[BOINC] [生命科学类] Rosetta@home

Youth

CASP7快要开始了，相关的介绍可以看3楼的链接，希望Rosetta@home可以继续取得好成绩！

Youth

April 27, 2006
Application upgraded to 5.06. New version includes a watchdog timer, and multiple checkpoints as well as some new science modes. For more information see this thread.

May 9, 2006
Application upgraded to 5.12. New version includes the ability to send out workunit descriptions and rescaled graphics for big proteins. For more information see this thread.

版本更新的详细信息可以看官方论坛中的这个帖子：
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1449

Youth

刚刚收到项目方的群体邮件,除了简述近期R@H计算程序的更新外,主要就是介绍CASP7并鼓励大家多多参加R@H!

另外,项目方正在努力降低计算程序的内存占用,希望能控制在100M之内(对于150个氨基酸组成的蛋白质)。

Firenet

引用 Youth 在 2006-5-10 14:29 时的帖子:
刚刚收到项目方的群体邮件,除了简述近期R@H计算程序的更新外,主要就是介绍CASP7并鼓励大家多多参加R@H!

另外,项目方正在努力降低计算程序的内存占用,希望能控制在100M之内(对于150个氨基酸组成的蛋白质)。

期待ing

Youth

We are sending out a newsletter that was written by the volunteers to all participants whose preferences allow (so, no, we've not become a SPAM host). The letter outlines the upcoming CASP contest and our greater need for computing power during that time. Sending out newsletters will be a very rare event - primarily because it is a big pain.

我们正在发送一封邮件通讯给那些愿意接收我们邮件的参与者。邮件中概述了即将到来的CASP竞赛以及我们对计算能力的渴求。另外，我们并不会经常发送这样的邮件通讯。

Youth

If you have seen any slowdowns in other computer applications when rosetta@home 5.12 is running, please post here. We are testing a potential fix on ralph, if you wish to help out!

如果你在运行5.12版本的计算程序时碰到了计算机变慢的情况，请在下面的帖子中报告。我们正在RALPH项目中测试一个可能有用的修复。
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1562

Youth

CASP7的第一个预测对象已经发布，大概明天之后就会开始分发相关的任务包了。

The first CASP 7 target was released today!

Here is its amino acid sequence:

MSFIEKMIGSLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSGGPTDWQDTKRIFGG
ILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKDTKTWMDKYRTKLNDSIGRD

can you tell from this what the three dimensional structure and function of this protein are?

The problem with proteins, of course, is that you can't read off directly from the sequence what the structure and function are, although both are completely determined by the sequence (the genetic blueprint, quite literally).

We are excited because this protein looks unrelated to any protein of known structure, and is not too much bigger than most of the proteins we've running tests on these many months, so it is a perfect challenge for the methods we've been developing. After some quick runs on RALPH to make sure work units behave properly, you should see work units for this protein by the end of tomorrow!

Firenet

引用 Youth 在 2006-5-11 21:19 时的帖子:
CASP7的第一个预测对象已经发布，大概明天之后就会开始分发相关的任务包了。

The first CASP 7 target was released today!

Here is its amino acid sequence:

MSFIEKMIGSLNDKREWKAMEARAKALPKEYHHAYKAIQ ...

我会收到吗？祈祷

windin

已经收到一个了正在运行

Youth

Rosetta@home updated to 5.13. New version fixes some debugging code that was causing slowdowns in a small fraction of clients.

计算程序升级到5.13版。新版本修正了一些可能导致少数机器变慢的调试代码。

Youth

The first workunits from the CASP7 blind trials have been queued to Rosetta@home.

CASP7盲试的第一批任务包已经进入了Rosetta@home的队列。

Youth

Rosetta@home has been updated to 5.16. In addition to matching the date, the new app has slightly lower memory requirements and includes some improvements that will allow us to test different science protocols. More info here.

计算程序升级到5.16。除了和日期对应（汗...），新版本对内存的占用稍有降低，算法上也有改进。详细请看这里。

Youth

Rhiju and I had fun looking at the lowest energy structures returned for T283 thus far. They are very similar in the first two thirds of the protein, but for the last third we see several distinct solutions. Based on our experience with the test problems over the past three months, we expect that with more sampling one of the solutions will clearly win out, and this should be (we hope!) the correct structure.

Thus far we have about 100,000 structures returned; we hope to have 10x more sampling before submitting predictions.

We made another step forward today in reducing the rosetta memory footprint. For a 175 amino acid residue protein, the standard ab relax protocol we are using for CASP took 222MB of virtual memory three weeks ago, and is now down to 108MB! Now a computer with only 256MB of memory should be able to comfortable process rosetta@home jobs even for larger proteins. The major memory hog now is the boinc graphics which can add on another 100MB or more--any experts out there who might be able to help with this? In any event, you should be able to run rosetta@home on low memory machines as long as you turn the graphics off.

A side benefit to some of the memory use reductions is that it should be relatively easy to reduce the sizes of some of the input files we send out with each work unit. Would a 30% reduction make a significant difference to dialup users?

Seven targets have been released thus far in CASP7. The list, which is updated daily, is at
http://predictioncenter.gc.ucdav ... er.org;page=casp7/.

175个氨基酸组成的蛋白质，三周前的老程序需要222M内存，现在的程序只需要108M！

windin

最近动作平凡。估计是前段时间主管被鼓励了，现在更加要屁颠屁颠卖力了。

Youth

主要原因应该是CASP7吧？