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[已转移到维基条目] 【WCG】新项目Uncovering Genome Mysteries 揭开微生物基因组之谜

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发表于 2014-10-18 11:23:07 | 显示全部楼层 |阅读模式
本帖最后由 超哥不郁闷 于 2014-10-18 16:33 编辑

这周WCG上有了新的项目,是时候更新咱们的WIKI条目了~
这次我就一口气做好维基条目算了,不想拖太长时间,有问题的话日后再修改。
这次我就以该项目的第一则新闻作为素材好了,因为个人觉得这个讲的通俗一些,普通人比较好接受,翻译起来也没有太大难度~



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参与人数 3基本分 +90 维基拼图 +10 收起 理由
昂宿星团人 + 10 我好惭愧。。
swh@home + 60 很给力!
CCCP0081 + 30 赞一个!

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 楼主| 发表于 2014-10-18 11:26:35 | 显示全部楼层
本帖最后由 超哥不郁闷 于 2014-10-22 23:35 编辑

新闻链接:https://secure.worldcommunitygri ... le.do?articleId=385

From the realization that the Penicillium fungus kills germs, to the discovery of bacteria that eat oil spills and the identification of aspirin in the willow tree bark - a better understanding of the natural world has resulted in many improvements to human health, welfare, agriculture and industry.                                                                                                                                           从认识到青霉素能够杀灭病菌,到吸油细菌的发现以及从柳树树皮里提取阿司匹林——对自然界更深的理解为人类的健康、福利、农业和工业带来了许多进步。

Diver collecting microbial samples from Australian seaweeds for Uncovering Genome Mysteries

Diver collecting microbial samples from Australian seaweeds for Uncovering Genome Mysteries
                                                                                                                              
Diver collecting microbial samples from Australian seaweeds for Uncovering Genome Mysteries
潜水员正在为Uncovering Genome Mysteries 采集来自澳洲海藻的微生物样本
                                 
Our understanding of life on earth has grown enormously since the advent of genetic research. But the vast majority of life on this planet remains unstudied or unknown, because it's microscopic, easy to overlook, and hard to study. Nevertheless, we know that tiny, diverse organisms are continually evolving in order to survive and thrive in the most extreme conditions. The study of these organisms can provide valuable insights on how to deal with some of the most pressing problems that human society faces, such as drug-resistant pathogens, pollution, and energy shortages.
我们对于地球上生命的认识因为基因研究而突飞猛进。但这颗行星上的绝大多数生命仍然未被研究或发现,因为它们及其微小,容易被忽视,并且难以研究。然而,我们知道那些细小但多种多样的微生物在不断进化着,以在最为极端的环境下生存并繁荣下去。研究这些微生物能为人类社会面临的一些最为迫切的问题提供有价值的解决方案,例如抗药性病毒、污染以及能源的储存。

Inexpensive, rapid DNA sequencing technologies have enabled scientists to decode the genes of many organisms that previously received little attention, or were entirely unknown to science. However, making sense of all that genomic information is an enormous task. The first step is to compare unstudied genes to others that are already better understood. Similarities between genes point to similarities in function, and by making a large number of these comparisons, scientists can begin to sort out what each organism is and what it can do.

好在快速的DNA测序技术能让科学家去解析很多微生物的基因组,而这些微生物之前很少受到关注或从未被科学界所认识。但是,理解所有这些遗传信息是一项艰巨的任务。任务的第一步便是将未被研究过的基因与那些已经被研究得较为透彻的基因进行比对。基因的相似性与功能的相似性是相对应的,通过进行大量的比对,科学家能够弄清楚每一种微生物的真面目以及它们能完成的事情。

In Uncovering Genome Mysteries, World Community Grid volunteers will run approximately 20 quadrillion comparisons to identify similarities between genes in a wide variety of organisms, including microorganisms found on seaweeds from Australian coastlines and in the Amazon River. This database of similarities will help researchers understand the diversity and capabilities that are hidden in the world all around us. For more on the project's aims and methods, see here.                                                                                 
通过Uncovering Genome Mysteries,世界公共网格的志愿者们要运行大约2亿亿次比对,以发现各种微生物之间的相似性,其中包括来自澳大利亚沿海的海藻和亚马逊河的微生物。这个相似性的数据库能够帮助研究人员理解隐藏在周围世界中的多样性和潜在能力。想要进一步了解该项目的目的和方法请参见这里

The specific goals of the Uncovering Genome Mysteries project are:

  • To create a database of protein sequence comparison information, based on the DNA found from diverse sources, for all scientists to reference.
  • To discover new gene functions, augmenting our knowledge about biochemical processes in general.
  • To find how organisms interact with each other and environment.
  • To document the current baseline microbial diversity, allowing us to understand how microorganisms change under environmental stresses, such as climate change.
  • To better understand and model complex microbial systems.

以下是Uncovering Genome Mysteries的目标:

1.创建一个蛋白质序列比对信息的数据库供所有科学家查询,其基于从多种渠道获得的微生物DNA。                                                   
2.发现新的基因功能,扩充我们对于生化过程的知识。
3.弄清楚微生物如何与同类和环境进行互动。
4.增进我们对于微生物多样性的认识,让我们理解微生物是如何适应环境变化的,比如气候变化。
5.对复杂的微生物系统进行更好地理解和建模。

In addition, a better understanding of these organisms will likely be useful in developing new medicines, harnessing new sources of renewable energy, improving nutrition, cleaning the environment, creating green industrial processes and many other advances.

此外,对这些微生物更好地理解将可能对“新型药物的研发”、“新型可再生能源的利用”、“食物营养的提升”、“环境的清洁”、“创建绿色的工业过程”以及其他很多领域有所帮助。

The timing of this project launch is a perfect way to kick off celebrations of another important achievement - World Community Grid's 10th anniversary. There's much to celebrate and reflect upon from the past decade's work, but it's equally important to continue pushing forward and making new scientific discoveries. With your help - and the help of your colleagues and friends - we can continue to expand our global network of volunteers and achieve another 10 years of success. Here's to another decade of discovery!

该项目的及时发起是庆祝另一重要事件的完美方式——WCG十周年纪念。纵然在这十年的工作中有太多的东西要去庆祝和回忆,但是继续推进新的科学研究同样重要。凭借您、您的同事以及朋友的帮助,我们将能够继续扩大WCG的规模并取得下一个十年的成功。这是下一个充满发现的十年!






















点评

辛苦啦~~: 5.0
辛苦啦~~: 5
辛苦了~刷墙党上!  发表于 2014-10-18 14:16

评分

参与人数 1基本分 +10 收起 理由
litimetal + 10 辛苦了!

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 楼主| 发表于 2014-10-18 14:51:19 | 显示全部楼层
本帖最后由 超哥不郁闷 于 2014-10-18 14:55 编辑

可能有很多人会问该项目与即将离开BOINC平台的SIMAP有何区别,因为我们知道SIMAP专门比较蛋白质的相似性(也是通过比对蛋白质序列,也要建立数据库),两个项目的研究方法很类似,估计算法方面也很类似。官方论坛上也有人在问同样的问题,但我们要明确的是该项目是专门进行微生物研究的,而且所研究的东西是从未研究过的:"To kick off World Community Grid's 10th anniversary celebrations, we're launching Uncovering Genome Mysteries to compare hundreds of millions of genes from many organisms that have never been studied before, helping scientists unearth some of the hidden superpowers of the natural. "
 楼主| 发表于 2014-10-18 15:52:02 | 显示全部楼层
 楼主| 发表于 2014-10-18 15:52:55 | 显示全部楼层

点评

很给力!: 5.0 辛苦啦~~: 5.0
很给力!: 5 辛苦啦~~: 5
赞!快去找女朋友!  发表于 2014-10-25 21:30
发表于 2014-10-19 14:29:32 | 显示全部楼层
本帖最后由 acp134 于 2014-10-19 16:01 编辑

嗯……要不要把WCG上面的项目简介翻译一下,挺长的
 楼主| 发表于 2014-10-19 17:37:11 来自手机 | 显示全部楼层
acp134 发表于 2014-10-19 14:29
嗯……要不要把WCG上面的项目简介翻译一下,挺长的

项目简介里的内容跟这个差不多,没有什么新东西。要进一步翻译的话,只有选项目的详细介绍。那个我还没有仔细看。
发表于 2014-10-19 19:17:14 | 显示全部楼层
超哥不郁闷 发表于 2014-10-19 17:37
项目简介里的内容跟这个差不多,没有什么新东西。要进一步翻译的话,只有选项目的详细介绍。那个我还没有 ...

我说的是这个,有时间我来做两段……大学比想象中的要忙……随便写个C程序我就要调试半天提交到评判系统还是错的……
About the Project   



The Problem

It often seems as though humankind is in a state of conflict with the natural world. Pathogens are evolving resistance to many of today's important antibiotics. We are consuming many of Earth's valuable resources at an unsustainable rate, while pollution in the air and water threatens the health and livelihoods of many communities.

Fortunately, we are beginning to understand that nature may have already developed solutions to many of these problems, and they are hidden in plain sight: in forests, oceans and soils. For example, studies of exotic soil samples and plant extracts have revealed substances with the ability to kill particular kinds of disease-causing bacteria. We have found exotic tropical plants that show promise as efficient, sustainable fuel sources. Microorganisms have been used to clean water in sewage treatment plants and even help consume oil spills. Most of these discoveries were uncovered through time-consuming trial and error. If we could better understand the amazing range of natural powers, we might be able to speed up development of practical technologies and solutions.


One approach to identifying nature's hidden "superpowers" is to analyze the genetic makeup of different organisms to help us understand how they function. Traditionally, this has been a very expensive and time-consuming process, but in recent years scientists have developed more affordable and effective methods to decode DNA. The result is an explosion of genomic data from animals, plants and particularly microorganisms. After DNA has been decoded, scientists must conduct further studies to discover the function of each gene and its corresponding protein. Each gene specifies the sequence of amino acids to assemble into a molecular chain which is then folded into a protein molecule. This is also known as the protein sequence.

Genes and their corresponding proteins play important roles in many life processes, and as a result, are often valuable in medicine and industrial applications. Some proteins are chemical factories, called enzymes, which can break down molecules into simpler components or help construct more complex molecules. Other proteins form the building blocks of all kinds of structures in plants and animals. Still other proteins play roles in controlling all kinds of activity in cells in response to various stimuli.

It is clear that there is a wealth of useful knowledge to be found by understanding what unknown genes and their corresponding proteins do. This knowledge might even help scientists solve many of the world's most pressing problems. However, there are two important challenges to this effort:




First, we are rapidly losing many valuable potential sources of DNA from diverse life forms. This is because many acres of unexplored pristine forests and water habitats are disappearing due to human development, climate change and other factors. We are losing the rich resources in nature that harbor valuable, yet hidden, solutions to the world's problems. We need more efficient and effective ways to discover what nature still has to tell us before it is too late.

And secondly, if we want to search for useful genes in unknown organisms, the scale of the task is staggering. Each organism may have thousands of genes, and there can be tens of thousands of organisms in even a small sample of water or soil. If we want to unlock nature's hidden powers, we need new methods to deal with the "big data" from the hundreds of millions of genes that are being decoded.



The Proposed Solution and Justification

Uncovering Genome Mysteries expects to examine close to 200 million genes from a wide variety of life forms, such as seaweeds from Australian coastlines and microbes found in Amazon river samples. Those genes are being compared against each other to assess their similarity. When two genes are similar, and the function of one gene is already known, this allows scientists to make educated guesses about the function of the other gene. This represents about 20 quadrillion (2x1016) comparisons. The total computation time is projected to take the equivalent of one computer running continuously for 40,000 years--no small feat, but feasible thanks to the computational power of World Community Grid. While DNA sequences from all forms of life will be processed, microorganisms will receive a special focus.






                What are microorganisms and why study them?        












Modern DNA sequencing technologies can now rapidly determine millions of DNA sequences at reasonable costs. New technological breakthroughs are being developed to augment this capacity by several orders of magnitude. This will allow scientists to determine all DNA sequences hidden in the unseen microbial world. They have already been doing this for many medical and industrially important unicellular and multicellular organisms, animals, plants and human individuals over the last few years. Since the 1990s, genome analyses have concentrated on studying three kinds of organisms: "model organisms" in biology, because they had been studied for decades in laboratories (such as E. coli, yeast, helminthes and mice); important human, animal and plant pathogens (like the bacteria that cause tuberculosis and leprosy, or crop pathogens); and finally, representative organisms in the "Tree of Life". In more recent decades, many scientists around the world have started sequencing and analyzing metagenome data from many additional biomes, enriching our knowledge about biodiversity in air, land and sea, from the arctic to tropical forests. From this work, a very complex picture of the diversity of living organisms on our planet is emerging.

The daunting task of interpreting this now huge and exponentially growing amount of DNA sequence data ("big data") is not trivial. DNA sequence information is only meaningful and useful if it can be decoded and interpreted by comparing it to other gene sequences of known or unknown function, a process called "genome annotation," while mapping variations. This decoding and annotation process requires vast amounts of computational power, and is currently a major bottleneck in making sense of genomes that have already been sequenced.

The Uncovering Genome Mysteries project aims to harness the computational power of World Community Grid to give biological meaning to gene-sequencing data available for microorganisms and other life forms. This will be done on the level of comparison between individual microbial genomes as well as on the level of the genetic information of entire microbial communities for the environment (metagenomes). Decoding genomes and metagenomes will provide new information on the functional role and diversity that microorganisms play in the environment. Comparison of this information with known functional data from other organisms already studied in greater detail will be crucial for the interpretation and annotation of the DNA codes.




Project Goals

The specific goals of the Uncovering Genome Mysteries project are:


•To create a database of protein sequence comparison information, based on the DNA found from diverse sources, for all scientists to reference.
•To discover new gene functions, augmenting our knowledge about biochemical processes in general.
•To find how organisms interact with each other and environment.
•To document the current baseline microbial diversity, allowing us to understand how microorganisms change under environmental stresses, such as climate change.
•To better understand and model complex microbial systems.

While the immediate computational results of this project are only an early step in achieving the above goals, they will be ultimately useful in many ways. For example, the resulting knowledge should help identify, design and produce new antibiotics and drugs against chronic diseases, as well as new enzymes for industrial applications, such as food processing, chemical synthesis or the production of green plastics or biofuels. In the long-term this knowledge should help us manage the diverse organisms' important functions in the world's ecosystem, in all environments, in industrial settings, and in human, animal and plant interactions.
 楼主| 发表于 2014-10-19 21:28:25 来自手机 | 显示全部楼层
acp134 发表于 2014-10-19 19:17
我说的是这个,有时间我来做两段……大学比想象中的要忙……随便写个C程序我就要调试半天提交到评判系统 ...

这里面就涉及到比较专业的东西了,不急,有时间就翻译一点,我最近也有些事情,周末有空的时候也来翻译翻译。
 楼主| 发表于 2014-10-19 21:31:28 来自手机 | 显示全部楼层
acp134 发表于 2014-10-19 19:17
我说的是这个,有时间我来做两段……大学比想象中的要忙……随便写个C程序我就要调试半天提交到评判系统 ...

我已经翻译的那部分中的“项目目标”就是取自这个详细介绍里的,也就是用这个替换了新闻里的对应部分,因为这个概括的全一点。
发表于 2014-10-19 21:36:46 | 显示全部楼层
超哥不郁闷 发表于 2014-10-19 21:28
这里面就涉及到比较专业的东西了,不急,有时间就翻译一点,我最近也有些事情,周末有空的时候也来翻译翻 ...

我是希望我们有时间把这个搞定,大概看了一下,这个部分还是很吸引人的。
应该不着急,毕竟这个项目刚上线,还有大把时间翻译。
 楼主| 发表于 2014-10-19 21:41:07 来自手机 | 显示全部楼层
acp134 发表于 2014-10-19 21:36
我是希望我们有时间把这个搞定,大概看了一下,这个部分还是很吸引人的。
应该不着急,毕竟这个项目刚上 ...

嗯~上官网看了下,该项目的累计计算时间已快达到100年。。。。https://secure.worldcommunitygrid.org/stat/viewProject.do?projectShortName=ugm1
发表于 2014-10-22 23:17:19 | 显示全部楼层
通读了一遍译文,除了第一段的“食用石油的细菌”可能需要在仔细斟酌一番外,余下部分都感觉十分流畅。
没有细看翻译方面的问题,如果接下来碧大与acp同学没什么意见的话,超哥就自己改一下帖子分类吧~

点评

很给力!: 5.0 辛苦啦~~: 5.0
精辟!: 5.0
没意见 ^_^  发表于 2014-10-25 21:29
很给力!: 5 辛苦啦~~: 5 精辟!: 5
  发表于 2014-10-22 23:34
 楼主| 发表于 2014-10-22 23:28:22 | 显示全部楼层
昂宿星团人 发表于 2014-10-22 23:17
通读了一遍译文,除了第一段的“食用石油的细菌”可能需要在仔细斟酌一番外,余下部分都感觉十分流畅。[em0 ...

OK~
 楼主| 发表于 2014-10-22 23:33:51 | 显示全部楼层
昂宿星团人 发表于 2014-10-22 23:17
通读了一遍译文,除了第一段的“食用石油的细菌”可能需要在仔细斟酌一番外,余下部分都感觉十分流畅。[em0 ...

查了一下,那个学名叫“吸油细菌”。

评分

参与人数 1维基拼图 +3 收起 理由
昂宿星团人 + 3 嘿,这么翻译清爽多了

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