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Rilian
Aug 31 2011, 21:51
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Проект "Drug Search for Leishmaniasis"

Проект запущен 31 Августа 2011

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Как присоединиться читайте в главном топике World Community Grid thumbsup.gif



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Дата основания команды - 28.02.2005 Капитан - rilian
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О проекте:

Mission
The mission of Drug Search for Leishmaniasis is to identify potential molecule candidates that could possibly be developed into treatments for Leishmaniasis. The extensive computing power of World Community Grid will be used to perform computer simulations of the interactions between millions of chemical compounds and certain target proteins. This will help find the most promising compounds that may lead to effective treatments for the disease.

Significance
Leishmaniasis is one of the most neglected tropical diseases in the world. Each year this disease infects more than two million people in 97 countries. To date, there are no available vaccines to prevent the disease, in spite of multiple research efforts. Leishmaniasis is caused by a protozoan parasite (genus Leishmania) transmitted between human and animal hosts by female sand flies. One form of the disease, the "visceral" form caused by Leishmania infantum in America, mainly affects children, who can die if adequate treatment is not provided promptly. Existing control measures rely upon drug therapy, insect control and education in the affected communities. However, the number of human cases continues to increase in tropical countries such as Bangladesh, India, Sudan, Ethiopia, Brazil, Colombia, Peru and many others.

The classical treatments for all forms of Leishmaniasis can cause severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many endemic countries. For these reasons, there is an urgent need for new, safe and inexpensive anti-Leishmania drug compounds.

Approach
A software program called VINA from The Scripps Research Institute in La Jolla, California, will be used to perform the virtual chemistry experiments. These virtual experiments will search to find which of millions of drug compounds might be able to disable particular proteins, essential for the parasite's survival. Screening for the best potential drug compounds is an early step in the process of developing effective treatments for the disease. With enough computing power, this screening can be done much more quickly than using conventional laboratory experiments. However, existing computer facilities available to the researchers would require approximately 120 years to perform the screening. The power of World Community Grid can reduce the time required to less than one year. Information about the best candidate compounds will be published by the scientists, and this information will be available in the public domain for other scientists to build upon with their research. Further laboratory work using the best candidates identified by this project could lead to the development of better drugs to fight Leishmaniasis.

About the Project

Leishmaniasis is a tropical disease caused by a parasite transmitted by specific insects. Infections of this disease have been increasing - with over two million people affected last year. Existing treatments can have severe side effects, including death. Currently, pharmaceutical companies have not been investing in extensive research to combat this disease. Therefore, the researchers at the University of Antioquia in Medellín, Colombia, are running a project on World Community Grid to search for chemical compounds which may lead to new drugs for treating this disease.

Leishmaniasis is caused by a single celled protozoan parasite. The genus of this protozoan is Leishmania. It is transmitted between human and animal hosts via the female sand fly. In the Americas, the genus of the sand fly is Lutzomyia and elsewhere it is Phlebotomus. The insect injects humans or other animals with promastigotes, the infective stage of the parasite. Once injected into the skin, the promastigote infects immune system cells such as macrophages and other mononuclear phagocytic cells. Within these cells, the promastigote transforms into the tissue stage of the parasite, known as amastigote, which multiplies inside the cell by simple division, moving on to infect other phagocytic mononuclear cells. Various factors of the parasite and host determine which form of the diseases appears in the host. The insects become infected by sucking infected cells of the host during a blood meal. In the insect´s gut, the cells rupture releasing amastigotes, which are transformed back into promastigotes. They multiply and develop in the insect's gut. After several days, depending on the species, the parasites migrate to the mouthparts of the insect, where they are ready again to be transmitted to a host, during the next blood meal.

The disease has three clinical forms:
* cutaneous - affecting the surface skin consisting mostly of ulcerated lesions, warty lesions or spots.
* mucocutaneous - affecting mucous membranes, particularly from the nose, laryngeal and pharynx.
* visceral - affecting bone marrow or internal organs, such as the liver, spleen and lymph nodes. Symptoms can include anemia, clotting problems, weight loss, enlarging of the spleen, liver and lymph nodes.

The classical treatments for all forms of Leishmaniasis are certain compounds of pentavalent antimony (e.g. sodium stibogluconate and meglumine antimoniate). These compounds can have severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many endemic countries. Several additional drugs such as Pentamidine and Amphotericin B have been used with variable success, but these drugs also have serious side effects and are expensive and difficult to administer, limiting their use as drugs of choice. More recently, Miltefosine (an oral drug) has been used with variable success in Central and South America against cutaneous Leishmaniasis and for visceral Leishmaniasis in India. A phase IV trial of this drug in India has shown an increase in the relapse rate, indicating that drug resistance may develop quickly. The visceral form mainly affects children, who can die if adequate treatment is not provided promptly.

The complete genomes of several Leishmania species have been decoded and are providing information about proteins and processes essential for the survival of the parasite. Certain Leishmania proteins have been identified as targets using information about the genomes and through prior laboratory experiments and computational work. If drugs can be developed to disable these proteins, they may prove to be an effective treatment for the disease. The first step in drug development is to find chemical compounds which attach to the target protein in a manner that disables the protein's function, thus preventing the progression of the disease. To accelerate the search for potential drugs against Leishmaniasis, the computing power of World Community Grid will be used to screen millions of potential chemical compounds as possible drug treatment candidates. Instead of performing expensive and time-consuming laboratory experiments, simulations of these millions of experiments will be performed using the software running on World Community Grid's member computers.

A software program called VINA from The Scripps Research Institute in La Jolla, California, will be used to perform the virtual chemistry experiments, more precisely known as molecular dockings. Molecular docking is the process of determining how well two chemical compounds (molecules) bind together. One of the molecules is designated as the target, in this case one of several proteins, essential for the parasite's survival. The other compound is from a collection of millions of compounds from various drug data bases, cataloging known compounds and their exact atomic structure. The docking experiments position the two compounds in all possible orientations and then compute the binding energy, which tells how well they stick together. If a compound binds to the target protein, it may be useful in disabling the function of that protein and thus reducing parasite multiplication and the progress of the disease.

The VINA calculations will be used to identify the most promising chemical compounds that may inhibit these proteins. The computer computations involved are very intensive and would take about 120 years to test the 12 million compounds against 70 Leishmania proteins, if using machines normally available to the researchers. World Community Grid will be able to reduce the time required to less than one year. Information about the best candidate compounds will be published by the scientists, and this information will be available in the public domain for other scientists to build upon with their research. Further laboratory work using the best candidates identified by the VINA computations could lead to the development of better drugs to fight Leishmaniasis.

Наименования рабочих заданий и их количество (обновлено 31 августа 2011)

Work unit numbering is in this format:
DSFL_TTTTTTTT_BBBBBBB_WWWW
T=Target
B=Batch
W=Work unit number

Сейчас кол-во целей (target) 5353, и в каждой 58 пачек (batch). В каждой пачке примерно 1000 заданий, с кворумом 2
Учитывая что время задания в среднем 6 часов, получаем 5353*58*1000*2*6= 3,725,688,000 часов = 425000 процессорных лет orly.gif censoree.gif
Добавляя 6% на разные ошибки и таймауты, получается ~450000 процессорных лет, или 450000/345 = 1300 WCG дней (если бы считался только этот проект) suicide.gif

Команда

Stan Watowich, The University of Texas Medical Branch (Galveston, Texas, USA) -- помошник, координатор DDDT2
Carlos Muskus, PECET, University of Antioquia, Medellín, Colombia
Andres Florez, PECET, University of Antioquia, Medellín, Colombia
Rodrigo Ochoa, PECET, University of Antioquia, Medellín, Colombia

Ссылки по теме:Как происходят рассчеты: программа подбирает структуру поглощающей поверхности и подвергает ее воздействию освещения. Поверхность выделяет электроэнергию и нагревается. Программа измеряет эти параметры со временем

Видео о проекте (скачать link.gif )


Как выглядит графический клиент:


График работы проекта


Це повідомлення відредагував nikelong: Mar 17 2012, 22:34
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tiss
Aug 31 2011, 21:54
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Срачно переключил на этот проект свои мощности smile.gif


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Rilian
Aug 31 2011, 21:56
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Я теж. Змагаємось, хто швидше збере сапфіровий бейджик?

Порахую 2 рокі (на сапфір), і обратно на HCC


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tiss
Aug 31 2011, 21:58
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(Rilian @ Aug 31 2011, 22:56) *

Я тоже. Соревнуемся, кто первый соберет сапфир?


Дон Алексус смотрит на нас как...


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Rilian
Aug 31 2011, 22:01
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ВЮ займає 70МБ пам'яті

непогано smile.gif

QUOTE(tiss @ Aug 31 2011, 22:58) *

QUOTE(Rilian @ Aug 31 2011, 22:56) *

Я тоже. Соревнуемся, кто первый соберет сапфир?


Дон Алексус смотрит на нас как...

Алексус кранчіт HCC, за що йому величезний респект і уважуха!


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Bel
Aug 31 2011, 22:14
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(Rilian @ Aug 31 2011, 22:56) *

Порахую 2 рокі (на сапфір), і обратно на HCC

Да там уже как кот наплакал тех заданий. Скоро можно добить HCC, и переключаться на что то другое.
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Rilian
Aug 31 2011, 22:26
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Додав у шапку інформацію про кількість та довжину РЗ (робочих завдань)


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Rilian
Aug 31 2011, 22:37
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Rilian
Sep 5 2011, 15:09
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Отримав бронзу! IPB Image

нажаль сьогодні було виявлено помилки в таргетах 6-8, і зараз проект видає дуже мало завдань -- для тестування -- таргетів 9-15

Рекомендую, якщо ви переключились сюди, додати HCC як запасний проект


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tiss
Sep 5 2011, 15:11
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(Rilian @ Sep 5 2011, 16:09) *

Отримав бронзу!

Та в мене вже срібло smile.gif


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Rilian
Sep 5 2011, 15:14
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QUOTE(tiss @ Sep 5 2011, 16:11) *

QUOTE(Rilian @ Sep 5 2011, 16:09) *

Отримав бронзу! IPB Image

Та в мене вже срібло smile.gif

ти крут! чекаємо першого командного сапфіра smile.gif koc.gif icon_trollface.png


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Brodyaga
Sep 6 2011, 10:41
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Задания в этом проекте примерно одинакового размера (в смысле по времени, необходимого для вычисления одного задания) или разные?


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Rilian
Sep 6 2011, 11:16
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QUOTE(Brodyaga @ Sep 6 2011, 11:41) *

Задания в этом проекте примерно одинакового размера (в смысле по времени, необходимого для вычисления одного задания) или разные?

однакові, орієнтуються на 6 годин

в кожному РЗ є 40 підзавдань


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london2004
Sep 6 2011, 14:39
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У меня есть задания и по 10 и по 18 часов


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Rilian
Sep 7 2011, 10:28
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завдання з 7 таргета можуть бути дуже довгими. Але все ок

QUOTE
I am looking into the estimated runtime per job and why the target 7 has caused such a large increase.

Thanks,
-Uplinger


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