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[BOINC] [生命科学类] Rosetta@home

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发表于 2006-8-17 13:26:00 | 显示全部楼层

Aug 16, 2006

Work flow is back to normal. The new work based credit values are being added to the database. They will be reported on our statistics pages tomorrow.

新的基于任务的积分值已经添加到了数据库,这些值明天将出现在我们的统计页面上。

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发表于 2006-8-20 10:38:57 | 显示全部楼层
Posted 19 Aug 2006 16:39:10 UTC by David Baker

It is an exciting time in the lab now as we are recovering from the craziness of CASP. While Bin and Rhiju are taking an incredibly well deserved vacation, the new HIV vaccine design project is starting to come into full swing. We now have computationally designed amino acid sequences for 15 potential vaccine candidates, and we will start the process of making them next tuesday; the first step is to synthesize genes which encode these proteins. We have also designed a whole series of novel enzymes which catalyze a wide variety of reactions, and are starting the gene synthesis process for these as well.

I'm particularly interested now in designing enzymes which destroy organophosphate compounds which are the key ingredients in many pesticides and nerve agents. On rosetta@home, we are carrying out calculations in which we are resampling regions of the landscape found to be low energy in initial sets of runs and we hope these will lead to significnat improvements in our abilities to find global minima.

I'm very sorry about some of the not nice things being passed about on the message boards, and I'm also sorry that my efforts to calm things down haven't helped, so I will be doing my communicating with the project solely through this thread for the next week. You are all making great contributions, and I ask people who have been annoyed by what has been said on one side or the other to try to think about the big picture and what we are all trying to accomplish together.

似乎要开始处理HIV疫苗相关的工作了。

///

Posted 19 Aug 2006 17:20:40 UTC by David Baker

A couple more things:

First, I will be describing all of your efforts at a conference on Monday on grid computing:
http://www.opensciencegrid.org/e ... ng0806/agenda.html. (should I
show some excerpts from the message boards?). I will of course describe the great work you have all done together.

Second, To answer a question which came up on the boards--we will NOT be backdating credit totals. The new system will go into place early next week, adding on to the current totals.

Again, I thank you all for your efforts and the many people who have volunteered to help recently!

新积分系统不会调整之前大家的得分,新的积分会直接加到旧积分上。

[ Last edited by Youth on 2006-8-25 at 10:31 ]

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发表于 2006-8-25 10:23:18 | 显示全部楼层

Aug 23, 2006

New crediting system: We have officially switched to a new work based crediting system. See our technical news section for details.

我们已经正式使用新的基于任务的积分系统,详情请看技术新闻。

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发表于 2006-8-25 10:30:05 | 显示全部楼层

August 23, 2006

We have officially switched over to a new crediting system that grants credit based on the amount of structures produced by your computer. Under the new system, the amount of credit awarded per structure for a particular work unit is determined by the average amount of credit claimed per structure using the standard BOINC credit metric over all Rosetta@home runs of that work unit to date. For each work unit type, we keep track of the total amount of claimed credits and structures from valid results returned by hosts, and we use these running totals to determine the amount of credit to award per structure. So if your computer returns 2 structures, the amount of credit awarded would be 2 * total_claimed_credit / total_structures where total_claimed_credit and total_structures are the sum of the claimed credits and structures from valid results returned by all hosts prior to your returned result for that particular work unit type, respectively. The first returned result will be awarded the claimed credit, the second returned result will get the average claimed credit per structure between the two multiplied by the number of structures returned by the result, the third returned result will get the average claimed credit per structure between the three multiplied by the number of structures returned by the result, and so forth. Under the same time frame, a faster computer will produce more structures than a slower computer and thus will be awarded more credits per cpu time.

新积分系统的技术解释,太长,懒得翻译了,有兴趣的看看吧。

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发表于 2006-8-25 10:38:24 | 显示全部楼层
Posted 24 Aug 2006 6:26:58 UTC

Today was an exciting day for the group! In our vaccine design and enzyme design calculations, the end result is an amino acid sequence for a protein predicted to be a good vaccine or catalyst of a chemical reaction. The next step is to make a gene--a piece of DNA--that codes for the amino acid sequence. Due to advances in technology, rather than having to laboriously synthesize each gene in the lab, we can buy genes for any amino acid sequence for not to much from DNA synthesis companies, and we are lucky to be collaborating with a startup company in Boston called Codon who can make them for us quite cheaply. Today we ordered genes for 16 potential HIV vaccines, 15 potential new enzymes, and 4 potential new protien-protein complexes. I say potential above because our design calculations are not perfect, and we won't really know if these proteins act as designed until after we get the genes back in a month or so. Then we take advantage of modern molecular biology techniques to put the genes into bacteria where they direct the cells to make large amounts of the designed proteins. We can then separate the designed proteins from the rest of the stuff in the bacteria using a special tag we include in each of them that provides a good handle. Once we have the purified designed proteins, we can see whether they bind the desired antibodies in the case of the vaccine designs or catalyze the desired reactions in the case of the enzymes. In this way, we will learn about both the strengths and weaknesses of the rosetta design methodology, and hopefully have crated proteins that can have a very positive effect on the world!

在疫苗和酶设计方面的进展:已经将一批设计结果拿到商业公司去进行合成(说是还比较便宜),然后还需要进行一些相关的实验。

As Hugo pointed out, we have not quite gotten the design methodology to the point we can run it on rosetta@home, but this should be coming in not too long as several people in my group are now focusing on this. Before this, look for protein-protein docking calculations where we are trying to predict the structures of the complexes between proteins which mediate much of the basic processes important to life. Chu Wang, a graduate student in the group, is close to having his docking methodology compatible with distributed computing, and we anticipate breakthroughs in this importnat problem as it also seems largely limited by cpu power.

这方面的设计工作目前还不能在Rosetta@home进行,但应该很快就能实现了。

Currently running on rosetta@home are the last of the casp tests on protein structure refinement (see the casp7 website) and tests of a general approach for estimating how much compute power is necessary to find the lowest energy structure for a sequence. I will describe the basic idea behind this approach in one of my next posts.

目前Rosetta@home上运行的是最后一批casp的任务包,同时也在测试对于一个氨基酸序列如何估算寻找到最低能量结构所需要的计算力。

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发表于 2006-9-13 12:42:07 | 显示全部楼层

Sep 12, 2006

Native structures for several of the CASP targets are beginning to be released. The prediction from Rosetta@home for target T0299 is quite accurate! For details and pictures of the predicted structures, see the top predictions page.

部分CASP7预测目标的自然结构已经公布,Rosetta@Home对编号T0299的蛋白质的结构的预测相当精确!详情请看最佳预测页面。

下图为自然结构:


下图为Rosetta@home的预测结果:

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发表于 2006-9-13 16:17:05 | 显示全部楼层
很好看的说~~
那个颜色是不是代表什么意思啊??
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发表于 2006-9-13 16:24:30 | 显示全部楼层
应该都有特定含义的吧,我也不懂生物学上的东东:)
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发表于 2006-9-25 16:23:28 | 显示全部楼层

又公布了一个CASP7的预测结果

Sep 25, 2006
The predicted model from Rosetta@home for CASP7 target T0363 and the users whose computers generated the lowst energy models have been posted on the top predictions page. Congratulations!

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发表于 2006-9-28 20:49:21 | 显示全部楼层
一个Rosetta的视频剪辑,可以看到项目组的成员,可以了解一些项目的原理:

http://www.lauralynngonzalez.com ... team/bakerSmall.mpg
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发表于 2006-10-13 17:28:16 | 显示全部楼层
Rosetta@home has been updated to version 5.32 -- our first update after CASP7. The new update has two major new features: 1. protein sidechains are shown in the graphics during Rosetta full-atom simulation stage (left) details; 2. a new type of structure prediciton task -- protein-protein docking is running on Rosetta@Home now (right)




Rosetta@home程序已经更新到了5.32,这是我们在CASP7后的第一个更新。这次的更新包括了下列主要的功能:1)蛋白质的侧链(支链)将以图片的形式在原子模拟中被显示;2)新的结构预测任务-蛋白质与蛋白质之间的反应-现在已经正在进行了

翻译技巧不好,请原谅~

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发表于 2006-10-13 17:46:24 | 显示全部楼层
有新任务哦,加油算
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发表于 2006-10-14 15:15:20 | 显示全部楼层
新的任务报以DOC_开头,名称中还有_pert_bench_的字串~

一个包以我这里的速度(2.66GHz)平均4小时半左右一个包,获得的积分在30左右。
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发表于 2006-10-14 23:35:10 | 显示全部楼层
我现在接受的还是FRA的啊?
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发表于 2006-11-22 13:58:41 | 显示全部楼层
Nov. 13, 2006
Rosetta@home has been updated to version 5.40. The update introduces a new type of simulation -- predicting the structure of amyloid fibrils.

Rosetta@home版本已升级至5.40.本次升级引入了一种新的模拟——预测淀粉分子的结构.

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