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[BOINC] [生命科学类] Rosetta@home

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发表于 2007-11-21 23:27:48 | 显示全部楼层
among the new things to come in the relatively near future include virtual drug screening by large scale docking of small molecules onto protein targets. accurately docking even a single small molecue onto a protien target is fairly computationally intensive, so if we want to dock 100 or 1000 possible drug candidates onto a protein target large scale computing will definitely be critical.

似乎是对 100与1000内的小分子蛋白质上的目标 药物筛选把!    还是不行啊英语差  看的懂不多
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发表于 2007-11-26 20:42:15 | 显示全部楼层
Nov 21, 2007
Our web site has been updated with the latest BOINC version. Please post any bugs or issues in this thread.
我们已经更新到最新的BOINC,有任何问题的话请在论坛里回报。

Nov 20, 2007
Rosetta@home has been updated to version 5.85. This version contains some fixes in the modeling of symmetric complexes and a much improved RNA energy function. For details, see this thread.
程序已经更新到5.85。这次修复了一些在对称复合的建模问题,以及改进了RNA能量测量功能。您可以在论坛里获得更多的资料。

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发表于 2007-12-1 09:06:18 | 显示全部楼层
我接到的第一个5.85的包就出错.物理内存占用达150M+虚拟内存估计要300M+,关了Boinc重新启动软件后,任务就显示完成并要上报了.
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发表于 2007-12-3 19:15:34 | 显示全部楼层

Posted 2 Dec 2007 19:34:01 UTC

I aplogize for the rosetta@home site being down mid last week. Fate was against us: just as David K. was going in for surgery on his arm, a problem arose with the job feeder; normally David would have caught this immediately but it took the rest of the team a couple of days to figure out what was happening and how to fix it. Thanks to Rhiju for fixing the problem in the end.

很抱歉上周项目网站的当机。运气不好,DK去做手术时,任务生成器就出了问题,一般DK在时都很快就能弄好,但却让我们其它人花了好几天才搞定,感谢Rhiju最终修复了这个问题。

We have a very early and preliminary version of the rosetta game ready for testing and will soon be looking for volunteers. If one of you can collect email adresses of people interested in trying it out, I'll post instructions on who to send it to later this week. We don't want to make it completely public until all the bugs are out and it is truly fun to play!

我们已经有了一个非常早期的rosetta游戏版本,很快将开始寻找志愿者进行测试,我们希望在所有可能的问题都解决后才正式发布。

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发表于 2007-12-4 22:18:55 | 显示全部楼层
原帖由 Youth 于 2007-11-21 16:45 发表
Among the new things to come in the relatively near future include virtual drug screening by large scale docking of small molecules onto protein targets. accurately docking even a single small molecue onto a protien target is fairly computationally intensive, so if we want to dock 100 or 1000 possible drug candidates onto a protein target large scale computing will definitely be critical.

我们最近打算进行高通量虚拟筛选,把大量的小分子对接到它们的蛋白靶点上。目前,纵使是把单个小分子对接到它的靶点蛋白上也是很费时间的,所以如果我们打算把成百上千个可能成药的小分子对接到一个蛋白靶点上,就需要有很强的计算能力。

==

感觉这个想法超过Rosetta的项目初衷了

[ 本帖最后由 feynord 于 2007-12-4 22:30 编辑 ]

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发表于 2007-12-5 23:07:09 | 显示全部楼层
原帖由 feynord 于 2007-12-4 22:18 发表

我们最近打算进行高通量虚拟筛选,把大量的小分子对接到它们的蛋白靶点上。目前,纵使是把单个小分子对接到它的靶点蛋白上也是很费时间的,所以如果我们打算把成百上千个可能成药的小分子对接到一个蛋白靶点上,就需要有很 ...



  蛋白质结构、了解蛋白质与蛋白质之间的以及蛋白质自身之间的相互作用  难道他拓展到其他的领域了?
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发表于 2007-12-11 21:52:37 | 显示全部楼层
对阿,扩展到研究小分子药物与蛋白质作用的方面,这就不是“基础生物项目”而是“现实生物项目”了
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发表于 2008-1-21 10:46:11 | 显示全部楼层
最近一直在算ROSETTA 我想加个团队  请问怎么加~
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发表于 2008-1-21 10:48:12 | 显示全部楼层

回复 #32 na4088918 的帖子

置顶帖中有详细说明:
1、推荐加入 Team China (原Rosetta@China) 小组,加入方法说明如下:
请先通过 http://boinc.bakerlab.org/rosetta/home.php 页面登录。然后请进入 http://boinc.bakerlab.org/rosetta/team_join_form.php?id=47 页面,点击页面中间的“Join Team”链接,就可以加入 Team China 团队了。

2、Team China (原Rosetta@China) 团队信息查看页面为 http://boinc.bakerlab.org/rosetta/team_display.php?teamid=47
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发表于 2008-2-8 21:30:26 | 显示全部楼层
Nov 28, 2007
The Linux executable has been updated for Rosetta@home; this fixes a small error in the prior update. For details, see this thread.
linux 客户端升级,修复了一些错误。详见:http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1449

Nov 30, 2007
The site is up and running again. For more details, see technical news.
重建了网站,详见技术新闻:http://boinc.bakerlab.org/rosetta/rah_technical_news.php

Dec 3, 2007
It looks like we've a left-over problem from the other day - we're working on this now.... .
我们似乎忘了解决一个问题,现在正在修复。

Dec 3, 2007
We're up and running again. A complete update of the scheduler and web site was made so please post any issues with the server and site in this thread.
我们又一次开始。完整地升级了网站和调度程序,请在以下帖子里报告所有的问题:http://boinc.bakerlab.org/rosetta/forum_thread.php?id=3752

Dec 13, 2007
Rosetta has been updated to version 5.89. Changes allow us to model proteins with complex symmetries, and improvements in the energy function used to simulate RNA. Please post any issues with the server and site in this thread.
客户端升级,能处理更复杂的模型,在RNA折叠方面做了些改进。请在以下帖子里报告所有的问题:http://boinc.bakerlab.org/rosetta/forum_thread.php?id=3819

Dec 20, 2007
Rosetta has been updated to version 5.90. Changes include a reduction in virtual memory usage and a better exploration of proteins with complex symmetries. For details, see this thread,
客户端升级,减小了内存占用,在蛋白质模拟折叠方面也有所改进,详见:http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1449

Dec 21, 2007
The linux executable for Rosetta has been updated to version 5.91, to fix an issue with the workunit timing. Thanks to lots of linux users for posting and to helping us fix this quickly! For details, see this thread,
Linux下的客户端升级,修复了一个时间计算的问题。感谢linux用户的查错!详见:http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1449

Jan 04, 2008
Rosetta has been updated to version 5.93. This version includes improved treatment of dihedral symmetry in rosetta. For details, see this thread,
客户端升级,改善了对两个平面的对称的处理(?),详见:http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1449

Feb 05, 2008
A new application called 'minirosetta' has been released. This application is a complete restructuring of the current rosetta applicaton and was designed to facilitate future development and science. Our goal is to gradually transition to this application as it matures. Graphics are not yet available but are currently under development. Please post any issues/bugs in this thread. We'll be issuing tasks in relatively small batches soon.
发布一个新的称为“minirosetta”的计算程序,这个程序是现在的rosetta计算程序的完整重构,它是为使将来的改进更容易而设计的,同时顾及了科技的发展。我们的目标是逐渐地使这个新的计算程序替代当前的计算程序。目前不提供图形,但是这个正在开发之中。请在下面的链接中报告所有的问题:http://boinc.bakerlab.org/rosetta/forum_thread.php?id=3934,我们将很快尝试这个计算程序。

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发表于 2008-2-10 11:19:50 | 显示全部楼层
Feb 05, 2008
A new application called 'minirosetta' has been released. This application is a complete restructuring of the current rosetta applicaton and was designed to facilitate future development and science. Our goal is to gradually transition to this application as it matures. Graphics are not yet available but are currently under development. Please post any issues/bugs in this thread. We'll be issuing tasks in relatively small batches soon.
发布一个新的称为“minirosetta”的计算程序,这个程序是现在的rosetta计算程序的完整重构,它是为使将来的改进更容易而设计的,同时顾及了科技的发展。我们的目标是逐渐地使这个新的计算程序替代当前的计算程序。目前不提供图形,但是这个正在开发之中。请在下面的链接中报告所有的问题:http://boinc.bakerlab.org/rosetta/forum_thread.php?id=3934,我们将很快尝试这个计算程序。

已经在用新的计算程序在计算了.从原来的2小时50分钟变成2小时49分钟.
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发表于 2008-2-10 18:35:30 | 显示全部楼层
呵呵,这个项目的计算时间是网站上设定的,和程序的版本没有太大关系:)
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发表于 2008-6-14 11:31:12 | 显示全部楼层
June 10, 2008
The minirosetta application has been updated to version 1.28. This version contains a fix for the graphics application and jumping and loop modeling protocols. Please report bugs in this thread.

minirosetta版本升级,修正了图形显示程序。

May 24, 2008
The minirosetta application has been updated to version 1.25. This version contains a fix for a file formatting problem that was causing certain jobs running abinitio folding to fail. Please report bugs in this thread.

minirosetta版本升级,修正一处文件格式问题。

May 21, 2008
The minirosetta application has been updated to version 1.24. This version contains a fix for a memory leak that was causing tasks with long run times to fail. Please report bugs in this thread.

minirosetta版本升级,修正一处内存泄露。

May 14, 2008
CASP8 is ramping up with a handful of targets released last week, and many more expected this week. The reason you haven't seen many CASP8 work units as we are making a final benchmarking of all the new structure prediction protocols we have developed over the past two years in the new miniRosetta code framework. The testing is on CASP7 targets--we want to determine which of our new methods are best before going all out on the CASP8 targets (yes, we would like to have completed the benchmarking before casp8 started, but there has been so much to do!). the testing should be complete monday and tuesday, and based on these results we will be sending out primarly casp8 work units next week using the approaches the tests currently running show are most successful.

I can't emphasize enough how critical all of your contributions are to our efforts to improve protein structure prediction methods! we have had many ideas on potential improvements which we have implemented, but the only way to know whether we are actually getting closer to the truth is to do rigorous testing (the casp7 targets for which we now know the structures are a perfect test set), and this would quite simply be impossible without your contributions! -- David Baker

from DB's Journal

casp8来啦~~

May 05, 2008
The minirosetta application has been updated to version 1.19. This version introduces several bugfixes for our CASP8 abinitio and template-based modeling protocols. We'll be testing small batches of workunits this evening and tomorrow morning. For details, see this thread, and please report bugs in this thread.

minirosetta版本升级,针对casp8修正了一些bug。

Apr 23, 2008
The minirosetta application has been updated to version 1.15. This version introduces an improved method for modeling larger RNA molecules. For details, see this thread, and please report bugs in this thread.

minirosetta版本升级,改进了对大RNA分子的建模方法。

Mar 13, 2008
Rosetta has been updated to version 5.96. This version introduces an improved method for modeling larger RNA molecules. For details, see this thread.

rosetta版本升级,改进了对大RNA分子的建模方法。

Mar 13, 2008
Rosetta has been updated to version 5.95. This version includes a new method for searching beta sheet topologies. For details, see this thread.

rosetta版本升级。

Mar 12, 2008
Minirosetta has been updated to version 1.09. New graphics for windows have been included, and graphics for the mac should be in by the next version. This update also includes a variety of new experimental protocols for fullatom minimization. Please post any issues/bugs in this thread.

minirosetta版本升级,有图像显示。

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发表于 2008-6-14 11:39:59 | 显示全部楼层
补全一下,太长就不翻译了。

Nov 30, 2007
DK, our primary site developer, is recovering from surgery and is out of contact. When the troubles arose DK's status wasn't known to the IT group, resulting in confusion. Rhiju stepped in and provided the fix. We apologize for the outage...

David Kim术后恢复中?

Nov 29, 2007
The feeder is failing over and over again thus no new work is being sent out. The feeder application needs to be rebuilt to handle the large number of applications that R@H has had. We know of the problems and will get this done as soon as possible.

任务包生成服务程序持续运行失败导致发放不了新任务包。

Sep 18, 2007
The RAID is rebuilt and now we're chasing down the next bottleneck....

RAID正在重建。

Sep 17, 2007
We're experiencing another hardware problem that is effecting the overall project, causing the validator and assimilators to fall behind. The temporary fileserver to which we've switched has dropped on of its RAID disks. We've found a replacement and the RAID is rebuilding now. Once finished the project should start catching up w/ itself...

又一次硬件故障,RAID丢盘。

Sep 08, 2007
Rosetta@home has experienced a horrendous hardware/fireware failure. We essentially lost the SAN partition upon which the project was running! The newest edition of our SAN hardware was shipped with a firmware revision that contained an insidious bug - one which caused the new SAN disks to vanish after roughly 45 days of service. We - or rather I (KEL) - apologize for the inconveinence, lost time and lost effort that you have endured during our outage. We know full well that your contribution hinges on the understanding that we make maximum use of your valuable resources - that we not waste your time, CPU cylces or good humor. We are planning to express our disappointment to our vendors in clear terms, specifically siting the importance of this project to our research effort. We'll keep you abreast of the outcome.

Aug 30, 2007
There was an unannounced service outage this morning at 8AM PST. The outage was planned - I just forgot to announce it to the R@H community. I (KEL) apologize. We had to upgrade the firmware on our SAN which required the hardware being offline for an hour. We don't anticipate any further issues along this line, but we'll work harder to ensure prior notification to our R@H partners - you.

July 31, 2007
We moved the backend of the BOINC system from our older fileserver (a dual 2.8 GHz Xeon w/ 2 GB RAM, running a 64-bit kernel and serving up 655 GB RAID5 disk (6 X 146 GB 10K SCSI)) to our fiber SAN. The SAN is a clustered filserver, running Polyserve's Matrix Server and serving up 16 450 GB SATA disks as a single RAID5 LUN via two Dell 2950s from within our group's fiber SAN. I'll post more information on and pictures of the SAN setup in the near future....

Apr 10, 2007
The UW campus experienced a large power service failure this morning around 9:15 PST that lasted for roughly 45 minutes. 14 buildings in the South Campus area were effected, including the datacenter in which Rosetta@home is hosted. The battery backup for this facility provides only 10 minutes or so of power to the datacenter floor; there is no backup generator at this site. As a result lost all power to all RAH hardware and had to bring everything back from a cold start. We are reviewing the situation.

Jan 11, 2007
Regarding the recent increasing graphic related errors, we suspect it is a problem of thread synchronization. Basically Rosetta working thread does the simulation which changes all the atom coordinates ( which are saved in shared memory) while the graphic thread tries to read data from that place to draw the graphic or screensaver. Currently there is no locking mechanism to ensure the shared memory is accessed by one thread at a time and this could generate some conflicts or memory corruption and then trigger an error. On one of our local computers, when screensaver or graphic is turned on, it caught errors at a rate of at least one per day on average and without any graphics, it ran flawlessly. The errors which have been observed include crashing(0xc0000005), hung-up (0x40010004) and being stuck( watchdog ending). All the errors were not reproducable with same random number seeds and we think that is due to the radomness in graphic process. Another side proof was that showing sidechains requires accessing shared memory more often and intensively, and after turning off sidechains and rotating, the graphic error rates drop but the problem is not solved completely. There seems to be an correlation between two. We are currently working on adding the new locking mechanism and we will post an update when it is ready to be tested out. Meanwhile, if you have experienced freqeuent client-errors, please temporarily disable the boinc_graphics/screensaver to reduce the problem. Thanks for everybody's support.

Oct 11, 2006
A batch of work units, the first protein-protein docking Rosetta@home experiments, were sent out yesterday that, unfortunately, were destined to fail. The actual work units were completely fine as they were tested on Ralph thoroughly but a rather unfortunate circumstance caused them to fail on clients. The work units had input files whose names ended with "map", and our downloads web server was configured to handle such files as image map files (the default apache setting) so the clients were not getting the actual content of the files and thus the jobs were failing with download errors. The web server's configuration has been updated so the errors should no longer occur, however, the batch was cancelled, so if you have any work units queued on your client whose names start with "DOC_" AND contain the text "pert_bench_1263_" please abort them. For example, "DOC_4HTC_U_pert_bench_1263_1000_0". We are very sorry this happened. It's unfortunate since there has been some recent exciting developments which include an updated application and screensaver, and docking.

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发表于 2008-6-25 09:40:38 | 显示全部楼层
June 24, 2008
As many of you have likely noticed, our throughput has decreased significantly in the last week. This was due to a couple bad batches that were sent out last week for CASP8 that were not caught by our Ralph tests. The issue was rather insidious in that the tasks would cause some clients to stall and sit idle so we were not immediately aware of the problem. The task names started with "t405". If you have any of these tasks on your client, PLEASE ABORT THEM. These batches have been cancelled. We are currently testing a fix on Ralph and an update will soon be posted. Sorry for any inconvenience.

大意:
请把以"t405"开头的任务包中止.因为这些任务会使客户端停止运行,并且处于闲置状态.

[ 本帖最后由 Tynox 于 2008-6-25 09:54 编辑 ]

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