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WCGrid News and Talking Points!!

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thks kid keep up the good work. I like to tell everyone what I do bye showing one post you did for the team.
 
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Pioneering new techniques in the fight against HIV


30 Sep 2015

By: Dr. Arthur Olson
Professor, The Scripps Research Institute

Summary
The team behind FightAIDS@Home is launching Phase 2 of the project, putting to use a more accurate simulation tool to help them determine which of the Phase 1 results merit further investigation. Phase 2 will also be applying this analysis technique at an unprecedented scale, which if proven successful, can benefit medical research not only for HIV but many other diseases as well.
emphasis, throughout, is mine.


Model of a complete HIV Virion with all of the component molecules.
There have been some amazing advances in the fight against the human immunodeficiency virus (HIV), including treatments that have improved and extended millions of lives. But the fight continues - HIV is continually mutating, and as it does it evolves resistance to existing treatments. With tens of millions of people currently living with HIV, and millions more infected every year, the search for more effective HIV treatments is as critical as ever. Our team is therefore launching a new phase of HIV research to build on the success of the first phase and more accurately analyze the most promising drug candidates we've identified so far.
or almost a decade, FightAIDS@Home has contributed to this fight by exploring different ways of disabling the virus. World Community Grid members have provided my team an unprecedented amount of computing power, enabling us to investigate a huge number of potential cures. To date, volunteers have performed over 20 billion comparisons between candidate chemicals and different binding sites on the virus.
The massive success of FightAIDS@Home has also generated a new challenge: thousands of potential 'hits' (chemicals that might form the basis of effective drugs) - a handful of which we're synthesizing for additional testing. But because there are so many, it is prohibitively expensive and time consuming to synthesize and lab test all of those chemicals. The project now needs a new computational method to double-check the promising Phase 1 results, and ensure that only the most thoroughly vetted and probable candidate compounds proceed for further investigation. Phase 2 of FightAIDS@Home will address both of these goals: refining the Phase 1 results and validating the technology needed to make more accurate simulations.
...a new analysis technique called BEDAM (Binding Energy Distribution Analysis Method).... BEDAM has proven effective at carrying out more accurate simulations in computational contests, but thanks to World Community Grid volunteers, we now have an opportunity to apply it to analyze molecules at an unprecedented scale. This is important because if successful, these techniques can be applied to other drug discovery searches beyond HIV.

Collaborating labs for the HIVE Center. Prof. Art Olson directs the Center and collaborators include Prof. Ron Levy, who is partnering with the FightAIDS@Home project.
Phase 2 is more radical than its name suggests - World Community Grid volunteers have the opportunity to help us validate a new promising research paradigm that can help the search for treatments for many diseases, not just HIV. It's only because of the commitment shown by volunteers that FightAIDS@Home has been able to accomplish so much thus far. We hope we can count on your continued support as we continue this important journey.


Awesome Sauce!! Once again the results we crunch are evolving into more than what was being researched. These stories of success, over and over, help me pay my electric bill. I, and the rest of you Crunchers, am changing the World, one WU at a time (or rather 8, or more, at a time. :p).

If IBM did nothing else, but WCG, they would be considered a success! When the history books get written, WCG, and IBM, will be there. So will all of us who helped!

Folding will be in there, too. Standford, I believe, was using our GPU's before IBM and WCG. I could be wrong? Anyway, Their work is groundbreaking, also.

I hope I live long enough to see Ebola gone, HIV/Aids gone, Malaria gone, Cancer considered no worse than the Flu and have a All Natural Solar Panel running my Clean Water cooled Photon Laptop.:laugh:

Keep Crunching! Toast those GPU's Folding! Your small sacrifice is changing our lives for the Better!
:lovetpu:
 
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Finding new avenues to attack Ebola


6 Oct 2015

By: Dr. Erica Ollmann Saphire, PhD
The Scripps Research Institute

Summary
Efforts to simulate matches between candidate compounds and one key Ebola virus protein are largely complete. Simulations of matches against another, newly discovered target protein are beginning now. Even as simulation work continues, the team is beginning to analyze these results and home in on compounds that could form the basis for effective new drugs against Ebola and other related diseases. Thanks to your help, and a new grant, the work is proceeding well.
Emphasis is mine, throughout.


Two Protein Data Bank structures for the ribonuclease H domain of HIV reverse transcriptase. We used structural and experimental data for this domain to optimize our analysis protocols for the Lassa NP exonuclease site.
(?):confused:

Thanks to the efforts of thousands of World Community Grid members, my team has continued to make progress on Outsmart Ebola Together, a project whose goal is to find new drugs for curing Ebola and related life-threatening viral hemorrhagic fevers.
I understand this part! :D

Outsmart Ebola Together began with a study of potential drug attacks against the receptor-binding site of the Ebola surface glycoprotein (GP). We then announced the start of work on a second drug target: the nucleoprotein (NP) of Lassa Fever virus. Specifically, we are looking for drugs that attack the newly discovered "exonuclease site" of Lassa NP. This exonuclease site helps conceal the virus's presence from the infected human cell by destroying the virus's own excess production of double-stranded RNA.

We have since prepared research tasks for testing the Lassa NP exonuclease site against millions of potential drugs. These tasks are now ready for use, and will be sent out to World Community Grid volunteers over the coming months.
OK, that makes sense, the picture is starting to focus...:D

At this stage in the project, we’ve gathered enough data that we need to begin focusing on analysis procedures for the data already returned by World Community Grid volunteers. We must analyze the data for both the Ebola GP receptor-binding site and the Lassa NP exonuclease site; and our analysis procedures must be sufficient to filter out false positives from the large quantity of results returned.
As has become the Norm, WCG Volunteers have flooded the Researchers with massive amounts of Data. Now, is when the doors are open and there will be amazing new discoveries flowing through it! :toast:

We are also happy to announce that a $50,000 grant to support this work has been provided by the Robert Wood Johnson Foundation President’s Grant Fund of the Princeton Area Community Foundation. With this grant and the vast computing resources of World Community Grid, our way to the successful completion of the project is clear.
As always, we close with a thank-you to the volunteers who have run this work for us. As you can see, we’ve already made significant progress but there is much work still to do. Make sure you’re signed up to contribute to this project, and spread the word about our lifesaving work!
:clap: Well done WCG, and to all those, like us here at TPU, that Crunch Numbers to make the World a Better place!!

:lovetpu: Link to Original Story
 
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I just noticed total crunching up-time for TPU has reached 5,200 years!...which got me thinking...
and if I figure things correctly, this is number is calculated overall from the use of one PC crunching?

tpu years crunching.png

If correct this means theoretically or broadly speaking that one person has been crunching
on one PC for TPU since the Bronze age!

Pretty amazing I thought!

And this is not including what time the Folding@Home crew do as well!

Source: https://en.wikipedia.org/wiki/Timeline_of_human_prehistory
 
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World Community Grid to Appear at South by Southwest Interactive 2016


21 Jan 2016

Summary
Thanks to votes from many World Community Grid volunteers, we were selected to present at South by Southwest on March 13, 2016 in Austin, Texas.

Cool!
What do clean water, nanotechnology, volunteer computing, and the world's greatest group of volunteers have in common? They are all part of World Community Grid's presentation at this year's South by Southwest Interactive conference (SXSW).

Dr. Francois Grey, a researcher on the Computing for Clean Water project, will co-present with Juan Hindo, World Community Grid's project manager. Together, they will talk about how the Computing for Clean Water team used World Community Grid to simulate water flow through carbon nanotubes. This led to a breakthrough understanding of a fundamental physical process which could lead to improved access to clean water for millions of people worldwide

SXSW's advisory board and staff received over 4000 submissions from people applying to present at this influential event....

Due in large part to the votes and supportive comments from hundreds of World Community Grid volunteers, we were selected, and a new and influential audience will now hear about the power and potential of volunteer computing.

Full Story, HERE
 
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manofthem

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Looks like the WCG is looking to get into the Zika issue. Embarrassingly, I wasn't even aware of this Zika til about a week when an online friend brought it up, and then it scared me considering Florida has ridiculous mosquitos :fear:

Anyway, I got this email from WCG though dated 2 weeks ago, but I found it interesting :)

WCG said:
We're Ready to Help Fight Zika



8 Feb 2016


Summary

As the Zika outbreak spreads, and World Community Grid volunteers ask if their donated computing power can be used to help find new vaccines or treatments, we are actively searching for Zika researchers who need to conduct computational research.





Other languages:
To read this article in Spanish, click here.
To read this article in Portuguese, click here.


Details

Last week, the World Health Organization declared a global public health emergency due to the spread of the Zika virus, which may be linked to birth defects in newborn infants whose mothers are infected as well as to neurological disorders. Thanks to the contributions of over 700,000 individuals and 470 organizations, World Community Grid has already enabled important scientific advances in childhood cancer, solar energy and clean water. We are now actively seeking new opportunities to apply this free and powerful resource to addressing the Zika crisis, and have begun conversations with several researchers and organizations to find out how World Community Grid can help. Specifically, we are looking to provide computing power to Zika researchers who wish to conduct computational research, such as virtual drug docking experiments, to discover a treatment for the disease.

We understand the urgency of this work and have a track record of responding rapidly to address critical public health needs, such as the launch of Outsmart Ebola Together, which began the search for antiviral drugs for Ebola at the height of the 2014 outbreak. Within 6 months, 30,000 our volunteers had screened over 5 million candidates, which could potentially also be used to treat related diseases in the filovirus family, including the Marburg, Sudan and Reston viruses.

Additionally, through the Discovering Dengue Drugs - Togetherproject, World Community Grid supported the search for drugs to help combat dengue, a devastating mosquito-borne disease which is thought to have similarities to Zika. During this project, World Community Grid volunteers screened 3 million chemical compounds, leading the researchers to identify a promising molecules which might have the potential to disable the dengue virus. Chemists are working on modifying the molecules in various ways, hopefully to improve their effectiveness, before proceeding with further testing.

We welcome research proposals of any size, and have the capacity to provide massive computational power, completely free of charge. For example, two of our projects are respectively considered to be the largest drug docking experiment and largest quantum chemistry experiment ever conducted to date.

Existing Software Tools

While we welcome proposals which use any computational tools, the following software tools have already been enabled to run on World Community Grid, and a project using one of these tools could therefore be set up very quickly.

  • AutoDock and AutoDock VINA (the world's most widely used and cited docking programs, both developed by The Scripps Research Institute). These tools have been used by a number of World Community Grid medical research projects and could prove to be helpful for Zika research.
  • BEDAM - Academic Impact (molecular simulations). This tool is currently being used on our FightAIDS@Home project to screen top candidates from VINA screenings.
  • Rosetta (protein folding)
  • Lammps (molecular dynamics)
  • Charmm (molecular dynamics)
  • Gromacs (molecular dynamics)
  • Q-Chem (quantum chemistry)
  • SSearch (genome comparison)

Any scientists with expertise in Zika research, who are involved with or planning projects requiring large computational power, cancontact World Community Grid. We thank the many dedicated World Community Grid volunteers who have already expressed an interest in contributing to the fight against the Zika virus.
 

manofthem

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Here's a little about Chris Elsass, a musician, science buff, and volunteer, who got involved with the World Community Grid.

"Sometimes you want to help others but you just don't know how," he says. "It is very important to me to 'be green' as much as I can, and I was attracted to the fact that World Community Grid's projects are humanitarian."

Musician, Science Buff, Volunteer
26 Feb 2016

Summary
Meet Chris, a multi-talented volunteer from France, who explains why he joined World Community Grid.





When Chris Elsass is not at work repairing electronic devices, he can be found pursuing one of his many interests such as his band (he plays multiple instruments), science fiction, following scientific progress, and spending time with his family, which includes his wife and three grown daughters.

Elsass became interested in SETI@home a number of years ago, and from there he found and volunteered for World Community Grid. "Sometimes you want to help others but you just don't know how," he says. "It is very important to me to 'be green' as much as I can, and I was attracted to the fact that World Community Grid's projects are humanitarian."


Elsass is particularly passionate about Computing for Clean Water, a project that led to an important breakthrough with possible applications for water filtration and desalination. "Water is the most vital element to life, besides air. This is one of the most important issues today, and it will be harder and harder for everyone to obtain. We need to find clean water solutions quickly," he says.


As for why he remains a World Community Grid volunteer, Elsass says he feels committed to the work and by participating in a variety of projects over the years he has learned more about subjects such as desalination and diseases such as dengue and leishmaniasis that are still prevalent in many parts of the world.


"Donating unused computer power benefits all of mankind," Elsass says. "What my computer does is just one drop of water, but combined with all the other drops, it makes an ocean."

Not a volunteer yet? Join Chris and thousands of other World Community grid members who are helping accelerate scientific research.


Already a volunteer? Contact us if you would like to share your story.
Link
 

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Researchers Identify Key Proteins in the Fight Against Leishmaniasis



Leishmaniasis, which is one of the most neglected tropical diseases in the world, infects more than two million people in 97 countries. There are no available vaccines to prevent the disease, and the treatments can cause severe side effects, including death. Furthermore, drug-resistant parasites are causing major problems in many endemic countries. For these reasons, there is an urgent need for new, safe and inexpensive drug compounds.

Since our last update in July 2015, we have been moving forward in several key areas: 1) we are conducting further research on the findings from Drug Search for Leishmaniasis, which has identified three important proteins, 2) we are publishing and presenting our results, and 3) we are planning for a second phase of the project, which may also involve World Community Grid.

Looks like another project will be in bound eventually :D

WCG News Article
 

hat

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I still want to see an epilepsy project on WCG. It's a serious, crippling disease which affects a lot more people than you might think.
 

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33.4 Million Virtual Experiments and Counting: An Update on Outsmart Ebola Together

By: Dr. Erica Ollmann Saphire, PhD
The Scripps Research Institute

21 Mar 2016

Summary
In this project update, Dr. Erica Ollman Sapphire covers many fronts on the fight against Ebola, from the long-term effects of the disease on survivors, to her team's continued experiments using World Community Grid and their work with other Ebola researchers.


So far, 33.4 million of these virtual experiments have been conducted by World Community Grid volunteers, the percentage of tasks completed is increasing, and will probably reach 100% soon. We are currently seeking a computational scientist (and funding to support him or her) to filter this tremendous body of work into the most meaningful compounds we can test in a laboratory.
Full WCG News Article
 
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looks like i should stop sleeping in the yard after my nightly "blood baths" o_O

mosquitos around here come @ You like storm troopers...

these insect borne diseases always get me a little too freaked out , srsly . i have to add some humor to it. makes my skin crawl/.
 
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World Community Grid Needs Your Vote to Win a Webby Award!







World Community Grid has been selected as one of five nominees for the prestigious Webby Awards in the Corporate Social Responsibility category, which honors corporations with a commitment to help make our world a better place. You can help us win this coveted award by voting today.


Voting for the Webby's People's Voice Award ends on April 21, so please vote today and help us spread the word. Thanks to everyone for your support!

Full WCG News Article
 

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Uncovering Genome Mysteries Hopes to Shed Light on Zika and Other Viruses



By: Wim Degrave, Ph.D.
Laboratório de Genômica Funcional e Bioinformática Instituto Oswaldo Cruz - Fiocruz

12 Apr 2016


Summary
Uncovering Genome Mysteries is analyzing protein sequences from Zika and related viruses in order to help scientists better understand them. Dr. Wim Degrave, who is deeply involved in Brazil's response to the Zika crisis, gave us this update to describe how these analyses fit into the larger work of Uncovering Genome Mysteries, and how the project could help scientists develop new tools to diagnose and treat Zika virus and similar diseases.
WCG News Article
 

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Mapping Cancer Markers Now Examining Ovarian Cancer


By: The Mapping Cancer Markers research team

21 Apr 2016


Summary
The Mapping Cancer Markers project now includes markers for the most common form of ovarian cancer, with a goal to understand the how this disease progresses from early-stage to late-stage.





The Mapping Cancer Markers project, which had been concentrating on lung cancer, now includes work units related to ovarian cancer. The researchers are seeking to identify the genes that are important in differentiating between early-stage and late-stage ovarian cancer.

Full Article Here
 
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Help an International Research Team Fight the Zika Virus


By: Dr. Carolina Horta Andrade
Universidade Federal de Goiás, Brazil

19 May 2016


Summary

The Zika virus was relatively unknown until 2015, when it made headlines due its rapid spread and its link to severe brain-related deficiencies in newborns born to mothers who contracted the virus while pregnant. Dr. Carolina Horta Andrade, the principal investigator for the new OpenZika project, discusses how she and an international team of researchers are using World Community Grid to accelerate the search for an effective anti-Zika treatment.





Introduction

Few people had heard of the Zika virus before 2015, when it began rapidly spreading in the Americas, particularly in Brazil. The virus is mostly spread by Aedes aegypti mosquitoes, although sexual and blood transmission are also possible. A currently unknown percentage of pregnant women who have contracted the Zika virus have given birth to infants with a condition called microcephaly, which results in severe brain development issues. In other cases, adults and children who contract the Zika virus have suffered paralysis and other neurological problems.

Currently, there is no treatment for the Zika virus and no vaccine. Given that Zika has quickly become an international public health concern, my team and I are working with researchers here in Brazil as well as in the United States to look for possible treatments, and we are using World Community Grid to accelerate our project.

...As a scientist and a citizen of Brazil, which has been greatly affected by Zika, I am committed to the fight against the virus, but my team and I will need the help of World Community Grid volunteers to provide the massive computational power required for our search for a Zika treatment.
In January of 2016, when the Zika virus outbreak in Brazil became alarming, Sean and I decided to expand our dengue research, and we included the Zika virus in our work, since these two diseases are from the same family of viruses.


Dr. Sean Ekins, CEO, Collaborations Pharmaceuticals, Inc.

The Open Zika Research Team
After Sean and I began our work on the Zika virus, he introduced me to World Community Grid. Sean has also collaborated with Dr. Alexander Perryman of Rutgers University, New Jersey Medical School, who was previously at The Scripps Research Institute where he played a key role in two World Community Grid projects: Fight AIDS@Home and GO Fight Against Malaria. Sean and Alex are both co-principal investigators with me on the OpenZika project.


Dr. Alexander Perryman, co-primary investigator, and Dr. Joel Freundlich, collaborator, Rutgers University New Jersey Medical School

The research team also includes my colleagues at UFG, Dr. Rodolpho Braga, Dr. Melina Mottin and Dr. Roosevelt Silva; Dr. Jair L. Siqueira-Neto from University of California, San Diego; and Dr. Wim Degrave of the Oswaldo Cruz Foundation in Brazil, who is already working with World Community Grid on the Uncovering Genome Mysteries project, among others.


The UFG team includes Dr. Rodolpho Braga, Dr. Carolina Horta Andrade, Dr. Melina Mottin and Dr. Roosevelt Silva (not pictured).
Our Goals
The Open Zika project on World Community Grid aims to identify drug candidates to treat the Zika virus in people who have been infected.

...Our work on World Community Grid is only the first step in the larger project of discovering a new drug to fight the Zika virus. Next, we will analyze the data obtained from World Community Grid’s virtual screening to choose the compounds that show the most promise.

...We are committed to releasing all the results to the public as soon as they are completed, so other scientists can help advance the development of some of these active compounds into new drugs. We hope that OpenZika will include a second stage, where we can perform virtual screenings on many more compounds.

...And without the resources of World Community Grid, using only the resources of our lab, we would only be able to screen a few thousand compounds against some of the Zika proteins, or it would take years to screen millions of compounds against all Zika proteins. This would severely limit our potential for drug discovery.

...Enlisting the help of World Community Grid volunteers will enable us to computationally evaluate over 20 million compounds in just the initial phase (and potentially up to 90 million compounds in future phases).

...By working together and sharing our work with the scientific community, many other researchers in the world will also be able to take promising molecular candidates forward, to accelerate progress towards defeating the Zika outbreak.
I love the Fact that so many previous project people are collaborating with current project people and even using data from other projects to engage in REAL WORLD solutions to problems. It makes me feel so good to read these News Releases, often they are above my understanding, technical terms and all, but, I am good with the context. Do things that help people. This is, at the same time, the best thing I do and the easiest. WCG, constantly amazing, even after all these years! LOL.
:rockout::clap:

The whole thing...
 
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Hi guys! It's been awhile, eh? So, my plan is, for the time being, to update this thread on Thursdays. At least until I RE-start school! Then it will be a crap shoot. Hopefully I can settle into a regular weekly post, even while in school. Unsure of my schedules, work and school, so I will have to wait and see. So, look for some updates here on Thursday!!
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FightAIDS@Home Team Re-Opens Phase 1


By: The FightAIDS@Home research team

1 Dec 2016


Summary
We are happy to announce that we are re-opening Phase 1 of the Fight AIDS@Home project. In collaboration with World Community Grid, and thanks to their affiliated volunteers around the globe, High Throughput Virtual Screening will be performed by targeting the HIV-1 capsid protein with the goal of discovering new chemical compounds to defeat the AIDS virus (HIV). Read more in this update.

Background

During the maturation of the HIV virus, the HIV-1 capsid protein (CA) assembles with thousands of copies to forms the capsid core [ref 1] with a characteristic conical shape (see Figure 1C). This core encloses the RNA viral genome. Upon the entry of the HIV in host cells, the capsid core is released into the cytoplasm, and it dissociates in connection with the reverse transcription in a not completely understood process. This leads to the importation of DNA viral genome in the host cell’s nucleus, where it is integrated in the host DNA to finalize the infection.


The critical role of CA protein, in early and late stages of the viral replication life cycle, has led to recent efforts on drug development, targeting the mature form of the protein. Currently, none of these molecules are used in clinic, and some face natural polymorphism and resistant mutations [ref 2]. Therefore, continued development of drugs targeting the CA protein is still needed...

High Throughput Virtual Screening

The FightAIDS@Home team is working with World Community Grid to find active compounds which could attach to the CA proteins and mediate the assembly of the capsid core. This computational experiment will be performed using the docking software AutoDock VINA [ref 3].

Thanks to the volunteers, around 2 million molecules will be screened across ~50 conformations of the capsid protein, and hopefully lead to a reduced selection of molecules. This will be the starting point of a drug discovery process targeting the HIV-1 capsid protein.

Four pockets of interest

Based on X-ray structures of CA protein, models of the core, and computational analysis of their flexibility, four pockets of interest have been selected on the surface of the hexamer assembly (see Figure 2).


More technical stuff, Here!

My interpretation, our work has helped them move forward in Giant Leaps. But, now that they have narrowed down a main culprit, they need us again! Let's give them the stuff they need! Help wave Goodbye to this nasty Virus!!

:lovetpu:
 
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Meet a World Community Grid Team Member: Keith Uplinger

6 Dec 2016

Summary
World Community Grid's technical lead not only relishes tackling all sorts of difficult challenges, he enjoys helping others do so as well. Meet Keith Uplinger in this article.

Whether he's coaching his children's sports teams, or helping scientists deploy a new sampling protocol on World Community Grid, Keith Uplinger is always up for a challenge, especially when it means helping others.


Earlier this year, Keith co-starred in a video of our
acceptance speech for the People's Voice Webby Award.
Keith grew up in a technology-oriented family in Austin, Texas, where his father worked for IBM. Always drawn to math and technology, Keith began programming while still in grade school. Once his family installed a dedicated internet connection, he became even more focused. "I was online almost 24/7, programming and researching
computer components," he says.

He earned a bachelor's degree in computer science at Texas Tech University, and began interning for IBM during his sophomore year. From the beginning, his work focused on grid technology, which involves linking computer resources from multiple locations to reach a common goal. Upon graduation, he was hired full-time to work at World Community Grid, which had recently launched.

Since then, he has touched nearly all parts of World Community Grid's platform, including developing project screensavers, server management, running the testing environment, website development, and working closely with the BOINC group to help with the open source platform on which World Community Grid runs. "I've stayed with World Community Grid for the challenges," Keith says. "Many people work on a single product, but our scope is broader. Every few months we have a new project that needs to go out to large groups of people all over the world."
Keith is currently World Community Grid's technical lead. His latest work-related challenge is leading World Community Grid's work on asynchronous replica exchange, a new sampling protocol being developed by the research team for FightAIDS@Home - Phase 2. He explains, "When World Community Grid receives completed work units (research tasks) back from volunteers' devices, we don't send the results back to the researchers until the entire batch of work units is complete. This isn't always ideal for researchers like the Fight AIDS@Home team, who need to process their results more quickly. With asynchronous replica exchange, these researchers will get their data back more quickly, which will help them analyze their data more quickly."



To the many volunteers that he has served over the years, Keith says, "Thanks for your ongoing efforts to help find answers to science's toughest questions. I hope we can grow to millions of volunteers, and someday I'd like to see us cure cancer."
I am sure we have the same, 'Thanks', and respect for Keith and all the IBM staffers that make WCG work so well.

No?

:lovetpu::toast: rest of article, Here!

 
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Release Notes for BOINC 7.6



Get it NOW!!!

Can you smell the freshness?
:laugh::laugh::laugh::laugh::laugh::laugh::laugh::laugh::laugh:
 
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Big Data and Big Plans: Next Steps for Uncovering Genome Mysteries

By: Wim Degrave, Ph.D.
Laboratório de Genômica Funcional e Bioinformática Instituto Oswaldo Cruz - Fiocruz

15 Dec 2016

Summary
World Community Grid’s role in the Uncovering Genome Mysteries project has ended, but the research team’s work continues as they analyze the results of the calculations and prepare to apply the data to medical, agricultural, and other real-world applications.



Background

The Uncovering Genome Mysteries project began on World Community Grid in November 2014, with the aim of analyzing protein sequences to help understand how organisms function and interact with each other and the environment. The project began with 120 million predicted protein sequences from close to 150,000 organisms. These protein sequences and organisms represent a wide variety of known or uncharacterised life forms in our biosphere. They came from organisms in samples taken from a range of environments, including water and soil, as well as on and inside plants and animals. Additionally, 70 million sequences, derived from prospective analysis of genetic information from microbial marine ecosystems from Australia were added, with the objective to add to the identification of possible functionalities of these sequences. In July 2015, we added yet another 20 million newly predicted sequences of proteins.

Thanks to the enthusiastic contributions of more than 76,000 World Community Grid volunteers, all of these protein sequences were analyzed in approximately 24 months. (!!!!!)(Yea Baby!)

Results to Date and Plans for the Future

So, what is next? The research team at Fiocruz has spent the last year designing and testing new algorithms to transform the output of the comparisons with distance calculations between the genomes of the organisms included. Scientific literature cites many different ways to do this, depending on the purpose of the analysis and the views on evolutionary biology.

The results of the Uncovering Genome Mysteries can be summarized as follows:

  1. More complete and precise information is now available on the structure and function of proteins encoded by living organisms in our biosphere. More proteins are being studied and experimented with each day in the thousands of laboratories around the world, and by using results from the comparison performed through the project, functional parallels can be drawn for proteins that show structural similarity between organisms. This is particularly valuable when predicted protein fragments are compared from uncharacterised organisms, for example in environmental and ecology studies, such as those originated from the laboratory of co-investigator Dr. Torsten Thomas, and his team from the Centre for Marine Bio-Innovation & the School of Biological, Earth and Environmental Sciences at the University of New South Wales, Sydney, Australia. The resulting database with these functional annotations will be made publicly available as the next version of our protein comparison database, ProteinWorldDB, in the coming months.

  1. Through comparison, new protein functions are discovered that can have medical, agricultural, technological or industrial applications. These can be as new biopharmaceuticals, bioinsecticides, biodegradation of waste, or enzymes for production of chemicals, but especially when part of new biochemical pathways in cells, that help laboratories to develop new green chemistry or energy production, or biosynthesis and transformation of new drugs. This also adds to the growing knowledge of biotechnology and synthetic biology.
  1. The group at Fiocruz has developed new ways to compare genomes from different organisms. Traditionally, such analyses consider what is conserved between genomes, resulting in distance calculations that are used for phylogenetic studies and the estimation of evolutionary relationships between organisms. However, we feel that this is only part of the picture, and the Fiocruz team designed a new algorithm that also takes differences into account. This was coupled to a new visualization method for such comparisons, resulting in a markedly faster way to add new data to the picture. We hope that this method will enable us to keep track of data from new organisms that becomes available, adding results to the growing ProteinWorld DBdatabase.
That's a lot of 1's!! Seriously though, something in the page formatting did that when I copy/paste-ed it...?

Thank you to all World Community Grid volunteers who supported this project, and we plan to keep in touch as we have further news about our ongoing research.

Interesting Stuffs, Here!!
:lovetpu:

:lovetpu:
:peace:
 
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Community Achievements in 2016


27 Dec 2016

Summary
We're grateful for the volunteers and scientists who worked with us this year to launch two new research efforts, make progress on existing projects, and spread the word about volunteer computing to new audiences. Here are some of the highlights of 2016, which wouldn't be possible without each of you.

Two new research projects, two awards, several conferences...and volunteers around the globe whose support made all of this progress possible. Because of you, 2016 was a great year for World Community Grid! Below are a few of this year's highlights.

I essentially Copy and Pasted the whole article here! I couldn't decide where to edit anything out! So, here it is, 2016 WGC view!

Helping Stop a Global Killer
Tuberculosis is one of the world's deadliest disease, killing approximately 1.5 million people every year. In March, researchers at The University of Nottingham launched Help Stop TB on World Community Grid to study the molecular structure of the bacterium that causes tuberculosis, so that scientists can learn how to overcome it.

Not sure where this Project is. I have not had any work from them since I restarted, a few weeks ago. In fact this is ALL I have ever had..."
Help Stop TB 6,281 3 0:002:01:15:56
:confused:


Reaching a New Audience
Thanks to votes from volunteers and supporters, an influential audience at South by Southwest (SXSW) learned how World Community Grid volunteers have supported humanitarian research projects since 2004, and heard how these volunteers helped scientists make a breakthrough that could bring clean water to millions. Listen to audio of our full presentation, which was given in March, or read about our experience.


Researcher Francois Grey,
who was part of the Computing for Clean Water project,
and program manager Juan Hindo presented the results
of the project at South by Southwest 2016.

One day, I will get down to Austin, WHEN THIS is there, also!! SXSW, sounds like a blast! Austin is a great city, also!!

Searching for Potential Treatments for Zika
The Zika virus began spreading rapidly through the Americas in 2015. In 2016, it continued moving north and was also reported in Asia. There is no effective treatment for Zika, no vaccine, and the virus as been linked to serious complications, including lifelong brain-related issues for infants whose mothers contract Zika while pregnant. In response to volunteer requests, we looked for a project to fight the virus, and in May, an international team of researchers launched the OpenZika project on World Community Grid to search through millions of chemical compounds for those that may become treatments.

OK, so, I love this woman's voice. :p:p


Getting Inspired by Changemakers
Program manager Juan Hindo was invited to attend South by South Lawn 2016 at the White House in October. This first-time event brought together leaders in art, technology, innovation, and social change who are helping to improve the world. Read about Juan's experience and how it inspired us to re-ssue our call for research projects that address climate change.

I wonder if THIS will ever happen, again. :confused:



Winning Awards
We appreciate awards because they recognize and raise awareness for the important work made possible by World Community Grid volunteers.

Thanks to votes from volunteers and supporters, we were honored to receive a People's Voice Webby Award in the Corporate and Social Responsiblity category. This award recognized our new online experience to help people learn about and join World Community Grid, which helped improve our sign-up rate. The Webby statuette traveled around the U.S. this summer and fall to spend time with each team member, as shown in the video below.

Funny? Cute? It is a fun video, though.

We also received a D&AD Wood Pencil Impact Award, which was created by the advertising industry to recognize programs that have a societal impact that helps change the status quo.

THIS AWARD is a good thing, however, the linkable site, sucks. Doesn't even give a short paragraph about WCG. :confused:

Thank You
Twelve years, 27 projects, and (as of November) 3 billion research results later, we are very grateful to the volunteers all over the world who are supporting basic science by donating unused computing time. Thanks for making 2016 a year of new beginnings and continued progress. Stay tuned for exciting news in early 2017!

Keep Crunching!!
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Nearly 3 weeks, tomorrow, and no new News. I will keep scanning the site, every couple days but it has been slow going recently. Apparently, I like to think, we have overwhelmed the researchers with data and they have their heads down working overtime to disseminate it!

Either way, Go Team TPU!

Keep Crunching!!
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Audio Device(s) Sonic Master/ onboard's/ Beeper's!
Power Supply ASUS brick, 17W i5/ 19.5 volt bricks/ Dell PSU/ 525W sumptin/ same
Mouse cheap GigaWire930, CMStorm Havoc and a Logitech M510 wireless/iGear usb x2
Keyboard Dynex, 2 no name, SYX and a Logitech. All full sized and USB.
Software WIN8.1-64bit/ Mint 18 Sylvia/ Opti-Con Mint KDE/ T3500's on Kubuntu/HP 3770 is Win 10
Benchmark Scores World Community Grid is my benchmark!!
Meet a World Community Grid Team Member: Jonathan Armstrong


19 Jan 2017

Summary
This Texan's role with World Community Grid focuses on helping the researchers' work run smoothly, and he's just as focused outside of work. Meet Jonathan!

Hi Jon!! :laugh::laugh: :laugh::laugh::laugh::laugh::laugh:
:laugh::laugh::laugh::laugh::laugh::laugh::laugh::laugh::laugh::laugh:


Originally hailing from the San Antonio area, Jonathan Armstrong is a lifelong Texan. He received a bachelor's degree in computer engineering from Texas Tech University, and interned at IBM during his senior year. Immediately after graduation, he was hired to work at IBM's Austin office in the services division.

Jonathan in IBM's Austin, Texas office

"Our focus was on disruptive technologies," he says. "In 2001, when I started working at IBM, these technologies included virtualization, automation, and grid computing." For several years, Jonathan was involved in proof of concept and customer engagement work on these technologies, helping to determine how they might have the best real-world applications for IBM's various markets. He also mentored a college student named Keith Uplinger (scroll up to see Keith!) who later became one of his World Community Grid teammates.

Jonathon checking out his new quadcopter drone.


A Drone's view of Jonathon!
Jonathan and his wife have been married for 19 years. They have three young children who are the primary focus of their time and energy outside of work. When he finds time he enjoys listening to live music around Austin. Jonathan also loves the outdoors, and spends time flying his new quadcopter drone.

Like all World Community Grid team members, Jonathan is grateful for the people who help make the work possible. He says, “A big thanks to the volunteers. Without you and the resources you contribute, we couldn’t do what we do.”
More about Jonathon, HERE!

Thanks Jonathon
 
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Mouse cheap GigaWire930, CMStorm Havoc and a Logitech M510 wireless/iGear usb x2
Keyboard Dynex, 2 no name, SYX and a Logitech. All full sized and USB.
Software WIN8.1-64bit/ Mint 18 Sylvia/ Opti-Con Mint KDE/ T3500's on Kubuntu/HP 3770 is Win 10
Benchmark Scores World Community Grid is my benchmark!!
Outsmart Ebola Together Approaches Completion of Initial Phase

By: Dr. Hal Wasserman

The Scripps Research Institute

26 Jan 2017

Summary
The Outsmart Ebola Together research team has conducted an enormous number of virtual docking experiments, and they are now ready to embark on a new stage of their research.


The Ebola virus killed many thousands of people in 2014 during the largest outbreak of the disease since it was first discovered in 1976. Significantly, research has shown that the virus's long incubation period and our highly connected modern world could allow the virus to spread to new geographies and across oceans. Currently, there are no approved treatments or vaccines for this deadly disease, and the search for an effective antiviral drug to treat the disease is a high priority.

Outsmart Ebola Together is now approaching completion of its first phase, having conducted hundreds of thousands of docking computations. In this phase, we have simulated the binding of potential small-molecule drugs against atomic structures of proteins of the filovirus family. We have in particular targeted the receptor binding site (RBS) of the Ebola virus glycoprotein (GP), which plays a key role in viral entry into human cells.
Our study now expands to consider multiple stages in the dynamic molecular transformations of GP and other Ebola proteins. These transformations are essential to the viral life cycle, and therefore represent an ideal target for the design of effective antiviral drugs.

Thank you to all volunteers who have supported this project.
More Info HERE!

I am sure we all want to Thank YOU for doing this research and God-Speed to finding the cure, i.e. antiviral, to this devastating VIRUS!!

Crunch ON!!
:lovetpu:
 
Joined
Apr 3, 2012
Messages
4,084 (1.47/day)
Location
St. Paul, MN
System Name LappyTop/ Bay2- Lowerbay- RushCity1/ HP 3770/ T3500-1+T3500-2+T3500-3+T3500-4/ Opti-Con
Processor i5 3317U/ i3 2120's/ i7 3770/ x5670's/ i5 2400
Motherboard ASUStek/ HP UltraSlim's/ HP mid size/ Dell T3500 workstation's/ Dell 390
Cooling Air/air/ air/ Big Dell Air/ Air
Memory 8GB Kingston HyperX 1600/ 2GB/ 4GB/ 12 GB crucial in each 4GB sticks in 3 chan/ 4GB sammy
Video Card(s) intel HD4000/ HD2000's/ HD 2000/ 1 MSI GT710, rest are MSI R7 240's/ HD4000
Storage 256GB Crucial Mx100 SSD/ ?HDD's/ 500 GB 7200rpm-er's/ 500 GB
Display(s) 1366x768/ one acer x223w between the rest
Case ALU, beauty!/ HP 8200 UltraSlim's/ HP 8200 mid tower/ Dell T3500's/ Dell 390
Audio Device(s) Sonic Master/ onboard's/ Beeper's!
Power Supply ASUS brick, 17W i5/ 19.5 volt bricks/ Dell PSU/ 525W sumptin/ same
Mouse cheap GigaWire930, CMStorm Havoc and a Logitech M510 wireless/iGear usb x2
Keyboard Dynex, 2 no name, SYX and a Logitech. All full sized and USB.
Software WIN8.1-64bit/ Mint 18 Sylvia/ Opti-Con Mint KDE/ T3500's on Kubuntu/HP 3770 is Win 10
Benchmark Scores World Community Grid is my benchmark!!
OK guy and Gals, I will be back on Sunday to update this thread with the New and Exciting News from WCG.

I was having issues with my lappytop this evening. Apparently the Kingston SSD card, used as a cache, by Windows, has died or, is well on it's way. It causes major hiccups and before I, finally, waited it out I had rebooted from a frozen screen 3 separate times!

Upshot is, now I have no time to post anything but this, coffee shop is closing! So, Sunday it is!!

Then, sometime next week it is time to pay the local comp shop, I can do it...Don't wanna spend the time...school and work leave little time for sleep. Doing this swap, is my sleep time deprived even more. I will just pony up and support the local shop!

See you Sunday!!:rockout:
:lovetpu:
 
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