WCGrid News and Talking Points!!

[Arjai]

Well, some dismaying news. One of my favorite bosses, laidback, friendly and of an even demeaner with a good sense of humor, was fired. Of course, the guy who fired him did not have a plan in place. He's a dweeb.

Upshot? I am attending school, leave at 6:28 am, then work until close, 7pm, if lucky, and get home after eight, often 8:30. Since the firing of my boss, I lost my Thursday off. I now only get Sundays. A lot to do in one day a week, including resting! So, my post's will be a little erratic for a few weeks as they find and replace my boss and then have to deal with the inevitable new Sheriff rules and scheduling! There are so few obvious changes that could make this job worth doing happily. I won't get into it, rather I will use the little time I now have, on Holiday from School, not work, to update the News!! Stay tuned...

 

[Arjai]

The Importance of Protein Social Behavior

13 Feb 2017

Summary

Which proteins are most likely to interact with other proteins, and how might these interactions affect disease, and life itself? Results from data computed by World Community Grid are being used to help create a protein sociability index, which could help future advances in biology and medicine.

Dr. Alessandra Carbone, the principal investigator for the Help Cure Muscular Dystrophy project, recently co-authored a paper that addresses one of the fundamental questions about protein-protein interaction. Using data from the project, which ran in two phases on World Community Grid, researchers devised a method to determine which proteins are most likely to interact with other proteins. Dr. Carbone says, "The idea can be summarized as 'tell me if a protein is sociable, and I will tell you who its friends are.'”

I have never met Dr. Carbone. I am sure, I would fall deeply in love with her. I should probably avoid meeting her.

​

How different proteins interact with each other is important to understanding life and disease processes. The first steps of identifying protein interactions include computationally searching for complementary surfaces among the collection of proteins, because those are more likely to interact, as was done using World Community Grid for the Help Cure Muscular Dystrophy project.

However, some proteins tend to evaluate as sticking to many proteins, hiding their true interactions. Dr. Carbone and her co-investigators found an algorithm to improve the accuracy of identifying true protein interactions using a sociability factor to compensate for the apparent "stickiness" of some proteins.

​

...Sociability is proved to be more discriminative than geometrical shape of interacting surfaces. This work brings to light new avenues of investigation on protein interaction principles which could become fundamental to solving this difficult computational problem of high interest for biology and medicine.

Thank you to all World Community Grid volunteers who contributed to the Help Cure Muscular Dystrophy project!

"Sociability is proved to be more discriminative than geometrical shape of interacting surfaces." Imagine THAT! Even Proteins are Social!!

Technical abstract:

Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico-chemical and geometrical properties determine who interact with whom remains far from fully understood.

More article and tech abstract and perhaps more "physico-chemical," talk! ...HERE!


​

 

[twilyth]

Just as an aside to this, many proteins are intrinsically disordered. IOW, they don't have a fixed 3 dimensional structure. They change shape depending on the environment and the molecules they encounter. Other proteins are partially disordered so that they have certain regions with a fixed structure but other regions that are fluid. This is something that has only been realized in recent years (since about 2001) and researchers are only beginning to get a handle on.

https://en.wikipedia.org/wiki/Intrinsically_disordered_proteins

 

[Arjai]

Well, imagine my surprise! One, our fearless leader has returned! Hip, Hip, Hooray! @Norton is back to guide us!!

The second big Surprise? No alerts from WCG in the BOINC Mgr. Me has a sad. One of the things I look forward to, on my single day off (soon to change back to two days, essentially I am getting my Thu. night's back!), is to hit up my favorite coffee shop and post up to update this thread.

Also, @twilyth , Thanks! I always enjoy your pearls of knowledge! I am unsure where you find this stuff but, 9 out 10, you amaze me and make me think! I believe one of the benefits of IQ is admiring different types and flavors of knowledge.

Anyway, I hope everyone is doing well. I am going to enjoy my late breakfast and cruise around here for a bit.

See you all, next time I have time!

 

[twilyth]

Thanks for the kind words. I try to read as much as I can about science and technology and have a particular interest in molecular biology. The exact mechanisms behind how we function as living machines has always been fascinating to me. I'm glad you find these things interesting too. It's nice to be involved with a group of people who are contributing to the advancement of knowledge in these sorts of areas.

 

[Arjai]

Hmmm, 2 weeks of silence from WCG...I wonder what is in the works! If it is taking this long to produce, could be a doozy! Or, could be they are just stuck in the doldrums of working hard on the new project and have no time to set aside informing us of all the greatness we do!!

That's fine. We need their work as they need ours. I am content with that, although it does make this thread a bit of a bore.

I will continue to keep my eyes open, at least once a week, to any new postings on WCG. Thanks everyone for the Thanks and the visits to this thread. Makes me feel good.

Take Care everyone!

 

[Arjai]

Well, still nothing from WCG. So, just a "Hello!" and I hope everyone is doing well!

On a personal note, I should hit 1.8 Million BOINC points, soon! Despite not having anything but my Lappy-Top Crunching! The little i5 that could!

Take Care Team TPU!!

 

[Arjai]

Well, Looky here! WCG must have heard my moaning!!

Meet a World Community Grid Team Member: Al Seippel

14 Mar 2017

Summary
This team member was an experienced coder by the time he was in his teens, and began working for IBM while still in college. Meet Al Seippel in this article.

Al Seippel may have been destined for a career in computer science from a very young age. He was born and raised in Austin, Texas, where his father worked for IBM. "I definitely grew up around computers and always found them interesting," says Al." We had an original IBM PC, with the 8088 processor. And I began to learn how to get around in DOS in order to get early video games running."

During high school, Al worked at a movie theater, where one of his co-workers was a fellow high school student who later became his wife. Two years into college, Al began working at IBM's AIX Support Center where he solved customer problems related to IBM's AIX operating system. (AIX is an open operating system similar to UNIX that was created by IBM.) Just as he had done as a child while learning about basic programming, Al studied as much as he could at night to learn more about the technology he was supporting at IBM.

Al completed a computer science degree at Baker College, and eventually transferred to IBM's Electronic Tools Support Team, where he helped manage the Software Service Request tool which was used to report software issues. While there, he helped to consolidate the suite of software problem reporting tools into one tool, to simplify the customer experience.

During this time, he heard about World Community Grid and became a volunteer. He also met Jonathan Armstrong, Viktors Berstis, and Keith Uplinger, who were already part of the World Community Grid development team. When a development position opened up within World Community Grid, he applied and became the newest team member in 2010. Currently, Al is responsible for managing the work unit build processes, creating project screen savers, and modifying science applications to run on World Community Grid. He also helps handle eblasts and website updates.

Thanks, Al!!

Al with one of his children, passing his computer skills along
to the next generation.
​

As a husband and father of two young children, Al's life outside of work revolves around his family. He is deeply involved in helping revamp the technology at his son’s school. He's also passionate about the work of

World Community Grid. “Since I’ve joined the team, I’ve lost two family members to breast cancer," Al says. "Like many volunteers, this is very personal for me. It's very important to me that my work is connected to something that helps others, and promotes progress that can benefit everyone in the future."

Thanks, AGAIN, Al!!

The Full Article, HERE!

 

[Arjai]

Findings from Nutritious Rice for the World Project Made Public

By: Dr. Ling-Hong Hung
University of Washington

8 Mar 2017

Summary
The data from the Nutritious Rice for the World project is now available on a web server built by the researchers, and they recently published a short paper about their findings.

The findings of the Nutritious Rice for the World project were recently published in an open access paper, making them available to the public and any researchers who wish to use the information for their own work.

We have described our work in a short paper that has been posted to Cold Spring Harbor Laboratory's BiorXiv pre-print server. Researchers can now read about how the Nutritious Rice for the World project’s rice structures were generated and the best models chosen. The paper also describes the web server which allows scientists to find a particular protein of interest and download the structures. The formats and query procedure are described in detail to facilitate the use of the server and the protein structures. The entire dataset can also be downloaded upon request.

Depending on the usage and response, we may submit the paper for publication in a more formal journal. However, publishing this paper officially concludes the project. We thank the members of World Community Grid for donating their time to the Nutritious Rice for the World project. It has been an honor to participate in this project and have support from so many volunteers.

More, HERE!

Awesome work!! I love how our work is always made public for others to use and hopefully benefit from!

 

[Arjai]

Help Stop TB Team Selects Data Analysis Tools

By: The Help Stop TB Team
University of Nottingham

28 Feb 2017

Spoiler

"Hello everyone, and thank you for contributing your computer time to Help Stop TB! We would have never completed so many simulations if it wasn’t for you!"

Summary
The Help Stop TB team is hard at work analyzing the data they’ve received so far from World Community Grid. They recently chose two new data analysis tools, which will help them better understand the behavior of the bacterium which causes tuberculosis.

Background

Help Stop TB was created to examine a particular aspect of the highly resistant and adaptable bacterium that causes tuberculosis. The bacterium has an unusual coat which protects it from many drugs and the patient's immune system. Among the fats, sugars and proteins in this coat, the TB bacterium contains a type of fatty molecules called mycolic acids. Our project simulates the behavior of these molecules in their many configurations to better understand how they offer protection to the TB bacteria. With the resulting information, scientists may be able to design better ways to attack this protective layer and therefore develop better treatments for this deadly disease.

Choosing Data Analysis Tools and Methods

Since our previous mini update in November, Athina has been focusing on analysing our simulation data, and at the same time she is writing up her PhD thesis. As a team, we have now achieved our main goal, which was to come up with a robust and efficient analytical strategy. This will enable us to efficiently process the heaps of data we’re receiving from the simulations conducted by World Community Grid volunteers, and will answer our questions about mycolic acids’ conformational behaviour and its biological implications.

I left a lot out of this section. If this interests YOU, the full article is linked at the bottom of this post.

Figures 1 and 2 below are examples of how we are looking at the shapes of mycolic acids. These structures are important as we are looking at all the possible conformations that mycolic acids can assume in order to try to understand how those molecules work, how their conformations dictate any biological implications and/or affect the disease itself, in the hope to find any links and discover more for prevention methods.

​

Additionally, the length of time that the molecules choose to remain in a certain adopted conformational pattern may also elucidate further biological implications. Each molecule assumes different shapes throughout its folding pathway and these shapes can be very dependent to each other. From the PCA clustering tool data, we have extracted important information regarding the dependency (Figure 1) between the different shapes the molecules assume.

Another analytical approach that we employed was the distance matrix analysis. We created and analysed matrices (Figure 2) of the distances of all the carbon atoms along the mycolic acid chain. This method can provide further insight into the frequency of the folding events and can also help us understand more about the flexibility of each structure.

​

That was all our news for now! Thank you again for your contributions, and let’s all wish good luck to Athina with her writing! Until the next time, happy crunching!

Wow, I must be a bit Brain Dead!! I couldn't muster the concentration to take all that in. So, These are some excerpts, from the article, that I had some understanding. The rest, HERE! And there is a lot more to take in!!

BTW, Good Luck Athina with the paper!!

Thanks to all of you for the Crunching Powerhouse TPU is!! Crunch ON!!

 

[Arjai]

OK, something to report!! Looks like they were sitting on these for a bit!! Good fortune was, I was about to pack it up, leave the Coffee Shop, and go home for a bit. I decided to do some updates on my software, every week there is something, especially the malware and antivirus, and such.

Let's hope Al keeps on his toes and doesn't throw updates out in bundles like this!! Keep them steady Bud!!

Take Care and Crunch ON!! TPU is King!!

 

[Arjai]

OpenZika Researchers Continue Calculations and Prepare for Next Stage

By: The OpenZika research team

21 Mar 2017

Summary
The OpenZika researchers are continuing to screen millions of chemical compounds as they look for potential treatments for the Zika virus. In this update, they report on the status of their calculations and their continuing work to spread the word about the project.

Project Background

While the Zika virus may not be getting the continuous press coverage that it received in 2015 and 2016, it is still a threat to the health of people across the globe. New infections continue to be reported in both South America and North America, and medical workers are just beginning to assess the effects of the virus on young children whose mothers were infected while pregnant.

The search for effective treatments is crucial to stemming the tide of the virus. In addition to the OpenZika project, several other labs are doing cell-based screens with drugs already approved by the US Food and Drug Administration (FDA) agency, but few to none of the “hit” compounds that have been identified thus far are both potent enough against Zika virus and also safe for pregnant women.

Also, there are a number of efforts underway to develop a vaccine against the Zika virus. However, vaccines do not help people who already have the infection. It will be several years before they are proven effective and safe, and before enough doses can be mass produced and distributed. And even after approved vaccines are available and distributed to the public, not all people will be vaccinated. Consequently, in the meantime and in the future, cures for Zika infections are needed.

Progress on choosing compounds for lab testing

We began the analysis phase of the project by focusing on the results against the apo NS3 helicase crystal structure (apo means that the protein was not bound to anything else, such as a cofactor, inhibitor, or nucleic acid) to select our first set of candidates, which are currently being assayed by our collaborator at University of California San Diego, Dr. Jair L. Siqueira-Neto, using cell-based assays. The NS3 helicase is a component of the Zika virus that is required for it to replicate itself.

In the second set of screening results that we recently examined, we used the new crystal structure of NS3 helicase bound to RNA as the target (see the images / animation above). Similar to the first set of candidates, we docked approximately 7,600 compounds in a composite library composed of the US Food and Drug Administration-approved drugs, the drugs approved in the European Union, and the US National Institutes of Health clinical collection library against the new RNA-bound structure of the helicase. Below are the results of this second screening:

• 232 compounds passed the larger collection of different energetic and interaction-based docking filters, and their predicted binding modes were inspected and measured in detail.
• Of the compounds that were inspected in detail, 19 unique compounds passed this visual inspection stage of their docked modes.
• From the compounds that passed the visual inspection, 9 passed subsequent medicinal chemistry-based inspection and will be ordered soon.

Um, Awesome! No?

Status of the calculations

In total, we have submitted 2.56 billion docking jobs, which involved the virtual screening of 6 million compounds versus 427 different target sites. We have already received approximately 1.9 billion of these results on our server. (There is some lag time between when the calculations are performed on your volunteered machines and when we get the results, since all of the results per “package” of approximately 10,000 different docking jobs need to be returned to World Community Grid, re-organized, and then compressed before sending them to our server.)

Except for a few stragglers, we have received all of the results for our experiments that involve docking 6 million compounds versus the proteins NS1, NS3 helicase (both the RNA binding site and the ATP site), and NS5 (both the RNA polymerase and the methyltransferase domains). We are currently receiving the results from our most recent experiments against the NS2B / NS3 protease.

A new stage of the project

Publications and Collaborations

Additional News

Fundraising

​

You can get Open Zika Merch, like that shirt and more (mousepads, anyone?) at their store page, HERE.
https://www.zazzle.com/openzika+gifts
Outreach

All those Headings, and more info, is available at the WCG Site, HERE.

Also, a link to the Video (of the NS3 Helicase), HERE.
https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=518

We are very grateful for all of the volunteers who are donating their unused computing time to this project! Thank you very much!!

THANK YOU!!!! Awesome work Team TPU AND Open Zika!

 

[Arjai]

Clean Energy Project Researchers Sharing Results and
Planning for the Future

By: The Clean Energy Project team
Harvard University

28 Mar 2017

Summary
The Clean Energy Project team is working on publicizing their results to-date. They have wrapped up the second phase of the project, and are also making decisions about their future work with World Community Grid.

The Clean Energy Project research team at Harvard would like to thank the volunteers who supported us through two phases of the project! Currently, we are getting ready to share our findings in at least one publication and a conference. We are also weighing different options for further work with World Community Grid, which might include new types of calculations on solar cells or perhaps a study with a much larger scope.

Publishing Our Results
We have completed our screening of non-fullerene acceptor materials for new organic photovoltaic devices. The findings were quite interesting and have kept us very busy! We describe our results in a manuscript that was submitted to the high-impact journal Energy & Environmental Science.

Steven Lopez will travel to San Francisco to present this work at the American Chemical Society national meeting in April 2017. Alán has presented the results of the Clean Energy Project in several forums and they have helped inform the screening for other materials, such as organic flow batteries, in his research group.

Future Work with World Community Grid
We have not been able to submit work units for volunteer calculation because we had been working to expand the number of molecules we will test by using a low-cost computational method to evaluate the properties of potential photovoltaic materials. With our efficient calibration scheme, this would allow us to screen 10-100 times as many candidates in the same amount of time. If this process can be fully optimized, we could begin generating these work units for volunteers. Benjamin Sanchez-Lengeling has pushed this aspect of the project forward; keep an eye on this rising star!

However, it is also possible that we may go in a different direction altogether. Another idea we are considering is to use these efficient computational methods to catalog the properties of molecules that benefit humanity and have applications beyond clean energy. Molecular Space is vast and full of useful molecules for the world.

We appreciate everyone’s patience while we take stock of the resources and personnel available in our lab, and make decisions about the best scientific use of the generous donations of computing time provided by World Community Grid volunteers.

Thanks again to everyone for your support of this project over the years,

Alán Aspuru-Guzik and Steven Lopez
On Behalf of the CEP Team

More about this News Item, HERE!

 

[Arjai]

Mapping Cancer Markers Team Analyzes Lung Cancer Data

By: The Mapping Cancer Markers research team

6 Apr 2017

Summary
In this project update, the Mapping Cancer Markers team describes how they are analyzing 45 million of the most promising lung cancer data results, and how they have begun to disseminate their early findings.

The Mapping Cancer Markers (MCM) project continues to process work units for the Ovarian Cancer dataset. As we accumulate these results, we continue to analyze MCM results from the previous Lung Cancer dataset. Below, we discuss one direction in which we are pursuing the analysis.

Patterns of gene-family signatures in lung cancer
In cancer, and human biology in general, multiple biomarkers (genes, proteins, microRNAs, etc.) can have similar patterns of activity. This may be because the genes serve redundant roles, or because the genes (or other molecules) participate together in a group to serve a biological function. A cancer signature composed of a set of specific genes may appear different than another signature composed of different, specific genes, and yet perform equivalently because the genes in each are functionally related. With this problem in mind, post-doctorate fellow Anne-Christin Hauschild is leading a study of frequently-occurring patterns (or motifs) of genes present in high-performing lung cancer gene signatures.

This project looked at the first phase results from the Lung Cancer MCM analysis, which was a systematic exploration of the entire space of potential fixed-length signatures. We began by selecting 45 million high-performing signatures derived from World-Community-Grid-computed MCM results. These are the signatures evaluated to carry the most information for lung cancer diagnosis.

Next, we divided all genes in the lung cancer dataset into 180 clusters (gene families), where genes in each family show similar activity in the lung cancer dataset.

To help understand the gene-families themselves, we can visualize each one with word clouds that describe the functions of the genes they contain, or the biological pathways they represent. We draw this information from databases such as Gene Ontology, pathDIP, or other sources.

From there, we looked for patterns in these gene-family signatures: which families appear unusually frequently (or rarely) in high-performing signatures, or families that tend to appear multiple times in the same signature.

Early project results presented at Personalizing Cancer Medicine 2017
We presented the preliminary results of this project to Canadian and international cancer researchers this February, in a poster at the Personalizing Cancer Medicine Conference 2017 in Toronto, Ontario. We gained many insights and ideas from discussing this early work, and we continue developing them further.

Thank you to members
This work would not be possible without the participation of World Community Grid Members. Thank you for generously contributing CPU cycles, and for your interest in this and other World Community Grid projects.

If this interests you, there is a BUNCH more in this article. I truncated it due to not wanting a two page post!!

Find more, HERE!

 

[Arjai]

World Community Grid Moves to IBM Cloud

24 Apr 2017

Summary
On May 15, World Community Grid will begin migrating to IBM Cloud, as part of an effort to modernize and enhance our infrastructure capabilities. Our system will be unavailable for approximately 48 hours while the migration takes place, but otherwise the move will not affect most volunteers.

We're happy to announce that World Community Grid is moving to IBM Cloud. Through this migration, we are leveraging more scalable and powerful hosting capabilities, as well as IBM and open source automation tools that make our development and deployment processes more efficient. This allows us to identify, diagnose and address major technical issues more quickly. Most significantly, IBM Cloud's global footprint of more than 50 data centers across 19 countries allows us to expand more easily and prepares us for years of growth.

The migration will begin on May 15 and is expected to last approximately 48 hours, during which World Community Grid will be unavailable. This means that volunteers will not be able to access the website, fetch new research or return completed work during that time.

No action is required by most volunteers, as our systems will resume sending and receiving research tasks once the migration is complete. However, for individuals or organizations who have restricted firewall rules, you may need to update those rules in order to continue contributing, by allowing connections to our new IP address (169.47.63.74).

Anyone with questions about this migration can post in this forum thread. We appreciate everyone's support during this migration, which will provide a modern hosting environment for volunteers and researchers for years to come.


I certainly hope this did not cause any problems!!

 

[Arjai]

“It’s not just big data. It’s for the good of humanity.”

27 Apr 2017

Summary
Three co-workers wanted their company to support World Community Grid, but they knew they’d need to convince many people to make their vision a reality. Here’s how they did it.

This, folks, is a great story!

It is all right HERE.

Spoiler: The best part!

Plans for the Future

The team is working on internal marketing efforts to continue to spread the word within SILCA, such as working with their communications team to put a World Community Grid widget on SILCA’s intranet site.

The team would like to extend the project to other groups within Crédit Agricole. “SILCA is just one subsidiary of Crédit Agricole,” says David. “We are presenting the results of our project to other groups, and it would be a great victory if others would join.”

 

[Arjai]

FightAIDS@Home Targeting a Key HIV Protein

By: The FightAIDS@Home research team

15 Jun 2017

Summary
FightAIDS@Home researchers restarted the first phase of the project at the end of 2016, and in just a few months, they have completed approximately 46 percent of their projected work on World Community Grid. Read about their progress on finding compounds that could stop HIV from replicating.

Background

FightAIDS@Home is searching for possible compounds to target the protein shell of HIV (called a capsid), which protects the virus. Currently, there are no approved drugs that target this protein shell.

The virtual docking techniques used in Phase 1 are an approximation of the potential effectiveness of promising compounds. Phase 2 of FightAIDS@Home uses a different simulation method to double-check and further refine the virtual screening results that are generated in Phase 1.

The research team is examining a library of approximately 1.6 million commercially available compounds to find promising treatment prospects. The team estimates that they will need to carry out roughly 621 million docking computations on World Community Grid to thoroughly test each potential compound. With the help of many volunteers who are supporting this project, they’ve already completed 46 percent of their goal.

You can keep up with the research team’s progress on their website, which includes frequent updates on their experiments and progress.

Please read below for a detailed look at the technical aspects of their recent work.

Insilico search for novel drugs targeting the HIV-1 mature capsid protein

The importance of the capsid protein

The capsid protein (CA) plays crucial roles in the HIV replication cycle1. After viral and host cell membrane fusion, the capsid core is released into the cytoplasm. This core, which corresponds to the assembly of ~1200 capsid proteins, contains and protects viral RNA and proteins from degradation. (edited)

To date, no drugs targeting CA are approved for clinical use. With the goal of identifying novel active molecules which destabilize the capsid core, we set up a high throughput virtual screening (VS) campaign in collaboration with World Community Grid as part of the FightAIDS@Home (FA@H) project.

Figure 1: PDB 4xfx, the hexamer structure of the native HIV-1 mature capsid protein. (Credit: Pierrick Craveur)
​

Targeted structures

The main target of the docking calculations was the recently solved structure of the CA hexameric assembly2. Four pockets of interest were selected at the surface of the hexamer in order to perform focused dockings, mainly at the CA-CA dimer interfaces.

Structural variability surrounding these pockets was analyzed by comparing this X-ray structure from the PDB (4xfx, see Figure 1), and the two full capsid core models assembled by Schulten's lab3(3j3q and 3j3y, see Figure 2).

Figure 2: The 2 models of the capsid core assembly. (Credit: Pierrick Craveur)​

Based on that, 36 different conformations were selected as targets for the VS, including the X-ray structure and structures from the models. Each target was set as full rigid and also with a specific combination of residue side chains defined as flexible.

An extended library of ~1.6 million commercially available compounds was used for the screening. Replicate computations were performed for each docking experiment in order to assess the consistency of the results. In total ~621 million docking computations will be performed on World Community Grid.

For the time being, ~46% of the computation is completed, with an ending date estimated at the end of 2017 if the computation does not increase in speed.

However, in one month we will be able to propose to our collaborators from the HIVE Center a selection of compounds (focusing one of the four pockets) for experimental binding and infectivity assays.

Progress being made! Because of what YOU do every day and many of you do more than their share! It is things like this that make me Proud to be a Cruncher! It was this site that got me going, with a Socket A computer! Time flies but, it can be marked by the innovation and discovery that our power bills provide! LOL!



OK! For more, go HERE!

 

[Arjai]

https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=527

Unplanned outage effecting their storage servers. The IT team is working on it. Link is to the WCG site and on that page is a link to the forum thread about it. There is currently 8 pages of people bitching, go ahead and add to it!

 

[Arjai]

Help Cure Muscular Dystrophy Lead Researcher Releases Two New Open Data Tools

29 Jun 2017

Summary
In this letter to volunteers, Dr. Alessandra Carbone, the principal investigator for the Help Cure Muscular Dystrophy project, announces the release of two new open access tools which can accelerate the work of researchers who investigate protein interactions.

Alessandra Carbone...I love that name, and this woman. She has done it again, Sharing and creating awesomeness!

​

Dear volunteers for the Help Cure Muscular Dystrophy (Phase 2) project,

I am writing to update you on the analysis of the dataset of docking conformations produced by the Help Cure Muscular Dystrophy (HCMD2) project. The project’s goal was to investigate protein-protein interactions for more than 2,200 proteins whose structures are known, with a particular focus on those proteins that play a role in neuromuscular diseases.

The complete cross-docking dataset containing these protein-protein interactions is under analysis. For this, we are using the various computational tools that we developed in parallel with the calculations run on World Community Grid.

JET2 Viewer: A Repository of Protein Interfaces

We have built a database of protein interfaces for the scientific community. This database, called JET2, is a milestone for the identification of protein partners.

We are now concentrating on extracting useful information relating to muscular dystrophy from the JET2 dataset that your support helped to construct.

BIS2Analyzer: A Server to Help Our Data Analysis

We have released a server, called BIS2Analyzer, to help identify signals of interaction based on coevolution analysis within proteins or between protein partners. This server, which is also openly accessible to the scientific community, is important because it can help to identify signals of protein interaction. It was useful to reconstruct the first protein-protein interaction network for viruses (see the reference below on the reconstruction of the network for the Hepatitis C Virus).

Thanking you again strongly for your contributions. I shall keep you updated on our results. Be assured that we are making progress, thanks to your support!

Best regards,

Alessandra

Thank YOU (!!) Alessandra!



P.S. Dr. Alessandra Carbone named "Woman Scientist of the Year"

P.P.S I found a picture, and a recording of her at a 2014 lecture on HCMD.

Her web page, listing all her Awards.

I have finally found her online. I did some searching, some time ago, and had some difficulty locating the Dr. This time, I found it. She is a remarkable woman in Science, a Mathematician and Italian. Um, Yea, just woke up from a wonderful fantasy. I think those three things add up to what I consider a Perfect woman, or some semblance of one! (in my mind)

Hearing her speak is mesmerizing, I need to turn it off. It is a well done speech, about WCG and HCMD.

Oh, The rest of the article on the WCG site...Much more good stuff there.



https://www.researchitaly.it/en/news/legion-of-honour-to-the-italian-alessandra-carbone/

This is a VERY good Beer, BTW.

**** post those pics in the thread manofthem linked ****

​

 

[manofthem]

Her web page, listing all her Awards.

I listened to the whole thing, but man I didn't understand 99% of it But thanks for sharing!

This is a VERY good Beer, BTW.

I'd recommend posting these goodies over in this thread so as to enhance the discussion

 

[Silvertigo]

Smoking in Oz eh.

http://www.abc.net.au/news/2017-07-...ter-punching-out-data-for-researchers/8687104

 

[Arjai]

Supercharging Environmental and Climate Change Research

10 Jul 2017

Summary
IBM invites scientists to apply for grants of supercomputing power through World Community Grid, meteorological data from The Weather Company, and IBM Cloud storage to support their environmental and climate change research projects.

more here...https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=529

 

[Arjai]

Short Planned Outage for Tuesday, July 18

17 Jul 2017

Summary
We will be performing some maintenance which will result in volunteers being temporarily unable to access the website or download new work at 14:00 UTC on Tuesday, July 18.

We will be temporarily disabling the ability for World Community Grid volunteers to access the website and download/upload results at 14:00 UTC on Tuesday, July 18. The window for this outage is 6 hours; however, we estimate that the interruption to volunteer-related functions will last for approximately 30 minutes.

The Whole Story...

Hope this isn't an inconvenience!! LOL. Thanks WCG for announcing something that most of us won't notice. I suppose transparency, is to blame.

 

[Arjai]

Planned Update to World Community Grid's Security Certificates

24 Jul 2017

Summary
We will be updating our security certificates on Tuesday, July 25 at 19:00 UTC.

Update: Our security certificates have now been updated.

Date of outage: Tuesday, July 25, 2017

Reason for outage: Secure Sockets Layer (SSL) certificates are used to encrypt communications between volunteers' web browsers and our servers, and between the software client and our servers. SSL certificates must be renewed periodically, and we are therefore updating our current certificates.

I was out of town, on Holiday, this past week. I am sure this went well, as I had no problems while I was gone.

 

[Arjai]

New Lab at Tsinghua University Created to Work on Computing for Clean Water Project Findings

By: The Computing for Clean Water team
Tsinghua University

25 Jul 2017

Summary
Dr. Ming Ma, one of the original members of the Computing for Clean Water research team, has created his own lab at Tsinghua University. Dr. Ma and his team continue to analyze the data generated by the project. Learn more about their current work and plans for the future in this update.

Background

The Computing for Clean Water project was created to provide deeper insight on the molecular scale flow of water through a novel class of filter materials. Thanks to the millions of virtual experiments that the team was able to run on World Community Grid, they discovered conditions under which water can pass through tiny carbon nanotubes much more efficiently. This groundbreaking understanding of a fundamental physical process could help improve access to clean water for millions of people through more efficient water filtration and desalination, and also may have applications in clean energy and medicine.

A Growing Team

It has been one year since the main team member, Dr. Ming Ma, returned to Tsinghua University, China, after doing research at University College London and Tel Aviv University. During the past year, as an Associate Professor in the Department of Mechanical Engineering, Dr. Ma recruited four new researchers as members of the team with the help from Prof. Quanshui Zheng, the leader of the Computing for Clean Water team. The new team members include one postdoc, Dr. Wei Cao; and three PhD students: Jin Wang, Kunqi Wang, and Yao Cheng.

Next Steps

The team is now working on two main tasks. The first task is to improve the algorithm used in the previous study (see the reference below) by incorporating new techniques developed during the last three years, and to implement them into LAMMPS, a molecular dynamics software. The second task is to investigate new systems with the algorithm being developed. With these tasks finished, the team wishes to bring new, interesting information into the volunteer computing community.

We thank everyone who supported Computing for Clean Water, and hope to work with you again in the near future.

More HERE.