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

vmzy

FightAIDS@Home project research application update for Android

24 三月 2014

摘要
New release of the FightAIDS@Home research application for Android users to address a recent issue causing more invalid results than expected.


We've just released a new version of the FightAIDS@Home research application that runs on Android devices to address a recent issue which caused the number of invalid results to be higher than expected.

No action is required by our members as this update will download automatically.

大意：
发布新版FAAH Android平台计算内核，解决了无效结果过多的bug。
译注：喜大普奔啊，最近Android的无效问题的确严重。任务老是出错的原因已经找到了，后台程序太多，可用内存过低时，才会出错。




Paper published about processing the results from the Nutritious Rice for the World project

24 三月 2014

摘要
A paper about innovations and performance improvements that were used to process the results data from the Nutritious Rice for the World project. The paper was published online on March 17, 2014 in the journal Bioinformatics.


Paper Title:

"fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data"

Lay Person Abstract:

The Nutritious Rice for the World project used World Community Grid to predict the structures of proteins in a number of genomes of rice. This is the first step in understanding the functions of those proteins and how they play a role in better nutrition and resistance to environmental stresses such as drought, pests and disease. The project has been processing the results computed using World Community Grid. To obtain more accurate structure predictions, various methods were used to combine information from groups of similar protein models to identify the most accurate models.
The Nutritious rice for the World project generated sets of protein models that were too large to be clustered into subsets by existing techniques which were too slow and used too much memory. New algorithms were devised that were orders of magnitude faster. The new software also exploits GPUs, multi-core CPUs, and on-chip co-processors to make the structural comparisons faster. The new methods use less memory and result in significantly more accurate structure predictions. The software and code has been made available to be used by protein folding community.
Using the new software, the entire Nutritious Rice for the World dataset was analyzed in 6 weeks.

Technical Abstract:

Motivation: fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project.
Results: fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60× faster than qcprot and 3× faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250× and 2000× faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco.
Availability and implementation: fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license.

Access to Paper:

To view the paper, please click here.

大意：
营养大米项目结果处理方面的论文发表与3月17日《生物信息学》杂志上
营养大米项目通过wcg研究大米的蛋白质，藉此了解这些蛋白质如何让大米更有营养，更具抗性（干旱、病虫害）。为了从wcg得到的结果数据里得到更准确的预测，我们创建了不同的模型来进行比对优化。老的算法很慢而且非常耗内存。为此我们开发了新的软件fast_protein_cluster，不但可以利用GPU、多核cpu以及集成协处理器来进行结构比对，而且内存占用以及速度都得到了大幅提升。
fast_protein_cluster目前已经开源，它使用OpenMP实现多线程cpu，利用OpenCL实现gpu计算。目前cpu平均提速60倍，gpu提速3倍。在传统的k-means和hierarchical计算中，并行算法可以提速250至2000倍。

vmzy

System Maintence: Sunday, April 6th at 1:00 UTC  
2 四月 2014          

摘要
Routine server maintenance will be performed on Sunday, April 6.

World Community Grid will be performing routine server maintenance this weekend starting Sunday, April 6, 2014 at 1:00 UTC.

The window for this update is 10 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 these updates. In addition, volunteer device may not be able to fetch work for a brief period of time during this outage. No action is required by the members as the BOINC/World Community Grid software application will automatically reconnect to our servers once the outage is over.
大意：
4月6日9点开始例行维护，大概10个小时，届时网站瘫痪，boinc偶尔抽风。

vmzy

Addressing issues with volunteers sending results   
8 四月 2014          

摘要
Volunteers may have recently experienced issues sending us their results. We have taken several measures to address this.

Over the weekend and into the week, volunteers may have noticed that the BOINC software application may have struggled to send your results back to World Community Grid. The server on which we upload your results became full, due to an influx of large results coming back from the Mapping Cancer Markers project. To address this, we have taken the following immediate measures:
To give members the ability to send us back their results, we have temporarily suspended sending out any tasks for Mapping Cancer Markers. Once this backlog clears up, we will enable Mapping Cancer Markers again, but run the project at a slower pace until a more long-term solution is found.

We implemented a process which prevents our system from becoming full again by disabling the results upload mechanism when a certain threshold is met. No action is required by our members in this case - once space is cleared up, our system would automatically resume receiving results again.

We have distributed the load for assimilating the results to allow for result files to be off-loaded from our system quicker.

We are investigating several options for resolving this in the longer term, which may include working with the Mapping Cancer Markers researchers to better anticipate and plan for larger research tasks.

We thank you for your patience and will update you once we determine the longer term solutions.
大意：
由于MCM的结果文件太大，老是把服务器空间占满，因此我们降低了MCM项目的优先级。
目前采取了如下措施：
1、暂停了MCM项目。
1、今后我们根据服务器空间状况随时可能暂停MCM项目，待空间足够了再恢复。
2、加快结果文件处理速度。
3、与MCM方讨论长效解决方案。

vmzy

Drug Search for Leishmaniasis project update

By: Dr. Carlos Muskus López
Coordinator, Molecular Biology and Computational Unit, PECET University of Antioquia
15 四月 2014

摘要
A project update from the Drug Search for Leishmaniasis scientists, describing the analysis of the data generated by World Community Grid volunteers.


Dear World Community Grid community,

Since we completed our work on World Community Grid, we have been running a second software program locally, which is searching for the best scoring protein-compound interactions.

The Drug Search for Leishmaniasis (DSFL) project produced files containing data on more than one billion interactions, so the work to search and filter the best docking results will still take some time. Currently, our new software program has searched approximately 85% of the DSFL data and a preliminary analysis of the results have shown interesting results.

As you probably know, Auto-dock Vina, was the program used on World Community Grid to evaluate candidate compounds for anti-Leishmania activity. The main score ranged between 0 and -16, with the more negative being better. In the table below, you can see the top 20 compounds with docking scores around -13, which are very good in terms of predicted interaction. These 20 compounds have been shown to interact well in silico, with three Leishmania proteins with ID's 2WSA, 3MJY and 3POI.

In addition, we are making an effort to get funds to test these and others compounds initially in vitro. We had submitted a proposal to a foundation called "€œOpen Lab",€ but unfortunately, our proposal was not approved for funding. However, we have approval to test between 10 and 20 compounds in vitro using resources of the consortium of the main Colombian funding agency (Colciencias).

Table 1. Details of the top 20 docking interactions with information about the detected compounds, protein targets, and molecular dynamics model of the proteins and their corresponding scores in Kcal/mol.

Score	Compounds	Structure	Model
-13,8	ZINC0583XXXX	3P0I	20
-13,7	ZINC0896XXXX	2WSA	30
-13,5	ZINC1270XXXX	2WSA	30
-13,5	ZINC0956XXXX	2WSA	80
-13,3	ZINC1209XXXX	2WSA	30
-13,3	ZINC1705XXXX	2WSA	30
-13,3	ZINC3312XXXX	3MJY	50
-13,3	ZINC3312XXXX	3MJY	80
-13,2	ZINC0497XXXX	2WSA	30
-13,2	ZINC0922XXXX	2WSA	30
-13,2	ZINC2194XXXX	2WSA	30
-13,2	ZINC2194XXXX	2WSA	30
-13,2	ZINC2214XXXX	2WSA	30
-13,2	ZINC0925XXXX	2WSA	40
-13,2	ZINC0961XXXX	2WSA	80
-13,2	ZINC1215XXXX	2WSA	80
-13,1	ZINC3299XXXX	2WSA	20
-13,1	ZINC0860XXXX	2WSA	30
-13,1	ZINC0891XXXX	2WSA	30
-13,1	ZINC0896XXXX	2WSA	30

Thank you for your support and we will keep you updated on our progress,

Dr. Carlos Muskus López大意：
DSFL的结果文件有10亿多个。我们现在正在分析筛选其中的有效结果。目前已经完成了85%，找到了不少有效结果（分数越低越好，下面有这20个蛋白质的数据列表）。我们准备拿10到20个蛋白质，进行实验室测试。但是目前缺少资金，我们向"€œOpen Lab"申请了资金，但是没批准。接下来我们将继续向哥伦比亚基金协会申请资金。


Live webcast for Nutritious Rice for the World: April 17th, 7:00pm UTC

15 四月 2014

摘要
Join us on April 17th at 3:00pm Eastern (7:00pm UTC) for a live online presentation that will review how our members helped researchers understand the structure of rice proteins. These results could support the development of better food for billions of people worldwide.


Rice supplies 20% of all the calories eaten by humankind. There are thousands of varieties of rice, with considerable ongoing effort toward breeding new varieties with better nutritional content. The motivation is clear: a better strain of rice could improve the lives of billions of people.

However, these breeding efforts are hindered by a gap in scientific knowledge. Scientists know that the rice plant has thousands of proteins - molecules that are essential to nearly every process within living cells. However, the structures and functions of these proteins are mostly unknown. If scientists could understand the structures of rice proteins, they could have a better idea of what these proteins do, and which ones are important for nutritious, hardy rice plants. Plant breeding efforts could then try to target those proteins and develop better strains of rice.

The Nutritious Rice for the World project, which ran on World Community Grid from 2008 to 2010, aimed to use the power of volunteer computing to make predictions about the structures of rice proteins. Since completing their modeling calculations on World Community Grid, the research team has been analyzing the data generated by our volunteers and will present their work on April 17th.

In this research, a team from the University of Washington set out to use the rice genome – its DNA sequence – to predict the structures of the proteins that are created from that DNA template. World Community Grid members contributed over 25,000 years of processing time to simulate over 10 billion possible protein structures in the quest to help researchers determine which structures likely corresponded to a given DNA sequence.

On Thursday's live online presentation, Dr. Ling-Hong Hung will review the goals of the project, explain how members were able to help in those efforts, and give an update about the further analysis they have done on data they received from World Community Grid volunteers. The team was able to publish structural information about thousands of proteins, and advance the field of computational protein modeling. These results – which were only possible because of the massive amount of donated computing power they had available – are expected to guide future research and plant science efforts.

This is a great opportunity to learn about how World Community Grid work can have important consequences for an essential real-world research topic.

Please check your browser capability and join the live webcast on April 17th at 3:00pm Eastern Time (USA) / 7:00pm UTC.
大意：
4月18号凌晨3点，营养大米项目开网络视频会。
在人类输入的能量中大米占了20%，全球有上千种水稻，目前主要采用杂交的方法进行水稻品种改良，以解决粮食危机问题。
杂交的改进速度比较慢。所以项目方在08-10年，利用WCG平台，基于水稻的基因，对水稻的蛋白质结构进行预测，对这些蛋白质的功能进行研究，以期望找到最佳的转基因改良方法，获得更有营养更具抗性的水稻品种。在18号的网络视频会中，项目方将对研究结果进行展示。

vmzy

Replay available: Nutritious Rice for the World project webcast  
24 四月 2014          

摘要
The Nutritious Rice for the World project predicted the structures of key proteins in the rice plant, providing information that can help scientists develop better strains of rice. Watch a replay of last week's webcast in which project researcher, Dr. Hung, discussed the project, the publication of its results, its findings and its significance.


On 17 April, Dr. Ling-Hong Hung of the Nutritious Rice for the World project team led a live online presentation, the first since the computing phase of the project on World Community Grid ended in 2010. Member who joined the webcast heard first-hand about the scope of the project, the results, and the important implications of this work for developing better food crops.

If you missed the webcast, you can read a summary and view the replay below:
http://www.youtube.com/embed/l7KKSBywD5k

Summary of the webcast:

Dr. Hung explained that rice presents a unique challenge to plant scientists. It is the most important single food crop, providing about one-fifth of all the calories consumed by humans. Past plant breeding efforts have produced strains of rice with higher yields and better nutritional content, and it is vital to keep improving this important food resource as the world’s population grows and its climate changes. However, it is slow and difficult work to improve rice further, because most of the basic building blocks of the plant – its proteins – are a mystery. The rice genome encodes about 50,000 proteins, but the structures of these proteins are mostly unknown, so scientists do not know what role each protein plays in the plant. If these roles were known, plant breeding efforts could be better focused and potentially much more successful.

Nutritious Rice for the World used modeling techniques to predict these protein structures based on the genomes of two strains of rice. Volunteers simulated about 100 trillion possible structures, from which the researchers selected the 300,000 best. This represents about 5 possible structures for each gene or set of genes that they studied. The structures are now publicly available for download from two websites maintained by the research team. Now that these structures are available, researchers can compare them to the known structures of other proteins from other organisms and get a better idea of the specific role that each protein plays in the rice plant.

In addition to the huge database of calculated protein structures, the project also improved the computational methods used to simulate the proteins themselves. These improved methods mean that future protein research will be able to deliver much more efficient and accurate results.

This work was only possible due to the massive computing power available from volunteers on World Community Grid. On behalf of Dr. Hung and the entire project team, thank you for helping advance this important research!
大意：
营养大米项目网络视频会回放（需翻墙观看）

vmzy

Computing for Clean Water project update  
By: Dr. Francois Grey
CNMM, Tsinghua University, Beijing, China and Citizen Cyberscience Centre, Geneva, Switzerland
25 四月 2014         

摘要
Researchers announce the end of the project as they complete further studies to confirm interesting results gained from World Community Grid data and prepare to publish their exciting findings.

Over the past six months, we have been doing further analysis of the results we obtained from the Computing for Clean Water project, in order to finalize a manuscript for publication. We've now reached a level of confidence in our findings that we don't believe any further runs on World Community Grid are necessary, which marks the end of the project on World Community Grid. We aim to submit our manuscript in the coming few weeks, once all co-authors have had a chance to review it.

As we've mentioned before, the results we got from Computing for Clean Water were surprising in several ways. Since Computing for Clean Water allows us to effectively extend simulations to a new flow regime that is closer to what happens in real experiments (see the diagram below), we're being very cautious about testing our surprising results in different ways, to make sure that what we see is a genuine effect, and not some unexpected artifact of the way we are doing the calculations.

We'll be able to tell you more about exactly why our results are so surprising once the article has been submitted for publication. At that point, we'll release a so-called electronic preprint, so that colleagues – and you, the Computing for Clean Water volunteers – can see the results, too. For the moment, though, suffice to say that we're very excited about having discovered a new mechanism that could make water filtration by nanotubes much more efficient. This mechanism appears to have been overlooked in previous studies because they did not have the computing power to simulate the flow process in the sort of detail that we can with Computing for Clean Water.

The diagram below succinctly captures the big step forward that Computing for Clean Water enabled us to make in terms of bridging the gap between the (high) flow velocity that prior simulations have managed to study, and the (low) range of flow velocities for which practical experiments on water flow in nanotubes have been carried out.



So you may be wondering, what exactly have we been doing for the last few months, since we stopped running jobs on Computing for Clean Water? Well, the first step, before asking for independent feedback from reviewers, is to have scientists involved in the project directly ask tough questions about the results. To answer those questions we have needed to do further computations, carried out on computing clusters in the UK and in Australia. (Technical aside: these tests represent a much smaller volume of calculations than the Computing for Clean Water project. However, each calculation generates much larger data files than a corresponding Computing for Clean Water task. So doing these tests on a dedicated computing resource makes sense.)

These further computations supported the initial conclusions we drew from analyzing the Computing for Clean Water data. And as mentioned above, this gives us the confidence we needed to move ahead with publishing these findings.

We want to sincerely thank World Community Grid volunteers for supporting our work and for allowing us to extend our simulations to such a realistic level. While our work on World Community Grid comes to an end, our research efforts continue and we look forward to sharing details of our exciting findings and any further developments in the coming months.大意：
清水项目进展
经过6个月的结果研究，清水项目不再需要计算了，决定正式结束项目。准备发表论文。
待论文发表后，我们会公布电子版供大家阅读。我们可以骄傲的说，我们发现了一个新的结构，可以让碳纳米管更高效的滤水，在之前我们都忽略了这个结构。由于c4cw项目的计算结果我们才没有错过它。
最后再次感谢志愿者们的无私奉献。

vmzy

Temporary pause of the Clean Energy Project  
1 五月 2014

摘要
The researchers at Harvard are relocating their servers which requires a temporary pause on any new Clean Energy Project tasks being sent out. Distribution of new tasks will resume automatically once server migration work is complete.

The research team at Harvard are migrating the Clean Energy Project servers to a new facility on Monday, May 5th, 2014. They anticipate to have their servers unavailable for 24 hours during the migration process. To avoid members experiencing a backlog while attempting to send back Clean Energy Project results during that period, we will temporarily pause the project starting Friday May 2nd. This will give you plenty of time to return results before the server outage occurs on Monday. This means that no new tasks will be distributed until Harvard's new servers are available again, which is expected to be on Tuesday, May 6th.

We will update you on the status of the migration by posting updates to this article.
大意：
由于CEP2项目5月5日服务器挪窝，所以项目计划于5月2日暂停（以便你有时间清算囤积的任务），待服务器部署就位后，项目计划于5月6日恢复。

vmzy

Behind the Scenes: The story behind our new look
By: Rodrigo Cardoso
Information Architect, IBM Interactive
6 五月 2014         

摘要
In the first of our 'Behind the Scenes' series, which will give members insight into the workings of World Community Grid, IBM designer Rodrigo Cardoso discusses the motivations and rationale behind the program's new look, including our new logo.


Hello World Community Grid members,

My name is Rodrigo Cardoso and I was the designer for the new World Community Grid logo and website. But I didn’t do it alone. The new logo and website design you see was a team effort and the result of several months of collaboration.

Our directive was to create a fresh look: one that was clean and simple yet bold and exciting. The intention was to come up with an approachable design that would appeal to a broader audience, including volunteers who are less technically inclined.

The color palette you see was borrowed from a portfolio of IBM palettes and expanded upon, reflecting the linkage between IBM and World Community Grid. This color palette is vibrant and extensive, giving us many options to work with to meet the needs of a diverse research portfolio. The two main colors selected to form the logo and the main color elements of the website are a bold orange and cooler blue that provides balance.

As for the logo specifically, we wanted to create a logo that focused on the community-powered scientific research that you support, and less on the technology used to do so. We therefore shifted the attention away from grid computing, and focused on the concept of people coming together, forming a community of volunteers to support researchers. The logo you see today is the result of many rounds of reviews and refinements as part of a design process that started out with 22 initial logo concepts. They all shared elements that symbolized people coming together and forming a community around the globe.

I thought you would like to see some of the logos that didn’t make the cut:


Our chosen logo is a representation of two people embracing, which symbolizes people coming together to form a community and support each other. This can signify both the volunteer community, as well as the volunteer-researcher relationship. In addition, the way the two figures embrace forms a hexagon – a representation of a chemical molecule, thus tying it to the program’s primary focus of supporting scientific research.

We’re excited about the program’s new look and hope you like it too. It’s a significant departure from the program’s previous design, but we felt it important to make a bold statement about what this program stands for, and the bold aspirations we have for it.
大意：
有关新界面和图标。
新界面的色调（深橙色和淡蓝色）与IBM官网保持一致。为了表达出这是个志愿者参与的公众项目，而且减少网格的概念，我们设计了很多图标。
最终我们选择的图标表示的是两个拥抱的人，代表了来自五湖四海的志愿者为了同一个目标聚在了一起。同时它形成了一个代表化学分子的六边形，表示我们是的主要目标是协助科研。
虽然新界面变化非常大，但是我希望大家能喜欢它。


May 7, 2014 @ 03:45 UTC - We have enabled sending new work for The Clean Energy Project - Phase 2. If you are still having issues uploading files, please comment inthis forum. -Uplinger
大意：
CEP2项目恢复发包。

vmzy

System Maintenance: Wednesday, May 21st at 14:00 UTC  
19 五月 2014          

摘要
Routine server maintenance will be performed on Wednesday, May 21st.

World Community Grid will be performing standard system maintenance this week starting Wednesday, May 21, 2014 at 14:00 UTC. The window for this maintenance work is 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 these updates. In addition, volunteer devices may not be able to fetch new research tasks or return completed work for a brief period of time during this outage. No action is required by the members as the BOINC/World Community Grid software application will automatically reconnect to our servers once the outage is over.
大意：
5月21日晚上10点开始例行维护，预计需要8个小时。

vmzy

New ways to visualize progress on your favorite research projects
29 五月 2014          

摘要
We're launching a new timeline feature that showcases project progress and highlights, and new badges for higher levels of contribution.

In the latest of our website improvements, we're rolling out a series of changes including two new ways to track how your contributions advance our research projects.

Visualizing research progress with new project timelines
We've just launched a new project timeline feature to show each project's progress at a glance. On the Research page, you'll see a progress bar for each active project to give you a sense of how much work has been done and how much more work remains. That project's individual pages now also display a detailed timeline highlighting the project's key achievements and milestones. Check out the timelines or learn more at our FAQs.

Recognizing higher levels of contributions with new badges
When World Community Grid first launched, it was hard to believe that members would one day donate years and even decades of computing time. But now, that’s a reality for many of our members. To recognize these extraordinary contributions, we’re unveiling new Diamond badges to celebrate 5, 10, 20, 50 and even 100 years of computing time donated to our research projects.

If you've already donated Diamond badge levels of computing time to a past or current project, the appropriate badge will automatically appear on your My Contributions page and within your My News feed. If you now have one of these new badges, thank you so much for your enormous contribution to world-changing research. And if you don’t have one yet, stay involved in our current projects and it will appear before you know it!
大意：
网站改版。项目页面加项目进度图片。增加了几个新勋章，祝大家刷墙快乐！

vmzy

Clean Energy Project update
By: The Clean Energy Project team
Harvard University
5 六月 2014         

摘要
The team at Harvard provides an update which includes details of how a recent team member addition is changing the way they determine which new molecules to investigate; their ongoing collaborations with other research teams to accelerate their results and calculate electrical conductivity of targeted materials; and upcoming paper publications.


Hello all!

It has come time again for another update on the Clean Energy Project (CEP) Phase 2 on World Community Grid. A lot has been going on in the last several months on all sides of the project. In January we told you about the change over in membership of the CEP team with Johannes moving on to an Assistant Professorship at the University of Bufallo, Sule moving on to an Assistant Professorship in Ankara, Turkey, and the team leadership transitioning to Ed who has joined us from Cambridge, UK.

One of the results of this change-over period was an important re-design of the scripts that we use for generating libraries of new molecules. Ed’s experience with crystal structure prediction was an invaluable asset in this process since his background gave us all more insight into the molecular mechanics calculations that were being used to generate the starting geometries of each molecule.

This overhaul of the library generation then rolled into more work on a new database backend. With the assistance of our software engineer, Kai Trepte, we have been working hard for several months to develop a new NoSQL database using MongoDB, that we believe will have some advantages over the current setup. The preliminary tests have been very promising and we hope to start parsing the raw data that is stored on the jabba disks into this new database in May.

Before we can process the raw data though, we had to move a number of our servers and storage machines to their new home in a secure data center in downtown Boston. The research computing team has done a great job helping us move them to this new location to accommodate the renovations that are being done as a part of Alán’s tenure package.

In research news, Ed and Martin have been working in close collaboration with members of a computer science research group at Harvard (Prof. Ryan Adams) to use techniques from the field of machine learning to try to accelerate the calculations that the CEP runs. This summer we will have two new undergraduate research assistants helping out with this exciting area of research!

Ed has also been working on incorporating some crystal structure prediction calculations into the CEP so that we can study the properties of promising molecules in greater detail. This is a particularly important part of the project moving forward because it is possible to learn a great deal more about a molecule if once we have some idea of how it will pack into a solid material.

Martin’s work with doing calculations on the electrical conductivity of a few targeted materials of interest that have been identified by our collaborators in the Bao group at Stanford and the Sariciftci group in Linz, Austria has been going well and resulted in two publications that are about to be submitted. We’ll post links to those once they have been peer reviewed and are published. Both of these collaborations have been going really well and there are plans in the works for a new molecular library based on compounds that the researchers in Linz think might make particularly good organic transistors and organic solar cells.

We recently submitted a progress report for one of the main grants that funds the CEP research and a final report for the Global Climate and Energy Project grant that came to the end of its lifetime. Hopefully our funding review goes well because we have been working very hard and feel that we are on the cutting edge of the big data/materials screening research.

We want to take a moment to congratulate Laszlo on winning a Fullbright Grant and also on his upcoming graduation from Harvard. We wish him all the best in the future!

As always, we want to thank all of you for all the hard work you put in crunching on this project. Your support is incredible – and we couldn't do it without you!

Your Clean Energy Project Team大意：
CEP项目信息更新
修改了新分子库生成脚本。准备把数据库迁移到MongoDB。新的数据库和分子库，于5月开始内部调试。同时我们给服务器搬家了。
在研究方面，我们打算利用机器学习优化算法。同时合并加入了一些晶体结构算法以获得更多的属性细节。根据已有的结果，我们写了两边论文，待同行评审并发表后，会公开。

vmzy

Better tools for AIDS drug research
24 六月 2014          

摘要
The Scripps research team published a paper proving the effectiveness of a method to more accurately predict bindings between protein targets and drug candidates, which could benefit FightAIDS@Home and other World Community Grid drug discovery projects.

Paper Title:

"Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge"

Lay Person Abstract:

The Olson Lab at The Scripps Institute collaborated to participate in the "SAMPL4 Challenge" which evaluated methods to predict protein target to drug candidate bindings. Olson's lab in cooperation with Levy's lab at Rutgers University were able to prove the utility of a method to reduce false positives and therefore potentially reduce the amount of laboratory work required to validate computational results. This should ultimately be a benefit to research projects such as FightAIDS@Home and other drug search projects on World Community Grid.

Technical Abstract:

To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein–ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new ‘‘Rank Difference Ratio’’ metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAMreplica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4’s very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational structure-based drug discovery tools and strategies that are being developed to advance the goals of the newly created, multi-institution, NIH-funded center called the ‘‘HIV Interaction and Viral Evolution Center’’.

Access to Paper:

To view the paper, please click here.
大意：
Scripps研究所改进了算法，减少了蛋白质变构点结合能的计算误差，提高了结果的有效性。

vmzy

System Maintenance: Sunday, July 6, 2014 at 01:00 UTC
1 七月 2014          

摘要
Routine system maintenance will be performed on Sunday, July 6th.


World Community Grid will be performing standard system maintenance this week starting Sunday, July 6, 2014 at 01:00 UTC. The window for this maintenance work is 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 these updates. In addition, volunteer devices may not be able to fetch new research tasks or return completed work for a brief period of time during this outage. No action is required by the members as the BOINC/World Community Grid software application will automatically reconnect to our servers once the outage is over.

There will be another planned outage to World Community Grid, on Saturday, July12, 2014 at 01:00 UTC, as we will be performing server upgrades. Please stay tuned in for additional information.
大意：
7月6日早9点开始例行维护。
另，初步计划7月12日早9点开始服务器升级，稍后会发布更多相关信息。

vmzy

Advancing and expanding Help Fight Childhood Cancer research
By: Dr. Akira Nakagawara, MD, PhD
President Emeritus, Chiba Cancer Center
2 七月 2014          

摘要
Dr. Nakagawara, the lead researcher for Help Fight Childhood Cancer, provides an update on his continued efforts to advance his neuroblastoma drug candidate discovery, his transition to a new role and his hopes for expanding his research on World Community Grid to other pediatric cancers.

I recently accepted a position as CEO of the Saga Medical Center KOSEIKAN, located at Saga City on the island of Kyushu, Japan. The Saga prefecture is my home region, and Saga's governor asked me to come back to manage the region's biggest general hospital. A new research institute is being set up within the hospital, which will be affiliated with Kyushu and Saga universities in the near future.

My association with the Chiba Cancer Center will continue - I am now President Emeritus and will keep my research position at Chiba's research institute as an official councilor. The collaboration between the Chiba Cancer Center Research Institute and Chiba University will also continue. In this capacity, I aim to build on the success of the first phase of Help Fight Childhood Cancer (the discovery of several drug candidates which in lab testing killed cancer cells, with no apparent side effects). While we will be closing out this phase of the project on World Community Grid, we will continue our efforts to seek pharmaceutical collaborations to advance these promising drug candidates through the drug development process.

I also plan to expand our research. We have started planning for a second phase to the project, possibly in collaboration with a newly formed pan-Asian oncology group, of which we are a founding member. While Phase I of Help Fight Childhood Cancer focused on neuroblastoma, we hope to expand the scope of Phase II to cover multiple pediatric cancers. We are in early discussions to define the scope of Phase II and look forward to working with our oncology collaborators and with the World Community Grid team to bring this project to World Community Grid volunteers.

We are so grateful of the support of World Community Grid volunteers and the role you've played in powering our Phase I research. We hope we can count on your continued support and participation as we prepare for Phase II.
大意：
HFCC项目进展。
负责人Nakagawara已调至佐贺县医疗中心当院长了。不过仍然担任千叶癌症研究中心的名誉主席。
1期项目已结束，目前发现的几种候选药物正在实验室进行抗癌性能测试（暂未发现有毒副作用）。我们希望将来能找到合作药厂进行进一步研究和药物生产。
我们计划与乏亚洲肿瘤组织合作开展二期研究，1期我们主要研究的是神经母细胞瘤，2期我们打算研究多种儿科癌症。目前我们还在寻找合作伙伴，商定研究范围阶段。
再次感谢大家在1期项目中所做出的贡献，让我们一起期待2期的来临吧。

vmzy

System Maintenance: Saturday, July 12, 2014 at 01:00 UTC  
9 七月 2014          

摘要
Routine system maintenance will be performed on Saturday, July 12th.

World Community Grid will be performing a hardware upgrade as we move to a high performance clustered file system, starting Saturday, July 12, 2014 at 01:00 UTC. The window for this upgrade activity is estimated to be between 16 to 20 hours, although we anticipate the actual 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：
7月12日早9点开始系统例行维护。升级硬件，并转至高性能集群文件系统。预计耗时16-20小时。届时全部功能停机。请大家提前做好屯粮准备。