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> RNA World (beta), исследование РНК оргинизмов: от простейших до РНК человека
nikelong
Jan 2 2010, 02:07
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Проект "RNA World (beta)"

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ТОП-20 участников:

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Дата основания команды - 03.01.2010 Капитан - distributed.org.ua
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Для присоединения к команде Украины:
1. Загрузите BOINC менеджер (Если его у Вас еще нет!)
2. Перейдите в "расширенный вид"
3. Выберите сервис ---> добавить проект
4. Введите адрес проекта http://www.rnaworld.de/rnaworld/
5. Введите свои регистрационные данные.
6. Найдите нашу команду. Она называется Ukraine. Нажмите Join чтобы вступить в команду.
7. Если есть доступные для загрузки задания Вы их получите и начнете расчеты.
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Новичкам: статья со скриншотами, как поставить и настроить BOINC-менеджер
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Полезная информация:
Для идентификации пользователя в BOINC могут служить 2 вещи:
1) пара e-mail/пароль
2) межпроектный идентификационный ID (Cross-project ID) - 32значное шестнадцатиричное число.

Если Вы пожелаете подключится ещё и к другому BOINC-проекту, то помните: чтобы не плодить новых аккаунтов при подключении к новому проекту или команде, нужно обязательно везде регистрироваться с одним и тем же Именем и EMAIL. если при регистрации в проекте указать другой e-mail , BOINC создаст новый аккаунт с тем же именем! В этом случае рекомендуется зайти во все ваши аккаунты и во все проекты и где надо поменять емейл на нужный. Через некоторое время ваши аккаунты сольются в один с одним cross-project-id.
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О проекте - общая информация (на английском):
RNA World занимается исследованием РНК разных оргинизмов: от простейших, до РНК человека
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Project description

RNA World is a distributed supercomputer that uses Internet-connected computers to advance RNA research. This system is dedicated to identify, analyze, structurally predict and design RNA molecules on the basis of established bioinformatics software in a high-performance, high-throughput fashion.

In contrast to classical bioinformatic approaches, RNA World does not rely on individual desktop computers, web servers or supercomputers. Instead, it represents a continuously evolving cluster of world-wide distributed machines of any type. As such, RNA World is very heterogenous and, depending on the sub-project, currently addresses Internet-connected computers running Linux, Windows and OSX operating systems - your computer could be an important part of it. The fact that hardware and electricity costs are shared among the volunteer contributors raises the possibility of performing interesting analyses which under economical aspects would often not be affordable. In return, RNA World is not for profit, exclusively uses open source code and will make its results available to the public.

In its present form, RNA World runs a fully automated high-throughput analysis software version of Infernal1, a program suite originally developed in Sean Eddys laboratory for the systematic identification of non-coding RNAs. The goal of this RNA World sub-project is to systematically identify all known RNA family members in all organisms known to date and make the results available to the public in a timely fashion. With your help, we also aim at supplying established bioinformatic databases such as Rfam2 with our results to help reduce their future maintenance costs.

In contrast to other distributed and grid computing projects, the RNA World developers are currently designing generalized user interfaces that, in parallel to the projects our own research team is following up, allow non-associated individual scientists to submit their own projects in a manner similar to using a web server interface - of course, free of cost.

RNA World is developed by the German non-profit association Rechenkraft.net e.V. and is solely operated by volunteers. At present, it is in closed alpha phase. Cooperation partners are the Philipps-University of Marburg (Germany) and the Indian Institute of Science in Bangalore (India); further cooperation partners are welcome. Scientists having suggestions for specific RNA relevant software that is worth considering integration into the RNA World distributed supercomputer are welcome to contact us with a brief proposal.

Why RNA?

Every protein in a cell is produced from a transiently synthesized messenger molecule, termed mRNA. This mRNA is then recognized by a cellular machinery that translates the base sequence of mRNA into its corresponding protein (which is a sequence of amino acids). This protein synthesis machinery, termed ribosome, is actually a ribozyme, i.e. it is a catalytically active assembly of several RNA molecules. Consequently, RNAs do not only serve as messenger molecules or perform structural functions as e.g. in tRNA but may also act as catalysts that perform biochemical reactions as is the case for protein enzymes. Of course, the ribosome also contains numerous proteins as it is a very complex ribonucleoprotein particle but these predominantly serve structural functions, e.g. to give the ribosome its shape.

Fascinatingly, the initial analysis of the human genome sequence revealed that, apparently, only a very small fraction of the DNA of our genome is encoding proteins. Scientists at first thought "what is all this junk DNA about?" or "can't we just delete it?". Today, it has become clear that probably a major fraction of regulatory events taking place in a human cell might be governed by small RNAs, the so-called miRNAs. Among other functions, these appear responsible for making sure that a skin cell becomes a skin cell while a muscle, liver or hair cell differentiates to a muscle, liver or hair cell during development and all this although the genetic material (DNA) of all of these very different cell types is essentially identical. On top of that it seems that many cancer types are accompanied by or even result from a deregulated miRNA profile in the affected cell. Moreover, viruses have been discovered to bring along miRNAs to modify the target cell's regulatory network leading to diseases.

Hence, we can clearly state that investing into RNA research, e.g. by supporting the RNA World distributed supercomputer project, will ultimately lead to important discoveries that might also have significant impact on future health care.


Подпроекты: (ссылка на официальную страницу)

Project: CRISPR

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The CRISPR elements are part of a prokaryotic defence system directed against external attacks by e.g. viruses and may be viewed as a simple immune system of microorganisms.

By employing RNA World to systematically screen organisms for the presence of the various types of this defence machinery, we hope to acquire important information on the global distribution and varieties of this system. There is an enormous repertoire of potential applications to the results of such analyses ranging from the improvement of industrially relevant microbial food production to novel ways of coping with multi-drug resistant pathogenic bacteria.


Project: GEMM

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The GEMM RNA motif is a so-called cis-acting riboswitch designed to detect the second messenger cyclic di-GMP. The bottom line is that GEMM is an upstream terminal part of an mRNA that can bind to this small signal molecule. Upon binding, its structure is modulated such that the downstream part of the mRNA which encodes a protein is affected in such a way that, depending on the type of GEMM motif, the corresponding protein production is either activated or inactivated. Hence, GEMM serves as an RNA-based molecular switch to control protein production.

The reason for why we are interested in this RNA module is twofold: (1) its switch properties make it very useful for synthetic biology applications and (2) GEMM controls production of proteins that are essential for the capability of certain pathogens to attack human cells. Examples for such pathogens are the cholera-causing bacterium Vibrio cholerae or Bacillus anthracis which is responsible for anthrax. What RNA World does is a systematical screen of all completely sequenced organisms in order to identify this GEMM motif.


Project: 6S

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6S RNA is a small non-coding RNA of about 200 nucleotides in size which is widespread among bacteria and occasionally even occours in multiple gene copies within a given species. It appears to represent a system to preserve RNA polymerase under conditions of nutrient limitation. Interestingly, due to its special structure, this RNA may serve as a template for bacterial house-keeping RNA polymerase to generate small miRNA-sized RNAs upon nutrient re-supply, thereby demonstrating that RNA polymerases can act as both DNA-dependent RNA polymerases and RNA-dependent RNA polymerases.

In this project we attempt to chart the presence of this regulatory system in all completely sequenced organisms.


Project: Thermo

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All organisms examined so far to this respect respond to a sudden decrease in ambient temperature by inducing a specialized genetic program termed the cold shock response (CSR). This cellular stress response is designed to cope with a broad variety of temperature-dependent modulations of molecular structures, transport processes, chemical reactivities, and many more.

The goal of this project is to systematically identify non-coding RNAs (ncRNAs) involved in thermoregulation in all organisms whose genomes have been completely sequenced.


Project: Mtb, Myctu, Mycle & Myc - изучает РНК туберкулезных палочек

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Mycobacterium tuberculosis is the the causative agent of tuberculosis (TB) which is a world-wide pandemic that is contagious and spreads through the air. Scaringly, more than two billion people, equal to one third of the world’s total population, are infected with TB bacilli. Even worse, multidrug-resistant TB (MDR-TB) is a form of TB that does not respond to the standard treatments using first-line drugs and is present in virtually all countries surveyed by WHO and its partners. Strikingly, a total of 1.77 million people died from TB in 2007, equal to about 4800 deaths a day which makes TB one of the world's major causes of death.

Since it is known that certain non-coding RNAs (ncRNAs) are required to control the ability of many pathogens to infect their hosts, in this project we undertake an exhaustive search to map all ncRNAs known to date in this organism. Moreover, including the leprosy-causing agent Mycobacterium leprae, we extend our bioinformatic analyses to all fully sequenced strains of the genus Mycobacterium and also compare pathogenic versus non-pathogenic strains to possibly identify ncRNA-based differences that might be involved in virulence processes. To validate the biological and medical relevance of our computational investigations, laboratory experiments are performed in cooperation with our research partners in India. It is clear that the potentially possible identification of a ncRNA which is essential for pathogenicity of this organism may represent an excellent novel drug target to battle TB in the future.


Project: sRib

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Ribozymes are non-coding RNA molecules that, like protein enzymes, catalyze chemical reactions. Examples are the hammerhead ribozyme, the HDV ribozyme, the hairpin ribozyme and many more.

In this project we are screening the kingdom of life for the presence of ribozymes. We also include artificially designed ribozymes in order to find out whether natural analogs exist.


Project: tRNA & tRNA-like

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tRNAs are essential components of the cellular protein production machinery but also serve a number of additional functions as e.g. regulating gene expression in conjunction with the T-box element or are utilized as primers for reverse transcription of the HIV genome, a process essential for viral integration into the host genome. Moreover, tRNAs are also required for building the bacterial cell wall and occur in certain lipids making them an extremely versatile molecule family. Interestingly, a number of tRNA-like sequences have been identified in plant virus genomes and appear to be linked to the regulation of viral replication.

In this project, we aim at compiling a complete survey on the occurrence of tRNAs and tRNA-like sequences hoping to identify even more variety in this fundamental molecule class.


Project: T-box

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The T-box leader is part of the 5' end of a number of mRNAs and represents an RNA element that serves a regulatory function in controlling protein production by interacting with non-charged tRNAs.

In this project, the RNA World supercomputer is utilized to identify T-box elements throughout the kingdom of life.


Project: GA

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Whenever a new genome sequence is published, its sequence of letters (i.e. the bases of the DNA molecules it contains) is annotated computationally. During this process, all regions are being identified that, based on the standard genetic code and a number of well-known rules, code for proteins. Besides ribosome-related RNAs such as rRNAs and tRNAs and a number of universally occurring non-coding RNAs, the majority of ncRNAs usually escape detection. In this project, we focus on exclusively filling in the gaps resulting from current protein-focused genome annotation procedures by systematically identifying ncRNAs and by adding our results to those generated by the standard methods.


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Ссылки по теме:
  • http://www.rechenkraft.net/wiki/index.php?title=RNA_World/en
График ППД команды "Ukraine"
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Це повідомлення відредагував nikelong: Sep 18 2010, 20:35
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Rilian
Mar 7 2010, 01:59
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Оптимизировали сервер и приоритеты подпроектов

QUOTE
2010-02-21: We have tweaked a bit server-side on the application priorities such that CMC WUs will go out preferentially compared to CMS WUs. This should help to avoid displacing CMC WUs that are already in progress by CMS WUs which have much shorter deadlines. Moreover, it should help those of you running many machines that differ in OS to make sure all systems are being served without having to disable the one or the other application manually anymore (as e.g. CMS on Linux x64). Additionally, it should reduce the need for setting up complex profiles for individual machines. Please note that CMC WU completion always is of major importance to us since this process represents the bottle neck for all of our current downstream analyses. Also, due to the floods of rather short WUs our server is having a hard time on the MySQL side. In response to this, we have altered the scheme by which work is fed into the RNA World system such that in the future the run time distribution can be controlled much better. At present, the server has some sort of a protection setting that simply reduces the server responsiveness if too many clients ask for communication in a very short period of time. At your end it might therefore look as if no work was there or as if the server is down. But be assured, both should not be the case, so just keep on crunching. koc.gif
Michael.


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Rilian
Mar 8 2010, 22:54
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Варнинг, ВЮ идут реально жирные, в требованиях от 950МБ памяти на ВЮ, но они могут сами увеличиваться до 2.8 Гиг (и это все на 1 ядро!)

замечено на заданиях с типами horse (лошадки), human (хумансы) и cattle (крупный рогатый скот)


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Rilian
Mar 9 2010, 15:29
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3/9/2010 3:26:13 PM RNA World Message from server: No work sent
3/9/2010 3:26:13 PM RNA World Message from server: cmsearch needs 1907.35 MB RAM but only 511.48 MB is available for use.
3/9/2010 3:26:13 PM RNA World Message from server: cmcalibrate is not available for your type of computer.



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Rilian
Mar 10 2010, 01:11
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В RNA World щяс идет пачка очень требовательных к памяти заданий проекта CMSearch, причем в них нету чекпоинтов (сохраняться нельзя). Замечены экземпляры до 7ГБ!

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Проблема с памятью известна, админы занимаются, дальнейшее тестирование в данный момент пока не нужно, поэтому рекомендую временно отключить проект на машинах с памятью меньше 4ГБ во избежание потери очков. На машинах с 2ГБ ВЮ вылетают довольно часто


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Rilian
Mar 10 2010, 03:22
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QUOTE(Rilian @ Mar 10 2010, 01:11) *

В RNA World щяс идет пачка очень требовательных к памяти заданий проекта CMSearch, причем в них нету чекпоинтов (сохраняться нельзя). Замечены экземпляры до 7ГБ!

Собственно, на сервере уже предприняты меры по недопущению машин с малым кол-вом памяти к рассчетам.

QUOTE
3/10/2010 2:50:40 AM RNA World Message from server: No work sent
3/10/2010 2:50:40 AM RNA World Message from server: cmsearch needs 953.67 MB RAM but only 511.48 MB is available for use.
3/10/2010 2:50:40 AM RNA World Message from server: cmsearch needs 1907.35 MB RAM but only 511.48 MB is available for use.
3/10/2010 2:50:40 AM RNA World Message from server: cmcalibrate is not available for your type of computer.


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Rilian
Mar 10 2010, 13:07
Пост #36


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Координатор проекта рассказывает о себе, о проекте, о том как устроена их работа итд. Довольно интересно

Just a few things for clarification (I always try to take comments serious although, sadly, sometimes people make it really very hard by the style they do communicate). RNA World is a bioinformatics project, so we do not need a lab at all. A few computers and a good webserver is sufficient. Still, as you can see from our cooperation partner list, we do clearly have the capabilities of performing lab experiments to validate our computational results. In fact, I work in an RNA lab every day with more than 10 years of practical experience in a diverse set of scientific fields. And yes, we do outsource server hosting to professionals while we keep server administration in house. This, to our experience, is the best and most economic way to do it. And we do indeed have at least some experience since we operate in DC for more than 10 years now. First we "only" participated in DC projects. Then we started the Yoyo@home project to help scientists not too firm with BOINC to acquire more volunteer support for their projects. We achieved that by wrapping a set of clients of non-BOINC projects we liked into the BOINC infrastructure and, apart from your crediting concerns, I think we did a nice job (and Yoyo is the driving force here). This scenario allowed us to gain a lot of practical experience over many years in this "business" (yeah, I hate that word in this context); also in terms of user requirements and support. And now, we are implementing our own scientific project in which we use established software plus own software developments to put into practice our own research ideas. You can say that we have evolved from a DC community to DC project developers. So, what is bad about that?

Finally, concerning myself (since you addressed this issue), maybe you have overlooked that I am not a Ph.D. student; I am holding a doc degree in natural sciences (Dr. rer. nat., chemistry) for quite some time now and I am the principal investigator at Rechenkraft.net you were seemingly looking for (and yes, I do not get paid for doing that like nobody at Rechenkraft.net gets paid for anything; it is just our spare-time interest but that has lasted in a sustained manner over a decade). That said, I would like to say that - as we witness in DC every day - volunteers can contribute significant efforts towards achieving meaningful scientific results. Hence, I do not give much on degrees (although from your writing it appeared to me that it seems important to you). Rather, a nice style of cooperative working together is what I have in mind where everybody can input small ideas. That, taken together, will ultimately give a nice overall picture. I believe, DC is not at all about competition as always claimed. If you look a bit beyond competition in terms of who has the fastest machine, you will find that a bigger goal is achieved COOPERATIVELY. And that, to date, to my opinion, is the most powerful principle in nature - not competition. But maybe let us better keep that aside for now. So to say as a philosophical side remark...

Michael.

пост: http://www.free-dc.org/forum/showpost.php?...34&postcount=38
весь топик: http://www.free-dc.org/forum/showthread.php?p=142234


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Rilian
Mar 12 2010, 11:57
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QUOTE
I think we found a solution for the RAM issue. But this might take some time to implement.

Michael.


QUOTE
Я думаю мы нашли решение проблемы с нехваткой оперативной памяти при рассчетах. Но это займет некоторое время, чтобы реализовать

Миша


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Rilian
Mar 12 2010, 19:40
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SlavaAltus
Mar 13 2010, 11:12
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Водку на работе пить не дают!, дома не дают драть обои... чё за фигня ваще((.. ?!




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Rilian
Mar 14 2010, 20:10
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3/14/2010 7:57:47 PM RNA World Message from server: cmsearch needs 3814.70 MB RAM but only 511.48 MB is available for use.

swoon.gif huh1.gif

геномы у млекопитающих беспощадны к оперативке sarcastic.gif


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tiss
Mar 14 2010, 20:41
Пост #41


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(Rilian @ Mar 14 2010, 20:10) *

3/14/2010 7:57:47 PM RNA World Message from server: cmsearch needs 3814.70 MB RAM but only 511.48 MB is available for use.

swoon.gif huh1.gif

геномы у млекопитающих беспощадны к оперативке sarcastic.gif


ппц. они там не охренели??? fool.gif


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Rilian
Mar 14 2010, 20:51
Пост #42


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tiss, если на компе есть свободная оперативка, то почему бы и нет? если нет оперативки - не считайте

если данные такие большие, и задача не распараллеливается (на данный момент), то что делать?


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tiss
Mar 14 2010, 21:13
Пост #43


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(Rilian @ Mar 14 2010, 20:51) *

tiss, если на компе есть свободная оперативка, то почему бы и нет? если нет оперативки - не считайте

если данные такие большие, и задача не распараллеливается (на данный момент), то что делать?


Память есть. Но если запущу, то тогда не смогу в даймсе отжигать.


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Rilian
Mar 14 2010, 21:18
Пост #44


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Ну, я говорю в общем случае (если память есть, бла бла ...)

RNA находится в стадии beta-тестирования, поэтому особой срочности в ресурсах нет


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Rilian
Mar 17 2010, 03:28
Пост #45


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QUOTE
We have a solution in place, which will be active for the next wu batch which is generated when the number of unsent wus goes below 1000.
But I think this will be only the first step in tweaking and tuning the RAM stuff.
yoyo
link.gif


через несколько дней, когда кол-во неотправленных ВЮ снизится до 1000 (сейчас их - 2500), админы RNA обновят сервер и приложения чтобы временно исправить проблемы с очень большой прожорливостью ВЮ (по отношению к памяти) thumbsup.gif

Пока что, если у вас есть 3ГБ памяти на ядро, ваши компы могут помочь ускорить наступление этого счастливого момента для обычных кранчеров shuffle.gif


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