Fold.it

So... I've been a long time proponent of Folding@Home. Its a good project that takes your extra CPU cycles and donates them to research protein folding. According to the site some of today's diseases, like Alzhiemers, Mad Cow, and Huntingtons are the result of proteins folding incorrectly. The project uses distributed computing to help crunch large amounts of data in a reasonable time because individuals, like me, donate extra CPU cycles.

The reasons for it are actually posted on this site:

“Why is protein folding so difficult to understand?
It's amazing that not only do proteins self-assemble -- fold -- but they do so amazingly quickly: some as fast as a millionth of a second. While this time is very fast on a person's timescale, it's remarkably long for computers to simulate. In fact, it takes about a day to simulate a nanosecond (1/1,000,000,000 of a second). Unfortunately, proteins fold on the tens of microsecond timescale (10,000 nanoseconds). Thus, it would take 10,000 CPU days to simulate folding -- i.e. it would take 30 CPU years! That's a long time to wait for one result! “

I couldn't agree with the quote more, that is a long time to computer a single result. This makes me believe that this problem is one known as an NP problem. Its an easy explanation as to why it would take so long to get just a small period of real time computed. So, like all these kinds of problems, the question is asked “How can we speed things up?” Currently the way to try and solve this particular problem has been to throw more technology at it. There are now versions of the program that user a computer's GPU to do these computations faster. Which has been known to show a significant improvement from the number crunching standpoint, however there is now another way.

This is where fold.it steps into the picture. Instead of using extra CPU cycles, fold.it turns the problem protein folding research into a game. Yes you heard me correctly, a game. As I understand things, players choose a puzzle, which is a protein that has already been folded, and the player that folds a particular protein closest to the natural protein wins points that particular puzzle, the top five or so players get points in the ranking system.

So I encourage you all to open an account, and play a couple of rounds of this interesting game for science. Or to show that you can fold a protein better than a computer. Oh, and don't forget to add me to your buddy list.

Happy folding!

Thank you ITT



So this is my first blog post, and I want to use it to tell a quick story.

 Being I am about to graduate college soon (that is a relative term of course); my mind has been juggling with the path to take next. I have about over five years of expirence being in IT including the last three as a Unix student worker at PSU, and none as being a programmer. So going back to IT would be really easy, and with a degree now the process of finding a job in a bad economy would become a easier. And of course going this route would remove the fear I have about becoming a professional programmer. Yes, I said it, I'm scared. I have no idea what the world of professional programming will expect from me. I'm fresh out of school and full of mostly theory, but not much in the way of practical experience. Sure I've done scripts for work. And yes my Capstone project (translate: required internship) does have me programming and interacting with a group of programmers towards a specfic goal, I can't help but feel a little anxious regarding the unknown.

And this internal struggle has been going on for a while now. Then about a month ago I was taking the MAX from downtown Portland to the airport. Along the way it passes by an ITT Tech Institute. The parking looked like it could hold about one hundred to one hundred and fifty cars, and it was full. And of course I remembered a couple of good friends of mine who graduated from ITT. And they seem to be doing well for themselves in these rough times. But it put all the effort I've been putting in since I decided to go back to school four years ago into serious perspective.

And so thanks for a full parking lot of an ITT students, I know that once I graduate college I'm going out into the world and finding a programming job.

Syndicate content