’re an alien research crew, above the earth. You’ve been tasked: “See that yellow stuff on that planet, figure out what that is, and what it does”. So to take a closer look you take your amazing camera and snap a picture. It comes out all yellow. Great, you’ve a galaxy class researcher, you’ve figured out it all looks yellow. Seeing as your paper titled “Yellow looks Yellow” won’t get published even in the “Galactic Journal for Yellow stuff” you decide to change your approach and take a closer look.
You zoom in on the savannah and you see all sorts of things moving about. Some move together, some by themselves. Some bigger and some significantly smaller. Some don’t move at all. Your paper now titled “Some things move, some don’t on yellow” still isn’t going to be published. You need a different approach.
Gotta catch them all!
Seeing as you need to figure out what’s different from each other, you go on a capturing spree, firing your abducting machine at accross the savannah, trying to get every area. Big grey dots… BAM! You’ll have those. Fast moving dot chasing after other dots? ZAP! Not as fast as my abduction machine loser! Your storage area fills up pretty quick of all sorts of thing. Grey thing with 5 legs, have plenty of those. Need a thing with a long neck? Got 1. Or 178156. Can’t tell, theres so much in there and you were like an Murrican. Shoot first and ask questions later. However, things start getting messy. No its chaos. The furry 4 legged thing is going crazy, jumping on anything that moves. Flappy thing is going after the small guys. Its straight up bullying. Some of your collection is in pieces. So you decide to get a couple of big nets, and anything bigger then the 4 legged furry monster goes through, everything else is on the other side. Then anything smaller then flappy boy goes into another section. Its relatively better now. You give the 4 legs furry monster fraction to your colleage next door. Its big, as sharp things and is scary. Nobody wants to study big things. Its complicated. Next you need to analyse your catch.
On the chopping block
You have alot of stuff, like alot of it. You need to automate the process of analysis. In your arsenal of image capturing devices, you have two weapons. You have the Big Boy, it can take really big pictures. Like really big. But its resolution isn’t very good. Its a little blurry and you’re sometimes not sure of the detail. But it generally gets a good overview of your sample. Next you have the Smol Boi. Smol boi is great, it can take very higher resolution of your sample. But its limited. There’s only so much you can get into one frame. Which one do you pick? Will it matter in the long term? Well lets continue.
You decide to do both, because your mission to study yellow stuff has unlimited funds. Well actually you don’t deal with the money, your boss does, and its his problem to get the money so you can do science. Because what you’re doing is cool and interesting. In your eyes anyway. So you prepare your samples. You give them a gentle shake, because your lab has rules that you need to be nice to you samples, but the lab accross the hall seems to be making frankstein. Lovely. Anyways, then you divide up your collection. Half goes to Big Boy, the other to Smol Boi. With Smol Boi, you need to get them to fit in the frame. So they all go into your blender and you give them a long pulse. Its getting pretty noisy in here so you put on those fancy noise cancelling headphones. Its was a great purchase, stops you hearing your co-workers constant dribble about how hard their life. Fabulous. The in thing on the galactic radio is mumbling rap. Good thing they make less then you, your job contributes to the understanding of the world, they just need to get a grip. Your sample has blended but tts a bit sparse and you wonder if its enough. You decide it isn’t so you get your exact-o-copy machine out. You aim in randomly and poof, a bit more of this, and a bit more of that. Brilliant and you set Smol Boi to work. With Big Boy, you just give that fraction a quick pulse and in it goes. You’ll be back tomorrow when they’re done.
Jigsaw puzzles
Smol and Big boy are done and its a success. Its taken a picture of every bit of your sample. There’s alot, like trillions of pictures. You start having an exatential crisis as you realise what you’re getting yourself into. You jettison your photographed samples out the spaceship. You don’t need those, and there’s plenty more where that came from. You really shouldn’t, its polluting the natural space, but plenty of more established galatic empires have done it in the past, you should be able to as well. What could possibly go wrong. Now you settle down and start arrange your pictures, Smol Boi first. You pick up the picture, its all yellow, you cry a bit because you now hate the colour yellow. Where does this picture fit into relation with the all the other trillion ones. You would need to compare this picture to every other picture and figure out where the next picture fits. Great… Luckily you notice something. Pictures that fit together should have the same colours on them. So you decide to catagories each of your pictures as numbers. You select some colours, blue, green, yellow and red and look at the proportion at which they occur in a picture. You reason, if the picture is has almost the same proportion of colour they should fit near each other. Giving each picture a number, rather then as a picture also allows you to sort them quickly with your computer, so you start making groups.
Problems and more problems
Your starting to piece together your picture, pictures of simular colours are fitting together nicely. However, its odd, more then one picture can fit in the same place. Both could be right, but how do you tell? Also, some pictures are just brown. Are they the same picture? or are some animals just all brown? You have no idea. You end up with alot of complete fragments of a puzzle. They are like islands, with nothing simular to anything else. Is this the complete picture of an animal, or am I missing bits? How do I tell?