Comp Bio is complicated

I finished up my first lab rotation two Fridays ago, here at UT Southwestern. It was a pleasant few months with an interesting project, consisting mostly of starting at a computer screen and writing Python scripts, running BLAST searches, and so on. To summarize, but leaving things vague (both for most-people-don’t-care reasons and the-data-is-unpublished reasons), the project was this:

There are currently a crap-ton (“crap-ton” is a standard scientific prefix) of bacterial and archaeal genomes published and available on NCBI‘s servers. Archaea, like bacteria, are single-celled prokaryotic organisms. However, they differ from bacteria genomically (and therefore metabolically) in many ways. Some archaeal properties are like those in eukaryotes (like us!), while others are like those in bacteria. So one of the huge unanswered questions in evolution is: how are bacteria, archaea, and eukaryotes related to each other? Or, how would we make a tree of life relating these three domains?

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More Puzzling

In a previous post, I discussed my attempt to write a program to solve a puzzle. I never updated that post because, well, I ran the program all night and it didn’t find the solution!

I had made up a fake puzzle that I knew had a solution for testing, and the program could solve it in 15 minutes. But it couldn’t solve the one I had recorded for the real puzzle. I figured (and hoped) that I had simply recorded it wrong and to check, I re-recorded the pieces and tried again. And it worked! Here’s how:

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Puzzling

My mother gave the fam a new game for Xmas called “The Impossible Puzzle.” Or maybe that was the company name. Either way, the label is certainly apt.

The puzzle is composed of nine, 4-sided pieces with interlocking parts in the shapes of the 4 card suits (hearts, diamonds, etc). There is only one way to lock the 9 pieces into a 3X3 square, and the game touts the fact that “there are over 300,000 combinations, only one of which is correct.”

Fig.1: An example of the puzzle pieces.

My mother, her bf, and myself all fiddled with this puzzle for a while before becoming too frustrated. There seemed to be no way to logically sort through the options of all possible arrangements and rotations of the pieces and clearly a brute-force method of trying all combinations would take way too long by hand. But maybe not for a computer. So, I figured this would be an excellent opportunity to try out my programming skills.

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Bioshock and F.E.A.R. 2 make me cry

Like a baby. And not just any baby. These games make me cry as if I am a baby whose teddy bear was taken out of one hand and shredded by an evil clown and whose candy was taken out of the other. And then the baby was punched in the face. After being flicked in the eyes.

I know that Bioshock is and old game at this point, which is why I bought it in the first place (on sale on Steam!), and I had often heard that it was quite creepy. But seriously. I crawl through the game, quicksaving every two or three minutes, afraid to go into any unexplored areas. The makers did an absolutely amazing job of making Bioshock as creepy as possible. I decided to quit playing last night after I was in a room that suddenly filled with steam, then heard running, and when the steam cleared I turned around to find a bloodied mutant surgeon with a weapon standing RIGHT BEHIND ME.

I had just finished downloading the F.E.A.R. 2 demo on Steam, so I thought I’d give it a shot to calm my nerves. The original FEAR was great and, though creepy at times (especially the last 10 minutes) was entirely bearable.

From the very beginning of the FEAR2 demo, it was clear that this was going to be a different game. The opening scene is creepier than any of the scenes in the older game, and that damn little ghost girl is back! The game starts with a massive explosion, and you find yourself waking up where everything is blood-red, you can hear your breathing and heart beating, and ghostly figures appear and disappear. After following the ghost girl into a fiery pit, your character wakes up for real next to a burned-out helicopter with its bent blades slowly spinning. There is, of course, blood everywhere.

Your character then makes his way into a school building (either high or middle), where you have to kill a few soldiers (who, like in FEAR1, are being controlled by the girl-ghost) and then suddenly ALL HELL BREAKS LOOSE. Some teammate speaks over your radio saying, “I hear a woman crying, I’m going to go check it out,” which is obviously a horrible idea.

Now you are wandering through hallways with barricaded classroom doors and lockers lining both walls. You start to see ghostly figures flying in front of you from one classroom to another, leaving the doors swinging. As you walk toward a hallway intersection, a bunch of chairs and things sitting in the middle are suddenly pulled away (by nothing). The poltergeist shenanigans gets more and more pronouned as you proceed, with locker doors opening, lockrs falling over, doors falling to the ground etc. Finally, your vision starts strobing between somewhat blurry color and black and white, and the lockers at the far end of the hall starting opening themselves, faster and faster, until whatever is opening them blows by you. At this point, you start seeing ghosts flying toward you, and bleeding soldiers stuck to the ceiling and moaning.

I was taking this slow, but eventually I had to just run for it. Finally, I got to a door and, as it opened, a guy grabbed me and stared me in the eyes saying, “Stay away from her, SHE’S MINE!” Presumably he was talking about the girl-ghost. This was the guy who had radioed me earlier. Then, the whirlwind poltergeist action slams him against the wall, and me to the floor, my vision goes red, and when the guy falls to the ground HE GETS DISINTEGRATED!!!

Everything calmed down at this point, but I had to stop. If Bioshock is creepy, then FEAR2 is ABSOLUTELY TERRIFYING. I was in a constant state of being adrenaline-pumped the entire time.

All in all, I only played both games for 20 minutes each before stopping, and then looked at cuteoverload.com for half an hour to calm down. There is nothing to stop an adrenaline leak like watching a sleepy kitten trying to stay awake!

Spore: please don’t buy it (yet)

I’ll write something longer about this later, but I just wanted to quickly add my expression of anger and frustration to the rest of the masses.

I had been looking forward to Spore’s release for years, quite literally. I pre-ordered it the first time it was supposed to come out and a major reason that I hooked myself up with a gaming desktop was so that I could play Spore for hours and hours before I took off on my traveling adventures.

Then I come to find out that, if I were to buy a copy of Spore, I wouldn’t actaully own it. I would only own three installations of the game. On top of that, it installs some kind of awful malware that EA uses to spy on you. And this is for paying customers. Meanwhile, the useless DRM was cracked several days before Spore was even release, and the pirates get to play the game without malware and without having to worry about losing their ability to play after a few installations. Maybe I should buy the game but then use the pirated version so that I don’t have to worry about breaking my computer…

In any event, I’m voting with my dollars along with a fairly substantial group of others. At $50, it makes no sense to pay for a game that breaks your computer and that you don’t even own. Vote with your dollars as well. Even just a thousand of us who want to buy it, but refuse to until the DRM is removed, will cost them $50,000.

Little Rocket Man

I got the gnome into the rocket! It ended up being fairly easy, with only a few difficult parts that made me want to punch something (like being chased by a helicopter in a vehicle that was not built to carry gnomes). I had mentioned this project in an earlier post, but I just decided to move it here with the remaining screen shots.

This is where I found him, underneath that shelf in the middle left of the picture.

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Ye Olde Halfe Life. And a Gnome.

I decided last week that it was about time I played through the original Half-Life games again. I had finally gotten to play through Episodes 1 and 2 of Half-Life2 just a few short months ago, and wanted to see if the backstory still made sense and actually built up to the plots of the newer ones. I finished regular Half-Life this weekend, and followed that with Blue Shift (which is an impressively short game). So far, everything matches up and makes more sense after playing the new games, and it was a lot of fun going back to this piece of my history that I have always looked back at so fondly. I haven’t started Opposing Force yet, but likely will soon.

This got me onto a Valve kick, and so I revisited Portal and Episode 2 to see what Achievements I had yet to make. The Achievements are something new for TF2, Portal, and Episode 2, where you are given random little tasks to try to complete. For example, in Portal you can try to destroy every video camera in the game (I managed to find all but three), fall 30,000 feet (which I did by lining up one portal above me, one below, and then fell for 15 minutes while I read Ayn Rand), kill one turret with another, etc. You also get achievements for beating the Advanced levels, which I have yet to finish (they’re friggin’ hard).

One of the more challenging and bizarre Achievements is set forth in Episode 2: carry a garden gnome through the entire game and then stick him in the nose cone of a rocket (the task is called “Tiny rocket man” or something similar”). I decided to do it, and put the game on easy to make it take less time.

[Edit: just finished the project and moved the pictures to a new post]