FR Folding@Home Project Update - We're are in the TOP250 teams and still climbing!!

soccer_maniac | 2-12-2006 | soccer_maniac

[soccer_maniac]

Welcome to the new FreeRepublic folding@home thread. The previous thread has gotten too large, so we move on to yet another.

While this folding@home team is not officially sanctioned by Free Republic, it's 250+ members comprised primarily of Free Republic members in good standing have banded together to donate their excess CPU cycles to a worthy cause. Via distributed computing, millions of computers around the world, contribute directly to scientific research, in the quest for a greater understanding of diseases such as Alzheimer's, Cancer, and Mad Cow (BSE).

Currently, the team is in 241st place, having moved up from 1200th place, a week earlier, and is now in the top 100 teams, for daily contributions.

This is an entirely voluntary program, and if you want to learn more, please see the links posted below (or read one of the previous 8 folding threads)

[texas booster]

It looks like we have just had our first 50K point day. We should finish with around 52,000 points. 2 million points should be hit on Tuesday.

Especially impressive since our friend Klutz still has systems that have not reported back in after their long weekend at Bernie's.

We also soon tally our 200th folder to register at least 1,000 points.

Way to go FReepers!

[auboy]

SNFFB :-)

[texas booster]

I looked up the p1808 protein that my system is working on. Here it is:

These projects concern the folding of the triple helix of collagen. Collagen is a major component of bone, skin, and other organs. It is in fact the most abundant protein in humans, taking a quarter of the protein mass. Collagen has a unique structure consisting of three chains wrapped around each other, hence the name triple helix. Mutations in collagen cause misfolding of the triple helix, leading to diseases such as Osteogenesis imperfecta and Ehlers-Danlos syndrome. We are studying the folding mechanism and how mutations affect it.

Points and deadlines:
p1800 - 77 points, 23 days;
p1801 - 66 points, 20 days;
p1802 - 77 points, 23 days;
p1803 - 69 points, 21 days;
p1804 - 123 points, 35 days;
p1805 - 130 points, 37 days;
p1806 - 19 points, 10 days;
p1807 - 19 points, 10 days;
p1808 - 153 points, 44 days;
p1809 - 153 points, 44 days;

Collagen triple helix

[texas booster]

The deadlines referred to (in days) for each protein tells us how long we have to complete a work unit before the work unit is considered "stale", and reissued to another cpu.

Don't worry if you have a system that seldom gets on the internet or is even turned on all that often. Once every two weeks is all that it takes to keep the Stanford server updated on progress.

I started this protein on Saturday about 9:00 pm and *should* finish it Monday about 3:30 pm. Folding will speed up once I go to bed and stop surfing, playing iTunes and running Outlook.

[auboy]

Fasinating!

Until ovrtaxt sent a FReep mail last Sunday, I had no idea what Folding@Home was. Thanks, ot, for the invite!

[processing please hold]

01100010 01110100 01110100 01110100

[houeto]

I have folded tinker core 1163 three times already. Why would it still be a "currently running project"?

[SC Swamp Fox]

Why would it still be a "currently running project"?

As I understand it, each WU is only a small piece of the entire project. I have two CPUs working on 1809 (again) right now.

[texas booster]

That's right. When one finishes a work unit you have not figured out every possible combination of folds for a protein, but only a very specific subset of folds for a molecule that makes up the protein.

Also, I understand that several folders will work on the same work unit for an integrity check. Sometimes the folding answers are physically impossible, sometimes the answers have small errors that creep in.

[Paladin2]

I've also found that using various combinations of cloned hard drives transferred to new m/b's and sneaker netted WU's caused the CPU count to be somewhat wacko.

[texas booster]

I found this interesting discussion on proteins:

**********

WHY DO PROTEINS "FOLD"?

However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carry out their function (eg as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."

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!

While the nature of the fold is determined by the sequence, it is encoded in a very complicated manner. Thus, protein folding can be seen as a connection between the genome (sequence) and what the proteins actually do (their function).

[dfwddr]

I have folded tinker core 1163 three times already. Why would it still be a "currently running project"?

Here are some snippets from my log file:

[08:36:04] " 393 p1152_L939_K12M_ext_from638
[08:36:04] 1 N 10.911244 -75.485219 63.120..."
[08:36:04] Protein: p1152_L939_K12M_ext_from638
[08:36:04] - Run: 70 (Clone 72, Gen 1)
[08:36:04] - Frames Completed: 0, Remaining: 400
[08:36:04] - Dynamic steps required: 5000000
[08:36:04]

[20:47:13] " 393 p1152_L939_K12M_ext_from638
[20:47:13] 1 N -2.573151 -108.572746 86.311..."
[20:47:13]
[20:47:13] Protein: p1152_L939_K12M_ext_from638
[20:47:13] - Run: 140 (Clone 96, Gen 6)
[20:47:13] - Frames Completed: 0, Remaining: 400
[20:47:13] - Dynamic steps required: 5000000
[20:47:13]

[09:21:28] " 393 p1152_L939_K12M_ext_from638
[09:21:28] 1 N -5.055652 0.731746 104.289..."
[09:21:28]
[09:21:28] Protein: p1152_L939_K12M_ext_from638
[09:21:28] - Run: 87 (Clone 71, Gen 9)
[09:21:28] - Frames Completed: 0, Remaining: 400
[09:21:28] - Dynamic steps required: 5000000
[09:21:28]

09:04:04] " 393 p1152_L939_K12M_ext_from638
[09:04:04] 1 N 22.067059 -118.190445 90.757..."
[09:04:04]
[09:04:04] Protein: p1152_L939_K12M_ext_from638
[09:04:04] - Run: 94 (Clone 76, Gen 5)
[09:04:04] - Frames Completed: 0, Remaining: 400
[09:04:04] - Dynamic steps required: 5000000
[09:04:04]

Note that the project number is the same - p1152_L939_K12M_ext_from638
Now look at the 1 N parameters and the RUN: numbers. They are all different. Each project has many, many little pieces to it. Each WU you download is just a small piece of a very large puzzle(project). And as texas booster said, they will often send out the same exact WU several times, as a confirmation of the results.

[Clara Lou]

So, you've been doing p1152 over and over again, too, I see. Likewise.

[Clara Lou]

I see that our team had 51,400+ pts. yesterday. I'm impressed! SISD needs to be looking over their shoulder.

[FreeAtlanta]

Same here.

[papasmurf]

Microsnot goes down TODAY!

:O)

P

[BreitbartSentMe]

Down goes Gates! Down goes Gates!!!

It just warms my little Mac-loving heart to see that. (sigh, I miss my Mac......)

[SC Swamp Fox]

We are 100 days from Apple Computer, Inc.

[Rate_Determining_Step]

> If you're on the folding ping list, you'll get pinged every time we start a new thread (usually once a week).

If you're sheparding the Folding Ping list, add me. I'm gonna get a little more serious about this.

[papasmurf]

Geez, you sounded just like Cosell :)

:O)

P