Українська команда з розподілених обчислень

Настраивай касперский (или у тебя другой антивирь ) Поставь их в довереные. Вчера тоже с протеомой парился.

при запуске БОИНКа в первых строчках Messages есть этот путь

Типа так

09/27/10 10:06:53 Starting BOINC client version 6.10.45 for windows_x86_64
09/27/10 10:06:53 Config: report completed tasks immediately
09/27/10 10:06:53 log flags: file_xfer, sched_ops, task
09/27/10 10:06:53 Libraries: libcurl/7.19.7 OpenSSL/0.9.8l zlib/1.2.3
09/27/10 10:06:53 Running as a daemon
09/27/10 10:06:53 Data directory: C:\ProgramData\BOINC
09/27/10 10:06:53 Running under account boinc_master
09/27/10 10:06:54 Processor: 4 GenuineIntel Intel® Core™ i5 CPU 650 @ 3.20GHz [Family 6 Model 37 Stepping 2]
09/27/10 10:06:54 Processor: 256.00 KB cache

Видимо пункт про антивирусы надо вписать в нашу стандартную "шапку" подключения к BOINC-проектам

Да вчера уже разобрался. Оказывается у протеомы исполняемый файл называется по хитрому я и не подумал вначале, что это он. Уже заработало

Да, вообще-то в WCG в исполняемых файлах на windows нету букв .exe. Надо тоже это в шапку прописать..

Это да. Но в других проектах хоть названия такие же токо сокращенно. А по протеоме в каспере был файлик, точно не помню уже типа Client....(тут не помню)... и вспоминания про институт Парижа (или Нью Йорка )и еще чото (длинное название), вобще думал это рекламка какаето. Оказалось именно оно .

Это чо в протеоме каждое задание считается по 15 раз Раньше разве тоже так было?

corsar83, всегда так было. задания немного разные, на самом деле. подробнее на англ в официальном форуме..

пользуюсь авастом, ставил в доверенные - один хрен. Помогло удаление-добавление проекта.
ЗЫ: начались траблы с этим проектом после переустановки виндовса, до этого считалось нормально.

что весьма кстати, если в офисе существует запрет на скачку исполняемых файлов и лень (а если правильно, то по соображениям безопасности не хочется) его отключать

Пресс релиз за Октябрь 2010

http://homepages.nyu.edu/~rb133/wcg/thread_2010_10_10.html

Долгожданный апдейт!

http://homepages.nyu.edu/~rb133/wcg/thread_2011_01_31.html

HPF2 Update - January 2011

Greetings WCG Community,

Happy new year! I have taken it upon myself to write a quick status update regarding the Human Proteome Folding project, in part to introduce myself and also to summarize a few of the tasks that lie ahead for us.

As of early January, the Bonneau lab team working on the HPF project has undergone a slight change of staff. Patrick Winters, from whom you have heard in previous updates, has moved on to other pastures, and I have taken his place. My name is Duncan Penfold-Brown, and I am coming out of a previous research position in the application of high-powered computing (both Grid and Cloud) to high-energy physics and astronomy. I have a degree in computer science, and have in the past focused on distributed and self-organizing systems. I also have experience (and a great deal of interest) in bioinformatics, which I look forward to increasing in my work on this project.

In short, I will be responsible for support and development of HPF projects and research. I am interested in pursuing a greater knowledge of proteomics - which seems to me like biological puzzle solving - and also the applications (medical, investigative) of the research we are completing together.

The immediate tasks we are approaching are to work on improving our pre- and post-analysis tools, in order to get more data to the Grid, and to better interpret what comes out. Goals for the immediate future include continuing the incorporation of phylogenetic data and evolutionary analysis of protein domains into our analysis process in order to enhance our annotation of select unknown proteins. This incorporation will provide us with a better understanding of the function of unknown proteins, as we can more accurately identify evolutionarily similar structures and cross-examine their structure-function relationships. With additions to our analysis process and continued work, we will ultimately be improving the end data of our research.

Speaking of data, here is a quick update of what is currently being turned over on the WCG:

Currently, all protein data being folded is from the Human Microbiome Project (HMP - see their site at http://commonfund.nih.gov/hmp/), with a focus on microbes found in the human gut. As of late January, we have completed pre-analysis on the last of the data that we will be working on from the HMP (for now), and have dropped it off to be picked up by the grid (see codes 'oh' - 'ok' in the following table).

We are now looking into new organisms - such as the malaria parasite Plasmodium Yoelii Yoelii (a model rodent malaria important for understanding the function of human malaria) - to analyze and send to the grid.

The following table describes the data that has recently been or is being processed by the WCG:


Thanks!

--

Duncan Penfold-Brown, Bonneau Lab

Считать американцам их микробиом. Слишком много чести. Хочу родной кефирчик.

Summary
The Human Proteome Folding project researchers have published a paper in the journal Genome Research, which announces the availability of their data base of predicted protein structures, their validation methods and how this augments other information about these proteins, thus helping to solve a critical problem for biologists.



Lay Person Abstract:

Lack of information about the structure of proteins is a critical problem for biologists and severely limits their ability to do further research and conduct experiments to understand the roles of proteins in disease processes. The researchers for the Human Proteome Projects have published a paper in Genome Research entitled "The proteome folding project: proteome-scale prediction of structure and function." The paper describes how they were able to use the computation results from World Community Grid to predict protein structure and protein function. Protein structure determines the function of proteins in life processes. Knowing the structure of these proteins helps scientists studying biological and medical processes and can, for example, hasten the process of discovering treatments for diseases. The human genome as well as 93 other genomes of importance to humans were processed. The paper describes the methods used to validate the accuracy of their predictions, which are now publicly available in a data base for all scientists to use.

Technical Abstract:

The incompleteness of proteome structure and function annotation is a critical problem for biologists and, in particular, severely limits interpretation of high-throughput and next-generation experiments. We have developed a proteome annotation pipeline based on structure prediction, where function and structure annotations are generated using an integration of sequence comparison, fold recognition, and grid-computing-enabled de novo structure prediction. We predict protein domain boundaries and three-dimensional (3D) structures for protein domains from 94 genomes (including human, Arabidopsis, rice, mouse, fly, yeast, Escherichia coli, and worm). De novo structure predictions were distributed on a grid of more than 1.5 million CPUs worldwide (World Community Grid). We generated significant numbers of new confident fold annotations (9% of domains that are otherwise unannotated in these genomes). We demonstrate that predicted structures can be combined with annotations from the Gene Ontology database to predict new and more specific molecular functions.

Access to Paper:

To view the paper, please click here.