找回密码
 新注册用户
搜索
楼主: 碧城仙

[BOINC] [生命科学类及其他] World Community Grid

  [复制链接]
发表于 2014-7-10 15:11:08 | 显示全部楼层
Help Conquer Cancer project update
By: Help Conquer Cancer research team
9 七月 2014          

摘要
The research team expands to advance their analysis of the millions of protein-crystallization images processed by World Community Grid volunteers. This will help scientists understand how protein structure can lead to better cancer drug design.

Dear World Community Grid volunteers,

Since you completed your calculations for Help Conquer Cancer (HCC) in 2013, we have begun analyzing the results you generated. Here, we provide an update on that analysis work as next steps to publish our findings and make the data publicly available.

Analyzing Results

Biologists and medical researchers use the three-dimensional (3D) structure of proteins to design drugs and understand protein function. Solving a protein's 3D structure requires a long and difficult sequence of steps. The protein needs to be made into a pure crystal (like you might do to crystalize sugar by slowly evaporating sugar water.) Then X-rays are shown through the crystal, and the neat array of protein molecules in the crystal creates a pattern on the film which can be analyzed mathematically to ascertain the structure of each protein molecule. Unlike sugar, protein is notoriously difficult to crystallize. HCC addressed this bottleneck in the pipeline: with a method for recognizing successfully formed protein crystals in images taken from a very large number of automated experimental attempts. For HCC, World Community Grid volunteers analyzed hundreds of millions of these images, but these results need to be processed further in order to generate reliable automatic image classifiers, discover trends in data, and ultimately improve our understanding how proteins form crystals. Our analysis work is in progress, and there are some exciting results we will be reporting on next time.

Additionally, over the last year we have devoted considerable energy and resources to our new project on World Community Grid - Mapping Cancer Markers (MCM), and other cancer-gene-signature projects that our research group is involved in. To help with both priorities and directions, our team expanded and we have a new Post-Doctoral Fellow (Dr. Lisa Yan) helping us with advancing our HCC research.

Publishing our results and findings

We have not yet decided the time-frame or the exact form of how we will make the HCC data you generated available to the public. Thanks to World Community Grid volunteers, our project's terabytes of raw image data have been transformed into terabytes of computed image features (morphological image properties used in automated image classification). The identity of proteins in the crystallization trials is largely unknown to us and partially unknown even to the Hauptman Woodward Institute (HWI), the source of the images. The features we have computed do not directly relate to crystallization outcomes or human-understandable image labels. A classifier is required to translate computed features to meaningful human labels or experimental outcomes. We have trained multiple image classifiers so far, but are confident that we can improve them. It is essential (and practical) that we finish this part of research, and publish our findings before releasing the useful data.

Paper publications

The Grid-computed results of Help Conquer Cancer have yet to be fully analyzed. Once complete, we intend to publish one or more papers based on the analysis, but cannot currently estimate a time-frame.

Collaborations

The High-Throughput Screening Lab at HWI supplied the original protein-crystallization image data, and indeed continues to generate more. Both HWI and the scientists who send them protein samples will benefit from the HCC research in two ways: better systems for automatically classifying protein-crystallization images (saving time and manual labour), and better understanding of the protein crystallization process.
大意:
自从13年完成HCC的运算任务后官人们一直在分析结果,现在跟大家汇报一下进展。
近1年来,我们一直在分析结果,试图对目标蛋白质有进一步了解。同时由于我们还在进行另一个项目MCM,所以进展略慢,不过对此已经增派了人手。
对于计算结果的公开时间及方式,我们还暂无定论。原始文件和结果文件非常大,需要对这些数据进行分类处理。待文件处理完后会发表论文,之后会公开数据。

评分

参与人数 1基本分 +30 维基拼图 +25 收起 理由
xx318088 + 30 + 25

查看全部评分

回复

使用道具 举报

发表于 2014-7-11 13:22:09 | 显示全部楼层
Project roadmap and first phase results from the Mapping Cancer Markers team
By: The Mapping Cancer Markers research team
10 七月 2014          

摘要
The lead researcher for Mapping Cancer Markers presents a roadmap for the project to analyze signatures for 4 types of cancer: lung, ovarian, prostate and sarcoma; an update on his team’s progress thus far, and an invitation to join the research team in an August cancer fundraiser.

On behalf of the Mapping Cancer Markers team, we want to start by saying thank you! In just 7 months, World Community Grid members have donated over 60,000 years of processing time to support our research. As a result, we are nearly done with the “benchmarking” portion of the project, which determines the characteristics of our search space. Over the coming months and years, we will pursue more targeted approaches to discover relevant gene signatures. Today we want to give you both a high-level roadmap and some further detail about what is happening with the project.

Project roadmap

The project is anticipated to run for two years, and we plan to analyze signatures for 4 different types of cancer. At the moment, we're enlisting your help to process research tasks for lung cancer, and will move on to ovarian cancer, prostate cancer and sarcoma.

Currently, the Mapping Cancer Markers project has two phases:
In the first phase we have been attempting to set a benchmark for further experiments.
The second phase will be geared towards finding clinically useful molecular signatures, initially focusing on gene signatures that can predict the occurrence of various types of cancer.
We expect a smooth transition between the two phases, with no interruption in work. The “benchmarking” phase of our project is important not only for our own research, but for other researchers around the world. Every year, numerous groups worldwide develop and publish interesting molecular signatures for various diseases, including multiple cancers. One of the challenges of interpreting these findings is that many of the reports are not directly comparable to each other. The benchmarking phase of our project is designed to set a standard benchmark so that we and other groups can estimate how well individual signatures perform.

You can think of this benchmarking phase as a bit like designing an IQ test. By establishing a standard test and scoring system, we can evaluate any person's intelligence. The results from the first phase of Mapping Cancer Markers will allow us to create such a test for existing and future gene signatures, so that we can tell which ones have the best predictive ability.

Benchmarking

Our preliminary analysis of the work units processed so far (roughly 26 billion gene signatures) is focused on the nature of genes in the signatures, measuring their quality by assessing how accurately they contribute to identifying patients with poor prognosis. On the analytics side, we have also been evaluating the use of a software package to aid with post-processing our results.

One of the goals of the first project phase is to understand if some genes might have better predictive ability than others. To do this, we took the top 0.1% of the gene signatures and identified the individual genes that make up each signature. For each gene, we looked at how many times it occurred within top scoring signatures and plotted the scores of those signatures (see figure below). The blue line shows the average of all of the genes together. The red line highlights the worst-performing single gene while the green line indicates our best-performing gene. The average of all the genes is very similar to the worst single gene. This is not surprising, because most genes are likely to have poor predictive ability. However, we are looking for the few genes that stand out from the field. In other words, if we have 1 million potential gene signatures, and we look at the top 1,000 scoring signatures, we can find groups of genes such as the one shown in green, which have better predictive ability.


This information is important because if we know which genes have the best predictive ability, it may help us and other researchers to evaluate the value of other signatures: if an unknown signature has one of the top genes in it, it is likely to be a useful signature for identifying, assessing, predicting or treating a disease.

As a side note, this benchmarking process is why members may have experienced shorter or longer than usual runtimes over the past several months. The core algorithm of the Mapping Cancer Markers engine, used to evaluate each potential gene signature, has a processing time that is highly dependent on the statistical characteristics of each signature. The search space targeted by a single work unit can sometimes contain time-consuming signatures, which together lead to a longer total runtime. This also means variability with the size of Mapping Cancer Markers results. A typical work unit will evaluate tens of thousands of potential gene signatures, many of which are of low quality. Signatures below a certain quality threshold are removed from the returned results. However, the search space targeted by a single work unit can sometimes contain a high proportion of high-quality gene signatures. If this happens, the result file is larger than usual.

Funding & Fundraising

We’re happy to report that there are several potential sources for further funding. Applications are in progress with the Ontario Research Fund, the Canada Foundation for Innovation, and the US Department of Defense. Of course, the free computing power provided by World Community Grid volunteers is absolutely essential to our research. However, additional funding will help us to both leverage contributions from volunteers, and fully utilize findings of the Mapping Cancer Markers computations, with a primary focus on lung and ovarian cancer.

Finally, if you will be in Ontario between 15-17 August, please consider donating to, or cheering on the Team Ian Ride from Kingston to Montreal, which raises money for the Ian Lawson Van Toch Cancer Informatics Fund at the Princess Margaret Cancer Centre (if you are interested, please contact us about joining the Team Ian ride this or next year). If you can join us, it will give you the chance to meet some of the research team, as well as raise money for a worthy cause and participate in an outstanding event. For more details visit: http://www.team-ian.org/
大意:
MCM一阶段结果以及项目路线图
首先,我代表MCM项目团队向大家表示感谢。你们在6个月的时间里贡献了6千年的计算时间。目前项目的评分标准计算部分已接近尾声,这将为我们后面的研究打下基础。
项目路线图
项目计划运行两年,我们将分析4种癌症(肺癌、卵巢癌、前列腺癌、肉瘤)的基因标识,当前正在处理肺癌,其他癌症计算将陆续展开。
当前MCM有两个阶段:
1、评分标准计算,为未来的研究设定标准。这不仅对我们有用,对世界其他研究人员也十分有用。2、寻找有用的临床特征分子,将来可以用于癌症检测。
当前每年全世界的很多组织机构都能发现很多的癌症基因标识,但是目前没有一套评分标准可以对他们进行横向比较。1阶段的目标就是设置一套类似了IQ测试的评分标准,以便能对这些基因标识进行评分。我们将筛选260亿个基因标识寻找最好的,将来用于临床检测。
附注:每个MCM任务包包含上万个基因标识,大部分都是比较差的,但有些包含好基因标识,它就需要耗费更多的计算量,所以MCM任务包的耗时波动比较大。这是正常的。理论上相对耗时越长的包,结果越好。

评分

参与人数 1基本分 +30 维基拼图 +50 收起 理由
xx318088 + 30 + 50

查看全部评分

回复

使用道具 举报

发表于 2014-7-14 20:05:25 | 显示全部楼层
GO Fight Against Malaria update: promising early findings for malaria & drug-resistant tuberculosis
By: Dr. Alexander L. Perryman
14 七月 2014         

摘要
Dr. Alexander Perryman describes the analysis and initial findings from the first phase of GO Fight Against Malaria, which include the discovery of several promising hits against key drug targets for treating both malaria and drug-resistant strains of tuberculosis. They are conducting further analysis and experimentation on the massive amount of data generated by World Community Grid volunteers.


Dear fellow volunteers of World Community Grid,

In under two years, World Community Grid volunteers performed the world's largest docking project, carrying out over 1 billion calculations to help us identify chemical compounds to advance the treatment of increasingly drug-resistant strains of malaria and other diseases - a process that would have taken over a hundred years on the type of computer clusters currently available at most universities.

Since we completed GO Fight Against Malaria (GFAM) calculations on World Community Grid a year ago, we've been analyzing the generated data. Although that process will continue for some time still, early analysis has revealed several promising findings.

First, we identified the first "œsmall molecule" inhibitor (i.e., drug-like compound) to block the activity of a particular malaria enzyme involved in infection, the first step in developing a potential treatment or prevention aimed at this malaria drug target.

Also, a subset of your calculations was conducted against a drug target for malaria which shares a similar atomic structure to a Mycobacterium tuberculosis enzyme. With extensively drug-resistant strains of tuberculosis on the rise, there is a pressing need to identify more effective treatments. We therefore included this particular tuberculosis drug target in our GFAM experiments. In doing so, we have identified several chemical compounds as potential inhibitors of this enzyme and have confirmed these results with initial laboratory tests. A very impressive number of the promising chemical compounds identified through the virtual screenings you computed on World Community Grid have gone on to perform well in additional lab testing: 20% were "hits", vs. less than 1% on average for other experimental ("œwet lab") high-throughput tuberculosis experiments.

We are now designing and synthesizing new derivatives of these inhibitors to further refine them as viable drug candidates. Read on for more details about this early analysis work, and we'll be able to share more information once we publish our findings. In the meantime, I want to thank GFAM volunteers for allowing us to advance this important and often neglected area of research.

Largest set of computational docking experiments ever performed

GFAM was launched on IBM's World Community Grid on November 16, 2011. Malaria is one of the three deadliest infectious diseases on Earth (the other two are HIV and tuberculosis). Plasmodium falciparum (Pfal, or Pf), the species that causes the worst form of malaria, kills more people than any other parasite on the planet. Over 200,000,000 clinical cases of malaria occur each year, and over one million people are killed by malaria every year. Over three billion people (almost half of all humans) are at risk of becoming infected with malaria, and every 30 seconds, another child dies of malaria.

GFAM ran on World Community Grid for 19 months, during which the tremendous computational power provided by World Community Grid volunteers like you helped us generate massive data sets against 22 different types of drug targets, to seed the discovery of new drugs to treat malaria. We performed "docking calculations," which explore how well different "small molecules" (pieces of drug-like compounds) are able to bind and potentially block the activity of critical pieces of the molecular machinery that the pathogens use to survive, replicate, and spread throughout humanity. Docking calculations use flexible models of these small molecules to explore the energetic landscape of atomic-scale models (on the scale of 0.0000000001 meters) of proteins that perform critical functions for the parasite'™s lifecycle and infection process. These calculations predict how tightly a compound might bind to the target (that is, how potent it might be), where the compound probably prefers to bind, and what specific types of interactions might be formed between the compound and the drug target. One docking calculation refers to the process of docking a flexible model of a single compound against one particular version of one target. In this first phase of GFAM, World Community Grid volunteers performed 1.16 billion different docking calculations that explored the potential activity of 5.6 million different compounds against drug targets from malaria (and against some targets for treating drug-resistant tuberculosis, Methicillin-Resistant Staphylococcus aureus (MRSA), filariasis, and bubonic plague, when the targets from those other pathogens had structural similarity to the targets from malaria). With the computing power that you generously donated, GFAM was the first project to ever perform a billion different docking calculations. Performing this many calculations could have taken over a hundred years on the type of computer clusters currently available at most universities. We could not have accomplished this feat without your help. We are also grateful for the $50,000 in seed funding provided by the IBM International Foundation, from part of the prize money that IBM's computer Watson won on Jeopardy!™. Thus far, that seed money has been the only funding that the project has received, but we are currently writing grants that focus on analyzing and extending the GFAM data.

Finding a "œhit" that inhibits a critical protein involved in malaria infections

"Hits" are compounds that have some inhibitory effect on the biological activity of one of these drug targets. But finding a hit is only the beginning of the process (a complicated process that can take several years to a couple of decades to complete). Scientists from around the world called "medicinal chemists" can then work with structure-based computational chemists like us to try to increase the potency and decrease the potential toxic side effects of these compounds, which involves processes called "hit-to-lead development" and then "œlead optimization". "œLeads" are larger, more structurally complex, potential drug candidates that generally display nanomolar potency (that is, they are around 1,000 times more potent than "œhits", which means that only a tiny amount of a leading compound is required to affect the activity of the target). In collaboration with Professor Mike Blackman's lab in the Division of Parasitology at the Medical Research Council's (or "MRC's") National Institute for Medical Research (or "œNIMR"), in London, UK, and with InhibOx, Ltd, we searched for the first small molecule inhibitors of the potential drug target "œPfSUB1" (see target class #6 onhttp://gofightagainstmalaria.scripps.edu/index.php/how-we-will-discover-potential-malaria-drugs). When the Blackman lab solved the first crystal structure of PfSUB1 (that is, the atomically-detailed, 3-D map of where all of its atoms are), they shared that unpublished structure with us, which allowed us to perform virtual screens against PfSUB1. These virtual screens are searching for "small molecule" inhibitors (that is, compounds with some similarity to pieces of known drugs) that can block the activity of this malarial enzyme. When malaria parasites replicate themselves inside a red blood cell, the "daughter" parasites eventually rupture the infected host cell, which allows the new parasites to escape and then invade and infect other red blood cells. The subtilisin-like serine proteases from Plasmodium falciparum (also known as PfSUB1) are involved in this ability of the malaria parasites to escape (or "œegress") an infected red blood cell. The Blackman lab has shown that the PfSUB1 enzyme has an additional role in "priming" the merozoite stage of the parasite prior to its invasion of red blood cells (in other words, it is involved in processing certain other malarial proteins in order to prepare and activate them, so that the parasite can invade our blood cells). Thus, PfSUB1 is involved in both the egress and the infection process. In the results of GFAM Experiment 27, we discovered the first small molecule inhibitor of PfSUB1 ever identified, and it displayed a proper "dose-response curve" (that is, at higher concentrations of the inhibitor, it shuts down the activity of PfSUB1 more and more effectively), which indicates that it is likely a "œspecific" inhibitor, instead of a non-specific compound that randomly happens to impede activity a bit for many different types of proteins (but this will have be tested against other types of proteins to know for sure). This compound, nicknamed "GF13", is a fairly weak inhibitor: at a 200 micromolar concentration, it blocks activity of PfSUB1 50%. Strong hits will block 50% of the target's activity in the 1 to 50 micromolar range (the smaller the # of micromoles per liter that are needed to shut down activity, the more potent a compound is).



Although GF13 (shown as the green surface with a cyan outline that is bound in the cleft in the center of PfSUB1, whose surface is shown in purple above) is a weak inhibitor, it is still a novel and significant hit: it provides a foundation on which we can build, and it could help us find more potent inhibitors of this potential drug target for malaria. After we write a couple papers on the GFAM results against the tuberculosis target InhA (discussed below), which could help us get some grant funding to enable additional analyses of GFAM data, we will write a paper on these results against PfSUB1. We then hope to extend this collaboration with Professor Mike Blackman's lab on this important malaria target (if we can obtain a grant to enable that extension).

GFAM experiment leads to the discovery of new hits against a key drug target for tuberculosis.

As mentioned earlier, when a drug target from Plasmodium falciparum had structural similarity with a target from another pathogen, we docked 5.6 million compounds against the targets from both pathogens. A potential drug target for malaria called "PfENR" (for Plasmodium falciparum enoyl acyl-carrier-protein reductase) has a similar atomic structure to the well-validated drug target for treating tuberculosis called "InhA". Consequently, we included theMycobacterium tuberculosis (Mtb) enzyme InhA in our GFAM experiments against PfENR. Few pharmaceutical companies perform antibiotic (i.e., antibacterial) research anymore, which means that it is up to scientists at universities and non-profit institutes to fill that research gap. If the scientific community cannot create new ways to defeat these superbugs, then the medical community will not have the capacity to treat these drug-resistant infections that keep occurring with increasing severity, frequency, and distribution. The situation is dire. Mtb infects 8.3 - 9 million people each year, and tuberculosis kills 1.4 million people/year. A few decades ago, multi-drug-resistant tuberculosis (MDR-TB) was not a serious problem. There are now a half million new cases of MDR-TB per year. Extensively drug-resistant TB (XDR-TB) has now been found in over 92 different countries, including the U.S.A. And "nosocomial" (i.e., hospital-acquired) XDR-TB is now a growing problem. Totally-drug-resistant TB (TDR-TB) has appeared in several countries and will continue to spread. No drugs exist to treat TDR-TB.

Professor Peter J. Tonge is the first person we encountered who was willing and able to test some of the predictions from GFAM, even though it is an unfunded project. Professor Tonge is the Director of Infectious Disease Research at the Institute for Chemical Biology and Drug Discovery at Stony Brook University in NY. He has done some pioneering research against MtbInhA and is a leading expert in the battle against XDR-TB. He offered to experimentally assess the potency of the candidate compounds we discovered in the docking calculations on GFAM that we performed against InhA. InhA (which is also called FabI) is part of a unique metabolic pathway (that is, it's an enzyme that is part of a metabolic pathway that is not present in humans), which should hopefully decrease the toxic side effects of InhA inhibitors. Specifically, ENR/InhA is part of a Fatty Acid Synthesis pathway (called "FAS II") that human cells do not have. One of the main drugs used to treat tuberculosis is called isoniazid (or "INH"), and it kills that deadly bacteria by shutting down the activity of InhA (and perhaps by also shutting down the activity of other target proteins in Mtb, as well). But drug-resistant mutants against which isoniazid loses its effectiveness keep evolving and spreading, which is why we are searching for new inhibitors of InhA that are able to counteract the main mechanism of drug resistance that allows Mtb to evade treatment with INH. Some inhibitors of InhA also block the activity of the PfENR target from malaria. By advancing the research against InhA, we might be able to simultaneously help advance the research against both totally drug-resistant tuberculosis and against multi-drug-resistant malaria.

In the results of GFAM Experiment 5, which screened the National Cancer Institute's library of compounds (that we can order for free from the NCI's Developmental Therapeutics Program), we identified 19 candidate compounds as potential inhibitors of Mtb InhA. These 19 NCI compounds were then experimentally tested in "wet lab" experiments (in test tubes and Petri dishes) by Weixuan Yu in Professor Peter Tonge's lab. Of the 16 soluble compounds, 8 candidates (at a 100 micromolar concentration) shut down InhA activity by ~ 30% or more. The most potent inhibitor we discovered displayed an IC50 value of ~ 40 micromolar (which means that when the compound is present at a 40 micromolar concentration, it inhibits InhA activity by 50%). Additional kinetic experiments were then performed on the best hits from this experiment, and the two most potent inhibitors displayed Ki values of 54 and 58 micromolar.



The binding mode predicted by AutoDock Vina for the most potent hit we discovered in GFAM experiment 5 is shown as a magenta surface, while the InhA target is shown in cyan as a ribbon above. The NAD cofactor of InhA is shown as cyan spheres. Finding new, low micromolar inhibitors of InhA is a significant achievement (and so is having a hit rate of 8/19 candidates from a virtual screen), but we will still need to optimize these compounds and make them at least a thousand times more potent before they become a drug-like candidate called a "lead". These virtual screens on GFAM (and, thus, the new inhibitors we discovered) were designed to target one of the main mechanisms that Mycobacterium tuberculosis has evolved in order to resist the effects of drug treatment with isoniazid. We are now about half-way through the process of writing a paper on these exciting new results. I hope to finish the first draft within the next month or so, and then I'™ll send it around to all of the co-authors to get their input and suggested revisions. After that manuscript completes the normal peer-review process, we will share the published version with all of you.

Discovery of additional new hits against a target for drug-resistant tuberculosis

The third GFAM experiment we analyzed led to the discovery of additional new hits against InhA, a key drug target for treating Mycobacterium tuberculosis, and could help seed the discovery of new drugs against extensively drug-resistant and totally drug-resistant tuberculosis.

In November of 2013, I joined Associate Professor Joel S. Freundlich'€™s chemical biology and medicinal chemistry lab at the Rutgers University €”New Jersey Medical School, in Newark, NJ. Instead of having to search for collaborators in other labs to experimentally test my predictions, and then waiting many months to years to find out whether the compounds actually work against the drug targets and then against the full pathogenic organism, I can now just ask my co-workers in the Freundlich lab to help test the computational predictions. The enzyme activity assays, anti-bacterial activity assays against whole-cell Mtb cultures, metabolomics studies to investigate the different targets that are affected, synthesis of new derivatives, and medicinal chemistry-guided optimization research are all performed within the Freundlich lab. I provide the computational chemistry core that can help analyze and guide some of these efforts. I'€™ve even started learning how to do some of these "wet lab" aspects myself, to expedite the assessment of my computational predictions. In the Freundlich lab, some of our projects againstMtb involve analyzing and extending the subset of GFAM data that involve targets that can advance the treatment of XDR-TB and TDR-TB.

In GFAM experiment 9, which involved docking the Asinex library of over 500,000 compounds against PfENR and Mtb InhA, we discovered additional new inhibitors of InhA that have very novel structures, as compared to the known InhA inhibitors. In collaboration with Dr. Sean Ekins of Collaborations in Chemistry (Fuquay-Varina, NC), this project also involves the creation, testing, and development of new types of computational workflows that can filter and prioritize the docking results, in order to increase efficiency and enhance the probability of finding active, potent, non-toxic compounds. We used an innovative new combination of docking-based filters, other types of filters (which we cannot discuss until after these results are published), and visual inspection to narrow down the docking results for those 500,000 compounds and identify 20 promising candidate compounds. These 20 Asinex compounds were then tested in enzyme inhibition assays against InhA by Xin Wang, a graduate student who recently joined the Freundlich lab. Since Professor Freundlich was a medicinal chemist in the pharmaceutical industry for over a decade, he applied a more stringent bar to define what we would consider as hits: a "hit" had to inhibit InhA activity by at least 50% when the compound was present at a 50 micromolar concentration. Using this more stringent criteria, 5 of the 20 candidates are novel hits against InhA. The most potent new InhA inhibitor we discovered has an IC50 of 19 micromolar (at a concentration of 19 micromoles per liter, it inhibits InhA activity 50%).



This new hit€™'s predicted binding mode against InhA is shown as a dark green surface, with the InhA target shown in light purple as a ribbon above. Having a 5/20, or 25%, hit rate against an enzyme from the results of a virtual screen was a great success, as was discovering another novel InhA inhibitor that was more than twice as potent as the one we found in our previous GFAM experiment against InhA. The 5 hits we discovered against InhA were then further tested for their activity against whole-cell Mycobacterium tuberculosiscultures by Dr. Mi-Sun Koo in the Freundlich lab. These "MIC99" assays (for the Microbial Inhibition Constant, or the amount of compound needed to inhibit the growth of 99% of the bacterial cells) take over a week to perform againstMtb, since Mtb grows very slowly. Because Mtb is an air-borne bacteria, these MIC assays have to be done in special "BSL3" labs (the second highest form of Biosafety Level), using the full-body "bunny suits" and respirators. Since Dr. Koo went on vacation before the assays were done, the final measurement was taken by Dr. Pradeep Kumar, of Professor David Alland'€™s lab at the Rutgers University-€”NJ Medical School. Of the 5 InhA inhibitors we discovered, one of these compounds displayed potency against whole-cell cultures of the bacteria that cause tuberculosis, with an MIC99 of ~ 2.4 micrograms per milliliter.



Its predicted binding mode is shown as a light green surface, with the InhA target displayed in light purple as a ribbon. Traditional, experimental high-throughput screens against whole-cell Mtb tend to display hit rates less than 1%, but 1/5 (i.e., 20%) of the compounds we tested were active against whole-cell Mtb cultures. Professor Joel Freundlich, Dr. Shao-Gang Li, Dr. Steve Paget, and I have already designed new derivatives of the top InhA inhibitor and the top MIC hit, to test their Structure-Activity-Relationships (to figure out how changing and adding different chemical groups to these molecules increases or decreases their activity) and to try to increase their potency. These derivatives are currently being synthesized by Shao-Gang and Steve, as part of the "hit-to-lead development" process mentioned previously. After these derivatives have been made, tested in InhA activity assays, and tested in Mtbgrowth assays, we will write a paper on these exciting new results. Professor Freundlich, Dr. Sean Ekins, and I have already written and submitted two different grants that discuss our new approach and propose applying it to the other 5 million compounds that were docked against InhA as part of the GFAM project, and we plan to write a couple more grants that involve the Mtb subset of GFAM data. We'€™ll let you know how it goes.

Personnel update and a request for action

Last year, the "sequester cuts" to the NIH eliminated the funding for my position in Professor Olson's lab at TSRI. Don'€™t be sad for me - €”please contact your members of Congress and ask them to restore funding to the NIH! The inflation in scientific equipment and reagents rises faster than normal inflation, but the NIH budget has still not yet been restored to even the pre-sequester level. It's not even close to the level of funding it should have, considering scientific inflation, the growing problems that the medical community faces, and the fact that pharmaceutical companies keep cutting their research budgets year after year (which puts the academic scientific community under pressure to fill this research gap, or else progress against diseases will not occur rapidly enough). In addition, every single dollar from the NIH and NSF generates approximately $2 in economic output, and NIH funding has led to the creation of nearly 430,000 quality jobs. Luckily, I was able to find a great new position in Professor Joel Freundlich'€™s lab at the Rutgers University-€”New Jersey Medical School, where I get to continue my fight against drug-resistant infectious diseases. But I know many scientists who are still not able to find a job.

Thank you all very much for donating your computer power to World Community Grid!!! We would not have been able to generate this mountain of data for malaria and tuberculosis research without your generous help. The massive number of virtual experiments you performed provides us with enough data to continue our research for years to come. Please be patient, and keep crunching! Many other projects still need your help.

Sincerely,
Dr. Alex L. Perryman

大意:
GFAM项目更新:发现潜在的治疗疟疾和耐药性肺结核药物靶点
GFAM已经在一年前完成了计算,现在我们在分析结果数据,以寻找治疗抗药性疟疾(以及其他疾病)的药物。
首先,我们找到了一个小分子抑制剂,可用于抑制疟疾在感染过程中用到的一种酶。
同时,我们还针对另外一种疟疾和肺结核杆菌通用的酶进行了计算。我们找到了几种潜在药物,并在试验中进行了初步测试。结果很喜人,抑制率高达20%,而其他药物只有1%。现在我们正在优化设计和合成这些抑制剂,以便将来能用于临床治疗。


GFAM开始于2011年11月16日,地球上最致命三大传染病疾病是艾滋、肺结核和疟疾。恶性疟原虫是导致疟疾的元凶,其中每年死于疟原虫的人数远超过其他寄生虫。每年大约有2亿人次临床感染记录,其中有超过1百万人死于疟疾。全球大约有30亿人口都在疟疾高危区。每半分钟就有一个儿童死于疟疾。
GFAM在WCG上运行了19个月。它利用结合能计算,来筛选能抑制病菌生长、复制、感染的分子药物。志愿者们完成了11.6亿次结合能计算,找到了560万种可能用于抑制疟疾(有些还能用于耐药性肺结核、抗药性的金黄葡萄状球菌MRSA、丝虫病、淋巴腺鼠疫,因为他们的结构与疟疾酶类似)的分子。感谢志愿者们的无私奉献,也感谢IBM提供的5万美元赞助(来自于沃森在Jeopardy节目中赢得的奖金)。


寻找疟疾传染蛋白酶的靶点
寻找靶点是药物研发的第一步,找到后需要对药物进行优化,及去毒性处理(整个药物研发过程很漫长,大概需要几年到数十年)。直到找到真正有效的药物(最终的临床药物要比初筛的药物更有效1千倍以上才行),也就是只需要很小的剂量就能起效。我们和Mike Blackman教授合作,发现了PfSUB1目标蛋白酶,他把未公开的蛋白质3D结构数据给了我们,让我们进行药物筛选。疟原虫在感染红细胞后会在红细胞内进行疯狂繁殖,然后胀破红细胞,继续感染其他红细胞。PfSUB1蛋白酶在入侵和胀破红细胞膜的过程中起了关键作用。在GFAM的27号模拟实验中,我们发现了一直潜在抑制剂GF13。不过它的效用还比较差,200微摩尔浓度的GF13能使PfSUB1活性下降50%。有效药物,应该能在1-50微摩尔的浓度下使PfSUB1活性下降50%。
虽然GF13的效用比较差,但是它至少打了个好基础。现在我们在写肺结核目标蛋白酶InhA的论文,等写完了,应该可以拉不少赞助,然后我们就有钱继续疟疾的研究了。


GFAM实验发现新的肺结核药物靶点
如前所述, 疟原虫的靶蛋白酶PfENR和肺结核的靶蛋白酶InhA在结构上有点接近,所以我们把可能有效的560万种分子,针对两种靶蛋白酶都进行了计算。当前很少有制药公司会研究靶向抗菌药,所以只有大学学者和非营利性机构来干这活儿。要知道每年有830-900万人感染肺结核,其中有140万死于该疾病。几十年前,耐药性肺结核杆菌还不是个事儿,但是现在每年大约有50万人(92个国家)感染耐药性肺结核。更可怕的是,现在出现了完全耐药性肺结核。目前没有任何药物对它管用。
Tonge教授,是肺结核方面的专家,也是我们遇到的一个愿意自费进行研究的学者(译注:向这位仁兄致敬)。InhA是一种肺结核专用的新陈代谢酶,这意味着针对它的抑制剂,靶向性更好,毒副作用更低。当前治疗肺结核的主要药物是异烟肼(INH),它通过抑制InhA(以及其他蛋白酶)的活性来杀死病菌。但是现在病菌的变异使它对INH产生了抗药性,所以我们急需研发新的药物。而且对肺结核InhA的研究和对疟疾的研究都是相辅相成,互相促进的。
在GFAM实验5中,我们对NCI数据库中的分子进行了筛选。发现了19种候选分子,随后在实验室进行了测试。在16种可溶性分子中,8种在100微摩尔浓度下使InhA活性下降了30%。最有效的分子,在40微摩尔浓度下使InhA活性下降50%,亚军是54微摩尔,季军是58微摩尔。


由AutoDock Vina生成的GFAM实验5图中,靶点是红紫色的表面,而InhA酶是上面的青绿色的带状物,InhA的NAD辅助因子是青绿色的球面。此次发现非常振奋人心,因为它可以以极低的浓度产生效用。当然真正用于临床的药物要比这有效上千倍才行。所以我们还要继续优化。目前我们正在写论文,已经写了一半了,预计下个月完成草稿。待完成同行评审发表后,我们会公开论文。


发现新的抗药性肺结核靶点
在GFAM的实验3中,我们发现了新的InhA靶点。在GFAM的实验9中,我们对Asinex库中的50万个分子进行了筛选,发现与现有的抑制剂结构完全不同的新抑制剂。最终我们找到了20种候选分子并在实验室进行了测试。测试后,发现有5种分子在50微摩尔浓度下可以抑制50%的InhA,其中最好的可以低至19微摩尔。


新靶点表面为暗绿色,InhA酶是淡紫色带状物。老靶点的有效率高达20%,但是新靶点比它多一倍。我们对5个候选药物进行了肺结核病毒全细胞MIC99标准测试(即对病毒细胞生长抑制率达到99%),最终我们发现,其中一种分子,能在2.4微摩尔浓度下达到MIC99标准。我们现在针对这个分子还在不断的进行优化和调整。待有新的结果后我们会通知大家的。


个人吐槽
去年NIH大幅缩减了财政预算,这导致医学研究经费日趋紧张,我也因此失业(不过还好现在找到了新工作),如果你有‘舅舅’在米国国会,请让他们给NIH增加预算吧。现在制药企业在逐年缩减科研支出,国家方面也在减。要知道NIH和NSF的每一美元投入最终都能得到2美元的产出。而且NIH还能产生43万个相关工作岗位。要知道我还有很多同事根本找不到工作呢。


最后由衷的感谢大家的付出。


译注:翻译了一天终于翻译完了,休息一下,累屎我了。

评分

参与人数 1基本分 +30 维基拼图 +200 收起 理由
xx318088 + 30 + 200

查看全部评分

回复

使用道具 举报

发表于 2014-7-16 20:14:06 | 显示全部楼层
Improved efficiency and processing capabilities for FightAIDS@Home
By: The FightAIDS@Home research team
16 七月 2014         

摘要
New methods and processes help the research team process World Community Grid data more efficiently and provide more accurate docking techniques.
As the volume of data generated by World Community Grid volunteers for ourFightAIDS@Home (FAAH) project has increased, so has our need to optimize how we handle and store that data. In this project update, we discuss new improvements in how we process the extremely high result data rate you generate, which is allowing us to focus more resources toward the analysis of FAAH data. Further, improved docking techniques are being created and applied from the results of deeper analysis coupled with ongoing experimental data from our collaborators.


Example of repositioned side-chain, histidine, by Vina cycling through the original space-filling representation, original stick representation (orange), and new position compared to old position (dotted black lines).
Processing your results faster

Managing the very large data throughput generated by World Community Grid volunteers for FAAH is a great challenge. Beside the scientific results we have achieved over the years, we also have developed novel software and protocols to process, analyze and store the results you generate quickly and efficiently.

Recently, we exploited the parallel computational resources available at Scripps. In the last few months, we have shifted our processing of the incoming World Community Grid data to our local High Performance Computing cluster, Garibaldi. Since the implementation of the AutoDock Vina software for FAAH last year, you have generated several terabytes of compressed docking results each month, which was putting a strain on our storage system. Until recently, most of our work and resources have been focused on processing this data to make it suitable for deeper analysis. We had to devote most of our local computational power to this processing. With our new methods, we have increased the processing rate by several orders of magnitude with the use of multiple processors and the optimization of processing scripts. Processing a batch that used to take between 30 minutes to few hours now takes just a few minutes. Streamlined scripts and parallel processing has yielded 180,000 processed batches in two weeks.

We have created new analysis programs using structural and statistical methods to mine more information from the results you generate. Statistical analysis tools will first be used to reduce over 5 million docked compounds to a few thousand top-ranking candidates. Structural information will then be used to cull the list further by filtering for key intermolecular interactions and against unfavorable interactions. A new database structure that will incorporate these programs is being developed to handle this large and fast-growing flood of results. Once optimized, the whole processing and analysis workflow will be fully automated.

Importantly, what we have learned and are learning from these refined methods to handle big data will be made available in the AutoDockTools suite, which is utilized by many research labs worldwide.

Improved protein-ligand binding modeling capabilities

Proteins are typically large molecules and often can bend or flex in various ways at various points and at normal temperatures they rapidly bend to many or all of the possible configurations (bent shapes). When searching for ligands that might attach to a protein target, the ligand might not match the shape of the protein in one of its configurations, but might match in another configuration of the protein. By considering more configurations of the protein, it is more likely that a ligand can be found which matches one of the protein's configurations. Since February 2014, we have been running flexible receptor side-chain Vina jobs on FAAH, which we expect to enhance our docking results. While our typical docking methods hold the protein structure rigid, the flexibility feature in AutoDock Vina allows selected residue side chain conformations to be sampled along with the flexible ligand molecule. This enables the protein pocket to adopt alternate shapes to better model protein-ligand binding and the so-called “induced fit”, minimizing the bias of using a rigid target structure. Currently, we are testing this approach on several sites (LEFGF, FBP, and Y3) in HIV integrase.

The downside of performing flexible receptor calculations is that the search complexity increases, and computing run-times are therefore 5 to 10 times longer. The World Community Grid staff has been adjusting their methods to account for the different Flexible Vina work unit. Once these dockings have finished and the analyses performed, we will be able to optimize our application of Flexible Vina on World Community Grid and extend it to other targets.

Another way to minimize rigid-protein bias in traditional docking is to dock to an ensemble of protein structures. Two ways to generate these ensembles, both used in FAAH dockings, are molecular dynamics (MD) simulations and simply using multiple available structures for a given protein receptor. The last hundred experiments have included ensembles ranging from tens to sometimes hundreds of receptor structures. Ensembles add another layer of analysis with the goal of achieving a more accurate ranking of compounds from several sources of data.

Further experimentation

Despite the encouraging results on the first hits previously reported, we are encountering experimental issues that are making the process of identifying hits very challenging. As often happens in science (and particularly in HIV-related experiments!), it is hard to achieve robust and consistent statistics from biological assays.

Experiment 30 Compounds (October-December 2009), Target: HIV Protease, Exo/1F1 Sites:
Five out of ten compounds had promising results from a differential scanning fluorimetry (DSF) assay, performed by the Torbett Lab. Unfortunately. X-ray crystallography by the Stout Lab gave inconclusive data; crystals had formed but diffracted poorly, so no binding sites were confirmed. The compounds were sent to our collaborators at Scripps, Florida, but complications with producing enough HIV Protease delayed these efforts. This obstacle was recently resolved with the help of the Elder Lab, and nuclear magnetic resonance (NMR) experiments are soon to be performed.

Experiment 33 (June-December 2010), Target: HIV Integrase, Active Site of the Catalytic Core Domain (CCD):
Preliminary results were mixed. The Kvaratskhelia Lab (OSU) recently reported promising results for 2 out of 10 compounds, but these compounds were considered poor candidates due to poor chemical properties that indicated poor specificity, meaning that although they may bind to HIV Integrase, they will probably bind just as easily to other proteins reducing their effectiveness.

We anticipate identifying many more hit compounds for all 3 proteins and their various sites by the end of the year and we’re grateful for World Community Grid volunteers for giving us the opportunity to learn more about HIV and its interactions.


大意:
提升FAAH结果的处理效率和能力
更快的处理结果
如何管理FAAH产生的天量数据,对我们来说绝对是个挑战。最新,我们启用了Scripps最新的并行计算系统Garibaldi。因为去年FAAH把计算内核更新为vina了,所以大伙每月都会上传数TB的结果给我们,这对我们的存储系统来说也绝对是个挑战。直到最近我们新的超级计算系统就位后,我们才开始对这些数据展开深度挖掘。新系统的处理能力提升了几个量级。以前处理一组结果要半个小时,现在只要几分钟。现今我们只需两周就能处理18万组结果。
我们开发了新的分析程序,使用结构和统计学算法,从结果中深度挖掘更多有用的信息。首先,统计算法将从5百万的分子中筛选出几千个最好的结果。然后用结构算法寻找其中关键的分子间作用和相反的作用。一旦优化完成,我们将写个自动化处理脚本,将来加入AutoDockTools套件中,供全球的实验室使用。

改进蛋白质结合能模型性能
蛋白质是一种结构在不停变化的大分子。以前FAAH算的都是静态结构,这样结果的误差就会很大。所以从14年2月起,vina核心开始计算动态结构。现在我们已经针对某些HIV抑制剂(LEFGF, FBP和Y3)进行了测试。不过这个算法的缺陷是会导致计算量增加到5-10倍。我们现在还在不停跟分析、优化算法。今后会对所有的靶蛋白进行动态计算。当然还有一种方法是利用分子动力学找出一组代表性的静态结构进行计算。

实验测试
尽管之前的报告发现了很多的候选靶点,但是实验结果却不尽人意。
30号实验:在10个候选分子中有5个虽然形成了晶体,但是没有发现结合点。由于现在缺少靶蛋白,我计划接下来用原子磁共振技术再次对这些分子进行测试。
33号实验:10个候选分子,有2个可能有效,但是数据很差,而且它们靶向性很差,很容易和其他蛋白质结合,导致效用进一步下降。

接下来我们将继续寻找更多的靶点。同时我们也会找机会给大家讲讲‘关于HIV的那些事儿’。

译注:向MH17遇难的艾滋病专家们表示沉痛哀悼!

评分

参与人数 1基本分 +30 维基拼图 +100 收起 理由
xx318088 + 30 + 100

查看全部评分

回复

使用道具 举报

发表于 2014-7-22 16:03:02 | 显示全部楼层
Pioneering a Molecular Approach to Fighting AIDS
By: Dr. Arthur Olson
Professor, The Scripps Research Institute
21 七月 2014          

摘要
World Community Grid is being featured at the 20th International AIDS Conference which begins today in Melbourne, Australia. Dr. Arthur Olson, FightAIDS@Home principal investigator, shares his perspective on how World Community Grid is helping his team develop therapies and a potential cure for AIDS.

The Scripps Research Institute’s FightAIDS@Home initiative is a large-scale computational research project whose goal is to use our knowledge of the molecular biology of the AIDS virus HIV to help defeat the AIDS epidemic. We rely on World Community Grid to provide massive computational power donated by people around the world to speed our research. The “virtual supercomputer” of World Community Grid enables us to model the known atomic structures of HIV molecules to help us design new drugs that could disrupt the function of these molecules. World Community Grid is an essential tool in our quest to understand and subvert the HIV virus’s ability to infect, spread and develop resistance to drug therapies.

http://www.youtube.com/embed/V6gzc8uUGJw

Since the early 1980s – when AIDS was first recognized as a new epidemic and a serious threat to human health – our ability to combat the HIV virus has evolved. Using what we call “structure-based drug discovery,” researchers have been able to use information about HIV’s molecular component to design drugs to defeat it. Critical to this process has been our ability to develop and deploy advanced computational models to help us predict how certain chemical compounds could affect the HIV virus. The development of our AutoDock modelling application – combined with the computational power of World Community Grid – represents a significant breakthrough in our ability to fight HIV.

By the mid 1990s, the first structure-based HIV protease inhibitors were approved for the treatment of AIDS. These inhibitors enabled the development of highly active antiretroviral therapy (HAART), which in turn resulted in a rapid decline of AIDS deaths where such treatment was available. In the intervening years, thanks in part to the U.S. National Institute of General Medical Sciences AIDS-related Structural Biology Program, we have learned a lot about the molecular structure of HIV. But the more we understand the structure of the virus, the more complex our computational models need to be to unlock the secrets of HIV.

World Community Grid has enabled our research to progress well beyond what we could have dreamed of when we started our HIV research in the early 1990s. Through our FightAIDS@Home project, we can screen millions of chemical compounds to evaluate their effectiveness against HIV target proteins – including those known to be drug-resistant. By deploying these and other methods, we have significantly increased our understanding of HIV and its ability to evolve to resist treatment. Using these computational capabilities, we have just begun working with an HIV Cure researcher to help us move beyond treatment in search of a cure.
大意:
创新性的利用分子技术抗击艾滋——第20界艾滋大会报告
FAAH利用WCG的虚拟超级计算机来对HIV分子进行模拟研究,以期找到能够治疗艾滋的药物。
自从80年代早期发现首例艾滋病,它已经逐渐蔓延,现今已经成了人类一大威胁。我们利用基于结构的药物研发技术,开发了AutoDock程序,来研发抗艾滋药物。
在90年代中期,发现了首个基于结构的抗艾滋抑制剂。并促成了(HAART高效高效抗逆转录病毒治疗。俗称鸡尾酒疗法)的形成。这大大降低了艾滋病的死亡率。
利用WCG,我们可以对已知的化学分子进行筛选,寻找潜在药物,并且我们可以对HIV有更深入的了解。

评分

参与人数 1基本分 +30 维基拼图 +35 收起 理由
xx318088 + 30 + 35

查看全部评分

回复

使用道具 举报

发表于 2014-7-31 21:56:06 | 显示全部楼层
Calling all climate change scientists
29 七月 2014          

摘要
In response to President Obama's call to action on the Climate Data Initiative, we invite scientists studying climate change issues to submit proposals for accessing massive supercomputing power to advance their research.

Extreme weather events caused by climate change, such as floods and droughts, can have a drastic impact on food production. For example, production costs for maize and other grains could double by 2030. How can individuals, communities, organizations and governments prepare to handle future climate impacts on food security and other key issues? To address this challenge, President Obama today announced the second phase of the Climate Data Initiative calling on private and philanthropic organizations to develop data-driven tools to plan for and mitigate the effects of climate change. In response, World Community Grid invites scientists studying issues affected by climate change, such as the resilience of staple food crops, and watershed management to submit research proposals. In addition, IBM is participating in a roundtable discussion convened by the White House today to discuss joint efforts to further advance the Initiative's goals.

To date, over 300,000 World Community Grid volunteers have already provided sustainability scientists with the equivalent of almost 100,000 years of computing power to support researchers in numerous fields, including energy, water and agricultural science:
The University of Virginia’s Computing for Sustainable Water project is shedding new light on the effects of human activity on the Chesapeake Bay watershed. Organizations and policymakers will be able to use this data-driven insight to guide their efforts to support the restoration and health of the area.

The University of Washington’s Nutritious Rice for the World project studied rice proteins that could help farmers breed new strains with higher yields and greater disease and pest resistance. New crops like these will be vital in areas that face changing climate conditions.

In what we believe to be the most extensive quantum chemical investigation to date, Harvard University’s Clean Energy Project has discovered 35,000 materials with the potential to double carbon-based solar cell efficiency after screening more than two million organic materials on World Community Grid. These discoveries could result in solar cells that are cheaper, easier to produce and more efficient than ever before.

We invite sustainability researchers who could benefit from massive supercomputing power to advance their work to submit a project proposal. In addition, anyone can contribute to understanding climate change and mitigating its impacts by joining World Community Grid and supporting our current research projects. Take a minute right now to start supporting cutting-edge climate science.
大意:
召唤气候变化科学家
气候变化会引起的极端天气,如:洪水和干旱。这会对粮食生产产生很大影响提高生产成本,影响粮食安全。为此,奥巴马召集了圆桌会议商讨对策。IBM有幸应邀参加。
WCG已经在30万用户的帮助下为相关项目提供了10万年的计算量。希望有科学家能利用WCG平台来进行气候相关的研究。

评分

参与人数 1基本分 +30 维基拼图 +20 收起 理由
xx318088 + 30 + 20

查看全部评分

回复

使用道具 举报

发表于 2014-7-31 21:56:16 | 显示全部楼层
Simulations indicate that policy coordination is key to sustainability efforts
By: Gerard P. Learmonth Sr.
M.B.A., M.S., Ph.D., Associate Professor, University of Virginia
30 七月 2014          

摘要
Preliminary analysis of the Computing for Sustainable Water data shows the importance of broad community-based coordination, so that environmental priorities can be achieved with a minimum of redundant effort. The project has also increased understanding of sustainability practices in other watershed areas.

During the volunteer effort for Computing for Sustainable Water, World Community Grid members returned over 19.1 million calculations. Now that the computing phase of the project is over, our research team has completed the preliminary analysis of these results, indicating the need for a coordinated approach to water quality management.

Our goal was to assess the impact of various programs intended to reduce the flow of nutrients (nitrogen and phosphorous) in the Chesapeake Bay Watershed in the United States. Excessive nutrient flow causes the development of algal blooms which eventually reduce the oxygen levels in the water, making it inhospitable for various life forms. When the level of dissolved oxygen in the water column gets close to 0, the area is termed ‘anoxic’. When the water column is not quite fully deprived of oxygen, the area is termed ‘hypoxic’. In the Chesapeake Bay, low oxygen causes a serious threat to a particular aquatic species - the Chesapeake blue crab - Callinectes sapidus. In other watersheds, comparable species are vulnerable to increased anoxia and hypoxia.

In the Chesapeake Bay Watershed, as in other areas throughout the world, various ’Best Management Practices’ (BMPs) are encouraged by watershed authorities to reduce the runoff of nutrients from agricultural fields as well as populated urban areas. BMPs include such programs as conservation tilling on farms, the planting and maintenance of riparian buffers along waterways, wetland restoration and urban nutrient management. There are typically subsidies available to encourage adoption of these BMPs. A question that intrigued the University of Virginia (UVa) team is whether these BMPs actually produce the reductions in nutrient flow that are expected.

Computing for Sustainable Water set about testing the effectiveness of 23 separate and popular BMPs to answer this question by relying on the help of World Community Grid volunteers. This was no easy task given the size of the Chesapeake Bay Watershed: 64,299 square miles (166,534 km^2) with a population of nearly 17 million people. A simulation model was built to replicate nutrient flow into the Bay in the presence of these BMPs. Each BMP was also modeled at three levels of effectiveness. The results, contained in a recently completed report that has not yet been made public, show that under the idealized condition that each BMP is implemented individually throughout the watershed, many have significant positive impact - that is, they offer real benefits for nutrient flow reduction. However, the more realistic condition of BMPs being used in various combinations showed, somewhat disappointingly, that the reductions in nutrient flow under these more realistic cases did not show significant reductions. The UVa team analyzed these results from a strictly objective perspective. Anecdotally, we believe that the uncoordinated and uneven application of BMPs throughout this vast area is, in fact, not achieving the desired impact. We have not analyzed all 19.1 million results yet but we intend to do so selectively over the next few months.

We do believe, as we speak with policy-makers and government authorities, that we can make a strong case that a more coordinated approach to nutrient management will prove more effective and will save taxpayers considerable expense as compared to implementing BMPs with little or no discernible impact.

As a result of this project, we have moved toward a deeper appreciation of the need to protect our watersheds and their surrounding ecosystems. We have been invited to discuss our project work in Brazil, Australia, the Pearl River Delta in China, Lake Michigan in the US, and now the US coastal areas along the Gulf of Mexico that suffer greatly from the effects of nutrient flow.

We have also moved toward using satellite data to produce land use and land cover maps to identify areas of particular concern. Our first application of these is along the Mississippi River Delta and the Houston/Galveston area of Texas in the US.

We sincerely appreciate the time and effort of the World Community Grid volunteers in making this project successful. We will post the availability of our report and any forthcoming publications.
大意:
WCG的用户一共返回了1910万个Computing for Sustainable Water任务结果。目前计算已经完成了,初步的分析结果也已经出来了。
我们的目标是评估各种试图减少水中营养物质的方法的有效性。当水中的氮磷超标时(富营养化),会引发水藻爆发,最终导致水中溶解氧减少。这样会影响水质,也会对水生生物造成巨大伤害。
在切萨皮克湾分水岭,为了改善谁的富营养化。专家们采取了一系列措施,包括:减少化肥用量,在水路安装缓冲器,恢复湿地,城市污水处理等。弗吉尼亚大学开展这个项目的目的就是研究这些方面的效率。
C4SW项目对23种不同的方法进行了模拟。单个方法都是有一定效果的,但是在同时使用多种时,如何让他们优化组合发挥最大的效用,就是我们的研究目标。不过我们的结果还没分析完。
我们相信,我们的研究结果,会对政府产生积极影响,用最少的钱办最多的事。为纳税人省钱。未来可能用于巴西、澳大利亚、中国珠江三角洲美国密歇根湖以及墨西哥湾的富营养化水体治理。根据卫星数据,我们决定首先在密西西比河和休斯顿进行初步实验研究。

评分

参与人数 1基本分 +30 维基拼图 +50 收起 理由
xx318088 + 30 + 50

查看全部评分

回复

使用道具 举报

发表于 2014-8-12 22:46:05 | 显示全部楼层
Database maintenance: Aug 12, 2014 @ 1500 UTC
12 八月 2014          

摘要
There will be an unplanned BOINC database maintenance on Aug 12, 2014 at 1500 UTC time.

At around 23:00 on Aug 11, our monitoring scripts detected a potential issue with the BOINC database. To prevent any harm, it disabled the transitioner automatically. This has caused members to have results waiting in a state of Pending Validation. As a result of this and to fix the issue, we will need to disable all processes that connect to the BOINC database.

This will disable sending of new work and disable members from uploading results.

We are estimating at this time the change window will take 8 hours. We will keep members posted about the progress here.

Thank you for your patience as we correct this issue.
大意:
2014年8月12日23点开始数据库维护,预计耗时8小时。
12号早上7点左右,监控脚本报告BOINC数据库存在潜在问题,为了防止问题扩大,监控脚本自动锁定了数据库。现在我们需要对数据库进行停机维护。请大家耐心等候。

评分

参与人数 1基本分 +30 维基拼图 +15 收起 理由
xx318088 + 30 + 15

查看全部评分

回复

使用道具 举报

发表于 2014-8-20 10:27:03 | 显示全部楼层
The Clean Energy Project - Phase 2 work unit issues
19 八月 2014          

摘要
Due to validation issues, The Clean Energy Project - Phase 2 work units are not currently being sent out. Beta tests to fix the issue are underway.

Due to validation issues, we have currently stopped sending out new Clean Energy Project - Phase 2 (CEP2) work units until we complete tests with beta work units. Once the CEP2 beta tests show the new work units are working well, we will begin sending out new CEP2 work again.

No action is required by those members participating in the CEP2 project, as the BOINC agent will download new work when it becomes available.

For additional information, please check this forum thread. We will also update this News article when the CEP2 work units are being sent out again.
大意:
由于任务出错,我们暂停了CEP2项目。新任务正在测试中,待问题确认解决后,我们会恢复任务发放。详情见论坛帖子。

评分

参与人数 1基本分 +30 维基拼图 +7 收起 理由
xx318088 + 30 + 7

查看全部评分

回复

使用道具 举报

发表于 2014-8-21 12:17:15 | 显示全部楼层
System Maintenance: Sunday, August 24, 2014 at 01:00 UTC
20 八月 2014         

摘要
Routine system maintenance will be performed on Sunday, August 24th.

World Community Grid will be performing a hardware upgrade as we move to a high performance clustered file system, starting Sunday, August 24, 2014 at 01:00 UTC. The window for this upgrade activity is estimated to be 8 hours, although we anticipate the actual outage time will be less.

During this time, various parts of the website will be unavailable as we perform the hardware upgrade. In addition, volunteer devices may not be able to fetch new research tasks or return completed work for a period of time during this upgrade. No action is required by the members as the BOINC/World Community Grid software application will automatically reconnect to our servers once the upgrade is over.
大意:
周日(8月24日)早9点开始例行系统维护(迁移至高性能文件集群系统),预计最多耗时8小时,届时全站停机。

评分

参与人数 1基本分 +30 维基拼图 +7 收起 理由
xx318088 + 30 + 7

查看全部评分

回复

使用道具 举报

发表于 2014-10-4 21:54:26 | 显示全部楼层
2014-10-02: World Community Grid, Global PC network gives researchers supercomputer power
全球计算机网格赋予研究者强劲的计算力。

An article published in the Toronto Star featured Dr. Igor Jurisica, the lead researcher of the Mapping Cancer Markers project. He discussed the value of the supercomputing power that is provided to researchers through a global network of home and business computers.

MCM项目领导者,Igor Jurisica 博士的一篇文章发表在加拿大《多伦多之星》晚报上。作者讨论了来自全球的家庭及商业计算机所带来的巨大计算力对于研究者的价值。

评分

参与人数 1基本分 +30 维基拼图 +14 收起 理由
xx318088 + 30 + 14

查看全部评分

回复

使用道具 举报

发表于 2014-10-9 09:48:26 | 显示全部楼层
System Maintenance: Sunday, October 12, 2014 at 02:00 UTC
8 十月 2014          

摘要
Routine system maintenance will be performed on Sunday, October 12th.

World Community Grid will be performing routine system maintenance starting Sunday, October 12, 2014 at 02:00 UTC. The window for this maintenance activity is estimated to be 6 hours, although we anticipate the actual outage time will be less.

During this time, various parts of the website will be unavailable as we perform the software upgrades. In addition, volunteer devices may not be able to fetch new research tasks or return completed work for a period of time during this upgrade. No action is required by the members as the BOINC/World Community Grid software application will automatically reconnect to our servers once the upgrade is over.
大意:
10月12日(星期天)10点开始系统例行维护,预计耗时6小时。届时网站下线,bonic间歇性下线。

评分

参与人数 1基本分 +30 维基拼图 +7 收起 理由
xx318088 + 30 + 7

查看全部评分

回复

使用道具 举报

发表于 2014-10-10 10:05:21 | 显示全部楼层
New badges for helping to grow World Community Grid
9 十月 2014         

摘要
To celebrate a decade of scientific discovery, we're launching new badges to recognize volunteers for recruiting friends and family to World Community Grid. Start earning your badges today!


As World Community Grid gears up to celebrate a decade of scientific discovery, we're excited to keep growing our community. Help us get there by inviting your friends to join World Community Grid today!

For the past few weeks, a small group of volunteers has helped us pilot new badges that are awarded for recruiting volunteers to World Community Grid. Thanks to their efforts, this initiative is now ready to roll out worldwide.

To recognize you for your efforts, we're launching 5 new badges for recruiting volunteers to World Community Grid. You only need to recruit 1 friend to earn your first badge:
  Bronze - earned for 1 member recruited
  Silver - earned for 5 members recruited
  Gold - earned for 10 members recruited
  Ruby - earned for 25 members recruited
  Emerald - earned for 25 members recruitedWe hope that some enterprising members will force us to create a diamond-level badge as well!

To start earning badges, share your personal link with friends, family, and anyone else who you think will support the mission of World Community Grid.

Your personal link is available in the “Recruited Volunteers” section of your My Contributions page. You’ll be recognized for anyone who joins using that link and contributes computing power to World Community Grid.

Questions? Check out the Frequently Asked Questions.

As we prepare to start our 10th anniversary celebrations, it’s important to remember the “community” part of World Community Grid. On behalf of the entire World Community Grid team and members everywhere, we say thank you to the volunteers who helped us test, improve and finalize this exciting initiative!

Thank you!
The World Community Grid Team
大意:
World Community Grid‘拉皮条’奖章起售
WCG马上要满10周岁了。为此我没新增了‘拉皮条’奖章。如下:
铜牌——拉1个
银牌——拉5个
金牌——拉10个
红宝石——拉25个
绿宝石——拉25个(译注:肯定是官人调皮,复制粘贴后忘改数量了)
‘拉皮条’方法,在官网My Contributions页面Recruited Volunteers找到你的分享链接,然后发给‘下家’。

评分

参与人数 1基本分 +30 维基拼图 +10 收起 理由
xx318088 + 30 + 10

查看全部评分

回复

使用道具 举报

发表于 2014-10-18 17:24:14 | 显示全部楼层
Project Launch: Uncovering Genome Mysteries
16 十月 2014          

摘要
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 world.

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.

Diver collecting microbial samples from Australian seaweeds for Uncovering Genome Mysteries

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.

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.

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.

Once published, these results should help scientists with the following goals:
Discovering new protein functions and augmenting knowledge about biochemical processes in general
Identifying how organisms interact with each other and the environment
Documenting the current baseline microbial diversity, allowing a better understanding of how microorganisms change under environmental stresses, such as climate change
Understanding and modeling complex microbial systems
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.

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!

To contribute to Uncovering Genome Mysteries, go to your My Projects page and make sure the box for this new project is checked.

Please visit the following pages to learn more:
Uncovering Genome Mysteries project overview
Frequently Asked Questions
大意:
新项目:揭开基因的面纱
为了庆祝10周年,我们开始了新项目,对比数以亿计的自然界基因,帮助科学家发现自然界的超能力。
从发现青霉菌可以杀死细菌,到发现吃泄漏原油的细菌和柳树皮里的阿司匹林。我们知道对自然界越了解,越能改善人们的健康、福利,农业和工业生产。
注:图片为潜水员为UGM项目采集澳大利亚水草。
自基因研究出现以来,我们对自然界的了解以及有了极大的进步。但是仍然还有很多未知生物有待研究。这些研究可能帮我们解决人类社会遇到的急迫问题,比如:抗药病菌、污染和能源短缺。
借助廉价的快速DNA测序技术,我们已经对很多生物进行了测序。我们目前要做的就是对这些数据进行统计,找出DNA和特定功能的对应关系。在UGM项目中,我们需要进行20万亿次比对,以帮助科学家了解我们周围生物的多样性和功能。
项目的主要目标包括:
寻找新的蛋白质功能,扩大对微生物的认知
确定有机体相互之间(以及与环境间)如何互动
为当前微生物的多样性建立基线,更好的了解微生物在环境(如:气候)变化的情况下如何变异
了解并建立负责微生物模型系统
开发新药,寻找新的可再生能源,寻找更有营养的作物,净化环境,建立绿色工业加工模式,等等……
友情提示:为了确保加入UGM项目,你最好去官网确认下是否勾选了它。
回复

使用道具 举报

发表于 2014-10-23 10:12:46 | 显示全部楼层
Get competitive for good with our 10th anniversary challenge  
22 十月 2014          

摘要
As we celebrate a decade of discovery, we’re inviting you to take part in a community-wide competition to introduce new volunteers to World Community Grid.


World Community Grid is 10 years old this November and we’re celebrating everything we’ve achieved together over the last decade, thanks to the help of volunteers like you.

But there’s a lot more work to be done and many more discoveries to make. That’s why, as part of our celebrations, today we’re launching our 10th anniversary challenge.

The challenge is to recruit as many friends as possible to World Community Grid to power another decade of scientific success. Put simply, the more friends you recruit – the higher your chances of becoming a World Community Grid Champion.

And there are some great prizes up for grabs. The three people who recruit the highest number of new volunteers by November 16 will each be profiled on worldcommunitygrid.org in December, win the opportunity to take part in an exclusive "Ask Me Anything" Q&A session with the World Community Grid team - a unique chance for a behind-the-scenes look at the program - and will also receive a special limited-edition World Community Grid prize. The top 20 recruiters will have their names showcased on worldcommunitygrid.org and will alos receive the special limited-edition World Community Grid prize.

Find out more about the competition and start spreading the word today!

Be sure to share your unique recruitment URL (accessible at your My Contributions page) with friends to receive credit for the new volunteers you recruit.

Here’s to another decade of discovery.
大意:
WCG十周年之拉客大赛开启
截止11月16日前三名将有机会把头像放在WCG主页,参加WCG团队的真心话大冒险活动,另有限量版WCG奖品。前20名有限量版WCG奖品。
回复

使用道具 举报

您需要登录后才可以回帖 登录 | 新注册用户

本版积分规则

论坛官方淘宝店开业啦~

Archiver|手机版|小黑屋|中国分布式计算总站 ( 沪ICP备05042587号 )

GMT+8, 2024-4-28 21:05

Powered by Discuz! X3.5

© 2001-2024 Discuz! Team.

快速回复 返回顶部 返回列表