RNA World 的 FAQ

Youth

也是RNA World的项目方在邀请大家来翻译，待翻译页面：

http://www.rechenkraft.net/wiki/index.php?title=RNA_World/FAQ/en

1. 有愿意帮助翻译的，请直接回帖（可以先占座）
2. 因为页面比较长，可以按一个个问题分开来翻译
3. 翻译结果上最好原文和译文一并放上来，方便大家对照检查


更新：目前的翻译结果已搬运至主站 http://www.equn.com/wiki/RNA_World:%E5%B8%B8%E8%A7%81%E9%97%AE%E9%A2%98%E8%A7%A3%E7%AD%94，请大家针对该页面中的内容进行校对，谢谢。

xuyongchen

我试试看吧。。。先占个。。。（希望再来几个人占座，怕翻译的不太好，第一次尝试翻译）

xuyongchen

43项中已完成：2、4、5、6、7、8、9、10、12\16、17、18、19、20、21、22、23、31、32、33、

放在论坛上编辑感觉有点麻烦（我没怎么弄过，格式什么的调起来很麻烦）全部翻译后看能不能上传一个word版的下载吧。那个会直观一些，也舒服一些。目前这个版本嘛。。。抱歉了，大家凑合看吧
2.What applications are currently supported by RNA World?
RNA World目前支持哪些项目？
type                                        application                                               purpose
  
INFERNAL 1.0.2        CMBUILD, CMCALIBRATE, CMSEARCH        RNA covariance analysis  RNA协方差统计
InReAlyzer 1.0                Converter to produce high-resolution graphics from INFERNAL output files (in-house development)  将INFERNAL项目输出的文件转化并制作高分辨能力的图像（内部支持）

4.Does RNA World support GPU/CUDA/STREAM processing?
RNA World支持GPU/CUDA/STREAM运算吗？
At present, RNA World applications do not profit from GPU processing, but we can think of applications that will and if that applies, we will certainly try our best to make clients available that support such performance improvements. 目前，RNA World尚未从GPU运算中受益。不过我们会为参与者考虑。一旦有相关需求，我们一定会尽全力让参与者获得对这类计算性能提升技术的支持。

5.Does RNA World support checkpointing?
RNA World有存盘点吗？
RNA World is a universal framework comprising a diverse set of RNA-relevant bioinformatic tools. Originally, these tools were not designed for incorporation in a distributed computing environment although most of these require significant compute ressources. Traditional checkpointing, however, must be supported by the scientific application. Consequently, checkpointing is not available, but: The RNA World development team is seeking ways to establish novel, universal checkpointing procedures. These novel methods rely on either creating "suspend RAM to disk" images at the system level or the establishment of RNA World as a system that generally runs in a virtual machine (VM). For the former we have a functional 32-bit Linux workaround that, however, requires that memory randomization is deactivated in the Linux kernel. For the latter we have a promising cooperation with CERN.RNA World是一个通用的框架，包括一系列有关的的生物信息工具。一开始，这些工具并没有设计在分布式计算环境内，尽管它们需要大量（显著）的计算资源。传统的存盘点必须要被科学任务所支持。因此，存盘点并未被RNA World所支持。不过RNA World的技术小组正在试图建立新颖的、通用的存盘过程。这些新颖的方法包括在系统水平上创建将内存（数据）存入硬盘（的功能）或者将RNA World建成系统以便在虚拟机上运行。对于前者，我们可以在一台32-bit的Linux工作环境中实现，不过（事先）要将随机内存功能从Linux内核中移除。对于后者，我们与CERN有着密切的合作且前景良好。

6.What is the RAM requirement of RNA World?
RNA Word 的内存需求如何？
type                                          application                                                  RAM requirements
  
INFERNAL 1.0.2        CMCALIBRATE        up to 2.5 GB of RAM,usually below 600 MB of RAM最多需要2.5GB，通常小于600MB
        CMSEARCH        up to 1 GB of RAM,usually below 100 MB of RAM   最多需要1GB，通常小于100MB
InReAlyzer 1.0                below 50 MB of RAM  小于50MB
Please note one important thing: If you are using a multi-core machine, RNA World might engage on all of your cores simultaneously. As long as we do not use the OpenMPI-based multi-threaded application mode, this means that the RAM required to successfully complete all of the work units is additive.请注意一个重要的事实：如果你使用的是多核处理器，RNA World可能会同时使用所有的核心，前提是我们不使用基于OpenMPI的多线程任务模式。这就意味着未来完成任务内存需求会增加。

7.What are the typical running times of RNA World work units using an Intel P8600 Core2Duo 2,4 GHz machine with Ubuntu Linux x64?
运行在Ubuntu Linux X64上的英特尔Core2Due 2.4GHz的计算机通常运行RNA World需要多长时间？
type                            application                              runtime
  
INFERNAL 1.0.2        CMCALIBRATE        20 minutes to 10 days,typically a day
20分钟-10天
通常1天
        CMSEARCH        a few minutes to 100 hours,typically a few hours
几分钟-100小时
通常几小时
InReAlyzer 1.0                a few seconds to 5 hrs,typically a few minutes
几秒-5小时
通常几分钟

8.Does RNA World support multithreaded (MT) applications?
RNA World支持多线程任务吗？
RNA World supports whatever its scientific applications support. In case of INFERNAL, multithreaded applications are nicely supported on the basis of OpenMPI. While MT applications run well in a local computing environment under Linux, validation of results generated in a distributed computing environment that employ MT applications for unknown reasons fails in a subset of cases, although technically MT applications work excellent. We have not yet identified the cause of this inconsistent behavior, but INFERNAL makes use of random number generation that is tied to the processor core time at which individual threads are started. On a multicore system, an MT application therefore is initiated at slightly different times on each of the cores involved. Consequently, on a different (distributed) system, the random numbers differ and so do the results - although differences are only minor. If the random number generator is supplied with a fixed value, issues are largely solved but, strangely, not entirely and that is a problem for BOINC-based WU validation. The RNA World team is currently corresponding with the INFERNAL developers to solve this issue to fully enable distributed MT applications as soon as possible.只要是它的科学任务所支持的，RNA World都支持。以INFERNAL为例。基于OpenMPI，多线程任务可以被很好的支持。多线程任务可以在Linux下的传统计算平台下良好运行，但事实结果证实了在分布式计算平台下多线程任务无故的在一些任务的子集中遭遇失败，尽管技术上认为多线程任务工作正常。我们还没有探明这些矛盾的行为的原因，不过INFERNAL使用率随机数生成技术。该技术与独立线程的初始点：核心时钟联系紧密。因此在多核系统中，多线程任务受每个核心的影响在不同的时间被创建（尽管时间差很小）。因此，在不同的系统下（分布式运算），随机数不相同，结果也是如此（尽管差距很小）。如果随机数生成器支持混合数值，问题将在很大程度（奇怪的是，并不是全部）得到解决。而这就是基于BOINC的WU的难题。RNA World小组现在正在于INFERNAL小组进行合作来解决这个问题，以期多线程任务可以尽早展开。

9.What is a multithreaded (MT) application?
什么是多线程任务？
A multithreaded application makes use of multiple CPU cores on modern machines to compute a single RNA World work unit. Our measurements for CMCALIBRATE running in a Linux environment showed that a quadcore crunches one work unit in even slightly less (!) than a fourth of the computation time that was required for singlethreaded computation of the same work unit. This shows that CMCALIRATE scales excellent in MT mode.多下城认为可以让现代计算机上多个CPU核心只运行单一RNA World任务。对在Linux环境下CMCALIBRATE运行情况的测量显示一个4核处理器处理一个任务所需的计算时间甚至少于同一个任务使用单线程所需时间的四分之一。这表明CMCAIBRATE可以在多线程模式下完美的运行。

10.Will RNA World research ultimately lead to the development of medications?
RNA World的研究最终是否会促进医药的发展？
Although nobody can forsee this for sure, it seems highly likely that the results generated by RNA World will contribute to the development of medications (see application section of this F.A.Q.).尽管没有人预见并确信这一点，不过看上去RNA World有很高的可能性可以为医药的发展做出贡献。（参见本FAQ中的任务（介绍）部分）

12.Will the RNA World project results be published and if so under what license?
RNA World项目的结果会被公开吗？是的话，在什么样的许可下？
All RNA World results will be published in high-quality peer-reviewed science journals, preferrably in those offering an open access policy for the general public.RNA World的所有成果将会发表在高品质，优秀的科学期刊上，尤其是那些为普通公众开放的期刊。

16.Does RNA World award project performance certificates?
RNA World有项目表现证书吗？
Yes.有

17.How can I save my work for non-checkpointed RNA World sub-applications when I need to turn my machine off?
RNA World项目无存盘点，当我要关机时将如何保存我的任务？
If you run RNA World on a laptop or if you have multiple operating systems installed, from time to time it will be required to turn your machine off. The current RNA World sub-applications INFERNAL and InReAlyzer dot not support checkpointing, so your work would be lost if you shut down your machine the standard way. To avoid loss of your work, set the machine to enter sleep mode. Under these conditions the entire RAM will be saved to hard disk and upon system reboot your work will be reloaded into memory such that even RNA World can continue to calculate where it left off.当您在笔记本电脑上或者在多系统计算机上运行RNA World，关机将是必须的。目前，RNA World的主项目INFERNAL和InReAlyzer均不支持存盘点，所以关机意味着任务的丢失。避免任务丢失的方法是使计算机进入休眠模式。在休眠模式下整个内存的数据将会被保存在硬盘中，当系统重新加载时数据也将一同重新加载，这样RNA World能够继续运行。

18.What operating systems (32/64-bit) are supported by RNA World?
RNA World支持哪些操作系统？（32bit或64bit）
Since RNA World is a framework consisting of many different bioinformatic applications, support of operating systems will always depend on the individual application. If its source code is available, the RNA World development team will do its best to make it available for as many operating systems as possible, i.e. Linux, Windows and OSX at the minimum. In addition, care will be taken to support 32-bit as well as 64-bit versions and special assembly codes (SSE, SSE2, etc.) wherever possible and useful.由于RNA World只是一个框架，它包括众多不同的生物信息任务，因此它所支持的操作系统将取决于个人。如果它的资源代码可以获得，RNA World技术小组将尽全力支持尽可能多的操作系统平台。至少包括Linux、Windows和OSX。另外，32bit和64bit系统一样会的得到支持，特殊指令集（SSE，SSE2等）也将被支持，因为它们十分有用。

19.What are the costs of participating in RNA World?
加入RNA World需要哪些花费？
None, except for your private electricty, network and hardware maintenance costs.无，只有电费网费以及硬件的维修保养费用。

20.Are there privileges that apply only to Rechenkraft.net team members?
特权只授予Rechenkraft.net team的队员吗？
As fairness dictates: No.为了公平起见：答案是否定的。

21.What are the plans concerning language support on the RNA World website?
RNA World网站支持哪些语言？
Just take a look here: http://www.rnaworld.de/rnaworld/language_select.php
只需点击即可获知。

22.Will there be CPU-optimized applications?
有（所使用的）CPU最适合的任务吗？
These are already implemented, i.e. the initially downloaded package contains a program that checks which type of application is optimal for your machine (x86/x64, diverse SSE versions).这些已经被实施了，初始下载包中包含有一个检测计算机最适合运算项目的程序。（包括X86/X64,各种指令集）

23.Is it possible to exclude participation in certain sub-applications?
参与者有没有可能（选择）免于计算某个子项目？
Yes. In your RNA World project settings you can decide on your own which RNA World sub-applications to support and which not. In fact, if you have an older machine it might be recommended, e.g. to exclude CMCALIBRATE as work units for this program demand huge amounts of RAM and often take a long time to complete.是的，在你的RNA World项目参数中你可以自己决定参与哪些子项目而又不参加哪些。如果你的机器相对较旧，推荐不参与CMCALIBRATE。该项目的任务单元需要大量的内存并需要很长时间才可完成。

31.What are the minimal CPU requirements for participation in RNA World?
参加RNA World所需要的临界CPU是哪一款？
Concerning the CPU, even processors lacking SSE such as Intel Pentium II (or older) could in principle participate since we have the appropriate applications ready for delivery. However, you should consider the average run times, deadlines and RAM requirements for certain types of work units as detailed elsewhere in this F.A.Q.考虑到CPU的话，哪怕缺少SSE的英特尔奔腾2（或更早的产品）都可以参与。因为我们准备好了合适的任务，只待发送。不过你得考虑某个类型任务的平均运算时间，截止日期以及内存的占用。这些细节你可以在本FAQ的其他问题下找到。

32.What are the network requirements for participation in RNA World?
加入RNA World需要什么网络设备？
Currently we recommend RNA World participation only for machines that are connected to the Internet on a 24/7 basis, i.e. all around the clock.目前我们推荐那些24*7即始终联网的机器参与RNA World项目。

33.Does RNA World offer a screensaver function?
RNA World由屏保功能吗？
Yes.有

nekoko

这么一篇长篇大论的……真是佩服，太有毅力了

xuyongchen

回复 4# nekoko

翻译的头都大了。。。。有种想撞墙的冲动。。。

nekoko

回复 5# xuyongchen

まあ～JUST DO IT

xuyongchen

回复 6# nekoko

慢慢来吧。。。

xuyongchen

有些地方的翻译（如项目的全称之类的）还没有进行查找和矫正，大家稍微等一段时间吧（有的是没有查，有的是查不到。。。。）感谢大家的耐心！

Youth

翻译辛苦啦~~建议内容适当拆分成几楼，看起来清楚些：）

xuyongchen

本来也想的，但是我是柿子捡软滴捏，先翻译简单的，所以整体上支离破碎的。要不我把翻译好的贴上来吧，没翻译好的就先撤掉。

xuyongchen

PART-2 更新15、24、28、41、42、43

15.Are the work units identical for different operating systems?
不同的操作系统下任务单元有所区别吗？
RNA World delivers work units based on available applications. If an RNA World application is available for more than one operating system then the work units assigned are usually identical. This, however, does certainly not mean that identical work units will be computed similarly fast on systems that have identical hardware but different operating systems. The reason for this, among others, is e.g. differences in compiler performance.RNA World传送任务单元是基于有效的任务。如果一个任务可以在多个系统上运行，那么任务单元往往会被特定化分配。不过这并不意味着特定的任务单元可以在特定的硬件上运行的更快，在其他的系统下却表现的不同。这样的原因是因为不同的编译程序的表现不同，而不是其他的原因。

24.Is it possible to enable/disable participation in alpha/beta tests using a simple switch in the RNA World user profile?
在RNA World中用户能否使用一个简单的转换即可决定是否参加alpha/beta 测试？
Yes.可以

28.How much hard disk space is required to run RNA World?
运行RNA World需要多大的硬盘空间？
The required disk space varies depending on the types of work units you are being assigned to. At present, RNA World core files require around 25 MB of hard disk space. CMBUILD and CMCALIBRATE work units should not require more than approximately 10 MB while CMSEARCH work units may use up 300 MB at maximum, typically between 2-20 MB. InReAlyzer hard disk space requirements cannot be predicted reliably because the number of images generated depends on the CMSEARCH output file size. However, we do not expect InReAlyzer to require much more than 1-100 MB. Remember that the sum of required hard disk space calculates from the sum of work units that have been downloaded plus the RNA World core files. Currently, a maximum of 10 work units can be downloaded per CPU core. Note that you can specify the maximum hard disk space that RNA World is allowed to occupy manually from either within you local BOINC manager or on the RNA World website.硬盘空间取决于你所申请的任务种类。目前，RNA World核心文件大约需要25M的硬盘空间。CMBUILD和CMCALIBRATE任务单元一般不超过大约10M的空间，CMSEARCH任务单元可能最多使用300M空间（不过）通常在2-20M之间。InReAlyzer任务所需的硬盘空间大小无法被可靠的预测，因为生成的图片数量取决于CMSEARCH输出文件的尺寸。不过我们不期望InReAlyzer的硬盘需求超过1-100M。需要记住的是，硬盘空间需求总大小是由下载任务单元以及RNA World核心文件累加而得出的。目前，一个CPU核心最大可下载10个任务单元。注意这一点的话，你便可以通过本地BOINC客户端或RNA World的网站明确硬盘最大允许占用值了。

41.Can't you refresh the server status page more frequently?
服务状态页面能否更频繁的更新？
We could, but we will not do that because we need to give priority to server performance. Updating the status page more frequently would cause a considerable increase in database queries which in turn cause additional server load. That power we prefer to dedicate to more important tasks as e.g. WU processing and serving. Anyway, the status page is refreshed every 10 minutes and if you browser shows something different, then you have a caching issue.我们能做到，但选择不做。因为我们把提升服务体验放在优先位置上。更频繁的更新状态界面将导致基于数据的询问显著增加。这些将导致额外的服务负荷。这些能源我们更愿意贡献给重要的任务，比如WU单元以及服务。不论怎样，状态页面每10分钟更新一次。如果你的浏览器显示了一些不同的内容，那么你有隐藏的问题

42.I started RNA World on my Debian Etch machine and got a lot of 'compute error' messages whereas running it on the same machine using RedHat gives no errors at all - is it possible that I experience an OS-dependent problem here?
我在Debian Etch计算机上运行RNA World，出现了很多的“computer error”信息。但是同样的机器安装RedHat系统运算却根本没有错误。是不是我遇到了一个系统种类的支持问题？
Yes. If you have an older glibc version, please check your Linux distibution for an upgrade that employs glibc version 2.4. This will resolve the problem.是的，如果你有一个较旧的glibc版本，请将你的Linux分布式（指一个系统程序）升级到2.4版本。这样问题将得到解决。

43.How can I monitor the RAM usage of individual RNA World WUs?
我如何监控单个RNA World任务单元的内存（RAM）使用情况？
The most simple way to do this under Windows is to use the task manager (TM). But you need to tweak its settings a bit: start the TM -> choose the tab for 'processes' -> go to the TM menu and click 'view' -> 'select columns' and now check the checkbox of 'Peak Memory Usage'.在windows系统下，最简单的方法是使用任务管理器（TM）但是你需要调整设置：打开TM->选择processes选项->进入TM目录并点击view->选择select columns并且点击Peak Memory Usage。

41问的最后一句caching issue表示鸭梨很大。。求解。。感谢！

feynord

占楼,翻第1,11,25. 计算机相关的部分就交给楼上的兄弟了:)

1. In simple words, what are the goals of RNA World and why should I participate?

RNA World的目标是什么?为什么我要参与呢?

RNA World focuses on RNA research and as such it is the first distributed computing project of its kind. If you take a look for what discoveries the recent Nobel Prizes in chemistry and medicine were awarded (telomerase, ribosome: all RNA-based cell machineries; and before that for RNA interference / miRNAs: small RNAs that regulate cell development and are involved in cancer), you will realize that RNA research is a highly important subject. But maybe you have also once taken antibiotics to help your immune system to battle a bacterial infection. Such antibiotics usually bind to the RNA components of bacterial ribosomes and thereby inactivate protein synthesis and consequently growth of these microbes. Other small RNAs in bacteria are required for attaching to and eventually even invading human host cells. And of course, many aspects of fundamental cellular processes where RNAs are involved are of additional interest to researchers, as e.g. the question whether microorganisms such as bacteria might even possess some sort of primitive immune system (CRISPR RNA family). So as you can see, identifying non-protein-coding RNAs in as many organisms as possible establishes a fundamental basis of knowledge for a diverse range of questions and may even promote the development of drugs to combat diseases. For further information, please see the project description.

RNA World是第一个致力于核糖核酸(RNA)研究的分布式计算项目.从基于RNA结构的细胞器如端粒酶,核糖体,再到能够调控细胞周期,应对癌症的小干扰核糖核酸(siRNA),关于RNA的研究一直是近年来诺贝尔奖的热点.我们平时为了抵御细菌感染而吃的抗生素,通常就是结合在细菌的核糖体RNA上,从而干扰细菌的生长,抑制它们的繁殖;而且,细菌也是依靠一些小RNA来依附和感染人体细胞的.正是因为RNA广泛的参与了许多细胞基础代谢过程,它们也吸引了广泛的研究兴趣,例如:是不是细菌也具有(由CRISPR RNA,即含有规律成簇的间隔短回文重复序列的RNA组成的)某种原始免疫系统呢?于是,在多种有机体内发现和鉴别非编码蛋白质的RNA,能够让我们更多地了解生命的基础,并且促进开发新的药物.如想了解更多的知识,请参见"项目描述".

11.What are potential applications of the RNA World project?
RNA World项目有什么潜在的应用呢?

RNAs like proteins are macromolecules of defined structure that serve vital cellular tasks. Consequently, structural knowledge of RNAs is of similar importance for drug design as is the case for proteins. What you know as antibiotics are actually small molecule drugs that mainly target RNA components of bacterial ribosomes. This illustrates nicely how important RNAs are and what huge potential they represent in the context of drug design. However, before we can take on RNA structures to design drugs, we first need to identify which RNAs are present and where exactly they are located in the genome of any given organism. This we presently try to accomplish in a global manner using the RNA World supercomputer.

核糖核酸(RNA)如蛋白质一样,是拥有精妙结构的大分子,在细胞内起着必不可少的作用.因此,了解RNA的结构就如同了解蛋白质的结构一样,对于药物设计有着重要的作用.也许你已经了解到,抗生素分子通常就是攻击细菌核糖体RNA,因此了解RNA的结构就可以帮助我们设计抗生素.但是,在我们利用RNA结构设计药物之前,我们首先需要了解在目标微生物中有哪些RNA,且都在哪里.这就是我们的目标,是我们需要大规模计算能力的原因.

25.Can I as a scientist submit tasks to RNA World?
我是一名科技工作者,我可以在RNA World上面提交我自己的任务么?

Hopefully soon. We are working on implementing user job submission interfaces for each of the various RNA World applications. However, you will have to register and receive a digital certificate such that jobs submitted to our system are clearly correlated to an individual known to us.

即将推出.我们正在添加用户作业提交界面,让您能够使用RNA World的各种功能.您需要注册并使用收到的数字证书,来确保我们知道每一个任务的来源.

xuyongchen

回复 12# feynord

也好，计算机部分虽然不是特别熟但也还凑合。
那个，请把你准备翻译的编号告诉我一下好么？我就跳过这些部分，避免多余的二次翻译~
谢谢啊！（这就是开双核嘛~）

nekoko

回复 13# xuyongchen

两位大大干脆都完整地翻吧~因为还有一种东西叫做冗余验证[em06]

feynord

回复 13# xuyongchen

我只是对生物的部分比较了解,刚才看了一下,跟生物沾边并且还没翻译的就只有1,11,25了~所以我差不多已经over了...
其他的好像都是软硬件方面的,我觉得你翻译的挺好的,加油[em05]
要是你觉得时间不够的话,也可以列几个编号给我,我尽力翻...