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WCGrid News and Talking Points!!

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#1
The goal is to post project updates along with interesting tidbits / opinions thrown in.



Suggestions are welcome, criticism, is not. :D PM me with stuff you'd like to see, and I will possibly respond.:rolleyes:

Finalized Format, Ver 1.0.

:lovetpu:

Spoilers contain links to the WU reports published here, in this Forum. Links to original content is contained in each post, near the end.


These Spoiler's are for News events in 2015 and before, to the start of this thread. There was an issue with editing this post, and by the time I had editing power, again, It was too daunting a task to update. I may tackle it, someday, but it becomes more of an issue as time goes on. We'll see if at some point, I can find time to at least start to update it!!
 
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#2
Decade of discovery: doubling carbon-based solar cell efficiency

22 Oct 2014

Since launching on World Community Grid in 2008, The Clean Energy Project has screened more than two million organic molecules, with the help of our volunteers – the most extensive investigation of quantum chemicals ever performed.


The Harvard team – who so far have been provided with the equivalent of 17,000 years of computing time – continues to investigate the most promising candidates for use in cheaper, more efficient and flexible solar cells.
Very good work has been done and it is amazing the quantity of data in such a short time. I am sure to revisit this theme again, I find it both amazing and encouraging that world wide people are volunteering their computers for this work! Bravo, World. :p

The rest of the story (I plan to borrow this phrase from Paul Harvey, indefinitely)
 
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#3
Get competitive for good with our 10th anniversary challenge

22 Oct 2014

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

And there are some great prizes up for grabs.


The rest of the story
 
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#4
A productive summer for the Clean Energy Project


23 Oct 2014

Another update from CEP2.

As you have probably seen in the forums, we have had a redesign of the structure of the work units. We want to thank everyone for their patience while we sorted out all the “teething” problems, but they now seem to be working well. The reason for these changes was to allow us to try and move onto slightly different families of molecules which we have identified as being particularly interesting. It is important for the CEP to be constantly updating the molecular libraries so we can really live on the cutting edge, and hopefully discover the next “blockbuster” Organic Photovoltaic molecule (the type of molecule the CEP is looking for). To do this, we have to push up against the limits of what is possible on the grid, and we really appreciate the patience of the crunchers when we occasionally push too hard!
I like their attitude!! Go BIG, or GO HOME!! :D

The Rest of the Story
 

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#5
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#6
HELP CURE MUSCULAR DYSTROPHY

October 28, 2014

An update from the Project that ended, Phase 2, last year.

Phase 1 of Help Cure Muscular Dystrophy has ended in June 2007 and Phase 2 has been launched in may 2009 and ended in the fall 2013.

The first and second phase of the project is supported by World Community Grid and by Decrypthon (a partnership between AFM (French Muscular Dystrophy Association), CNRS (French National Center for Scientific Research) and IBM).
MORE ACCURATE PREDICTIONS OF INTERACTION SITES
We previously developed a tool, Joint Evolutionary Tree (JET) for the prediction of protein-protein interfaces [Engelen et al. 2009]. JET assumes that interaction sites are formed by a highly conserved core, surrounded by multiple concentric layers of less conserved residues, but with specific physico-chemical properties. Although this assumption is verified in the majority of interfaces, there are some cases where the interaction site only extends in a preferred direction from the retained core. In order to refine the definition of interaction sites predicted by JET, we have introduced a geometric criterion to describe the protein surface and have coupled this with conservation and physico-chemical properties. The new version of JET encourages extensions of interaction sites to protruding areas in the protein that appear to be highly exposed to the solvent. Depending on the system studied, JET is now able to automatically determine the combination of the most relevant criteria. These changes have significantly improved the performance of JET on different types of protein [Laine et al complexes. 2013- post Berlin]. We are currently setting up a database for all PDB structures, including those structures studied on the WCG grid in the HCMD2 project.
A bit technical but, it essentially means that they have found a way to use all the data produced by WCG, despite earlier failures described in the article, here.

4) Carry out a refined analysis of the large database of protein interactions that you generated (!) to characterize interaction networks and binding promiscuity. During stage two of the Help Cure Muscular Dystrophy project (HCMD2), the resources of the World Community Grid (WCG) were used to dock all possible protein pairs within a set of 2200 proteins, potentially important for understanding and treating
neurodegenerative diseases. This data will be analyzed to characterize key “hub” proteins and network structures, first, with the existing energetic and residue conservation data and then with the new methods resulting from 1-3.
As a layman, and an intelligent one, I can sort of grasp the concept and experiments. What I truly understand? This project is becoming a Grand Success!!

:clap:
 
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#7
Sub'd :toast:

Suggestion- how about links to the articles/items you're posting in the OP? Spoilered and arranged by date/title/etc..

Example:
- 10/22/2014 Decade of discovery: doubling carbon-based solar cell efficiency
http://www.techpowerup.com/forums/threads/wcgrid-news-and-talking-points.207154/#post-3192643
- mm/dd/yyyy Title
link
- mm/dd/yyyy Title
link
Might make for a rather large opening post....But, also a one stop shopping spot. In fact, I may just link to my posting, that contains the link to the original story. Deal? :toast:
 

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#8
Might make for a rather large opening post....But, also a one stop shopping spot. In fact, I may just link to my posting, that contains the link to the original story. Deal? :toast:
That's what I'm suggesting, a link to your postings ;)

Using spoilers will allow the OP to stay reasonably shorter
 
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#9
Early-stage results from the Mapping Cancer Markers team

27 Oct 2014

Thanks to your help, the Mapping Cancer Markers team is nearly finished with benchmarking their first set of genetic markers.
The Mapping Cancer Markers (MCM) team would like to extend a huge thank you to World Community Grid members everywhere. As of October 27, 2014, we have surpassed 89,000 years of computation, a goal that simply would not be possible without your help.
Que my amazing face!

The first half of the “benchmarking” experiment involves determining the performance of markers as the size of the signature changes. For instance, when we compare successful 5-marker signatures against 20-marker signatures, which markers are consistently useful? Which ones increase or diminish in predictive power? Is there an optimum size for signatures? And most importantly, can we identify seemingly minor players that are critical, but not yet in clinical use that can discriminate between normal and disease states?



In the above network, 20 out of 24 important proteins we have identified on World Community Grid (right hand side) can be linked through known protein interactions and 56 other proteins (left hand side).
I love it when our computed research drives the researchers in new directions with the results. :toast:

The Rest of the Story.
 
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#10
Decade of discovery: achieving a breakthrough in childhood cancer


28 Oct 2014

Through the Help Fight Childhood Cancer project, World Community Grid volunteers powered the screening of over three million drug candidates for neuroblastoma – a common and dangerous form of childhood cancer. Through this screening, researchers identified seven drug candidates that showed great potential for drug development – a breakthrough that could save many young lives.
Over the course of two years, World Community Grid volunteers helped the researchers screen three million molecules - a search that would have taken more than 55,000 years on a single computer. Following this testing, in February this year the researchers announced the discovery of seven promising molecules that proved effective at activating the self-destruct function and destroying neuroblastoma cancer tumors when tested on mice, without any apparent side effects on healthy tissue.

This was a significant breakthrough - particularly because over the course of the last 20 years, very little progress has been made in improving the cure rate for this deadly disease. What makes this discovery even more important is the fact that it could aid the research of many adult cancers including breast, lung, pancreatic, prostate and colon cancers.

Building on this success, in July lead researcher Dr. Nakagawara announced his plans to develop a second phase of the project on World Community Grid to cover multiple additional childhood cancers.

Speaking to the volunteers who made this crucial project possible, Dr. Nakagawara commented: “We are so grateful for the support of World Community Grid volunteers and the role you've played in powering our phase one research.”
Exciting news!! And a possible new project in the works!! :clap:
 
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#11
Community Grid Fosters Microbial Discovery

October 22, 2014

An international team of volunteers is putting their spare computing power to work unlocking the secrets of microbes from around the world. By plugging in to IBM’s World Community Grid, contributors are creating a supercomputer that can carry out genetic comparisons of a wide variety of tiny organisms that are too small to see with the naked eye. But don’t let their size fool you, the smallest of earth’s lifeforms have profound implications for human health, agriculture and industry.

The Uncovering Genome Mysteries project is administered by University of New South Wales (UNSW) in Australia and the Oswaldo Cruz Institute of Brazil. The project seeks to make about 20 quadrillion comparisons of 200 million proteins underlying a wide variety of lifeforms, such as microorganisms found on seaweeds from Australian coastlines and in the Amazon river. The computing involved in such an immense undertaking would take 40,000 continuous years on a typical PC, but the capacity of the World Community Grid will reduce the task to mere months.

News article from HPC
 
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#12
Sydney Scientists Are Linking Home Computers Around The World To Create A Huge Super Processor

CHRIS PASH, OCT 22 2014

The team at the University of NSW are using an international group of volunteers sharing their spare computer capacity to create a research supercomputer.

The project has the aim of making 20 quadrillion, or 20,000 million million, comparisons of genes from a variety of tiny life-forms invisible to the naked eye.
“But we know very little about them. Scientists have studied less than 1% of microbial diversity around the globe. Valuable discoveries await us if we can learn about the remaining 99%.”

The Uncovering Genome Mysteries project is hosted on IBM’s World Community Grid.
With enough volunteers the project could be completed within months. But it would take 40,000 years for a single PC to make 20 quadrillion computations.

Microbes are vital to sustaining life on Earth, producing half of the oxygen we breathe, soaking up carbon dioxide and recycling nutrients.
Half the AIR we breath? Hmmm...learned sumptin today!

:eek:

Business Insider, Australia article
 
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#13
Citizen IBM Uncovering Genome Mysteries

October, 21st 2014

Our understanding of life on earth has grown enormously since the advent of genetic research. A decade ago, the Human Genome Project added humans to the list of a
dozen organisms whose genomes had been completely sequenced. Today’s rapid
DNA sequencing technologies have decoded the genomes of thousands of additional organisms, including many microorganisms that previously could not be studied via conventional methods.
Today, we’re launching Uncovering Genome Mysteries on World Community Grid to examine nearly 200 million proteins from a wide variety of life forms – including microorganisms found on seaweeds from Australian coastlines and in the Amazon river. Through this work, we will learn more about the functions of millions of genes and the proteins they encode, enabling scientists to better understand complex microbial systems, identify how organisms interact with one another, and analyze how microorganisms change under environmental stresses, such as climate change.
Wim Degrave, Ph.D., of Oswaldo Cruz Foundation (Fiocruz), and Torsten Thomas, Ph.D., of the University of New South Wales, lead the Uncovering Genome Mysteries project.
A wide ranging project that could help solve a whole Bunch 'O Things!!
:laugh:

Citizen IBM article

 
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#14
Decade of discovery: New precision tools to diagnose and treat cancer


3 Nov 2014

When it comes to cancer, a doctor's diagnosis affects how aggressively a patient is treated, which medications might be appropriate and what levels of risk are justified. New precision medicine techniques are enabling physicians and scientists to refine diagnoses by identifying changes and patterns in individual cancers at unprecedented levels of granularity - ultimately improving treatment outcomes for patients.
To study the feasibility of automating tissue microarray analysis, we partnered with IBM's World Community Grid in 2006 to launch the Help Defeat Cancer project. At the time, we were pioneering a new approach that nobody else was investigating, and it was met with tremendous skepticism by many of our colleagues.

However, with the support of more than 200,000 World Community Grid volunteers from around the globe who donated over 2,900 years of their computing time, we were able to study over 100,000 patient tissue samples to search for cancer signatures.
Thanks to World Community Grid and the Help Defeat Cancer project, we demonstrated the success of using computer-based analysis to automatically investigate and classify cancer specimens based on expression signature patterns. We were able to develop a reference library of cancer signatures that can be used to systematically analyze and compare tissue samples across large patient cohorts.
Awesome Face!!

More Awesome, Here...

:peace:
 
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#15
Teamwork yields experimental support for FightAIDS@Home calculations


6 Nov 2014


The "exo-site" discovered in HIV protease (shown here in green), showing the original bound 4d9 fragment (shown here as red and orange sticks) and the volume (shown as the orange mesh) that is being targeted by FightAIDS@Home. (image credit: Stefano Forli, TSRI)

Our lab at the Scripps Research Institute, La Jolla, is part of the HIV Interaction and Viral Evolution (HIVE) Center - a group of investigators with expertise in HIV crystallography, virology, molecular biology, biochemistry, synthetic chemistry and computational biology. This means that we have world-class resources available to verify and build upon our computational work, including the nuclear magnetic resonance (NMR) facility at the Scripps Research Institute, Florida. NMR is a technique for determining the molecular structure of a chemical sample, and therefore is very useful for validating some of the predictions made during the computational phase ofFightAIDS@Home.
In fact, the first results from the NMR experiments validated the exo site we so thoroughly investigated in FightAIDS@Home. As a result, we now have experimental evidence that a small molecule binds to the exo site in solution with structural effects that seem to perturb the dynamic behavior of protease, even with a known inhibitor in the active site.
OK? Got it? :laugh:

More scientific gobbledy gook to try and wrap your head around, HERE!

The upshot, context, is, We are awesomely providing these guys with the stuff they want. They are very Thankful.

:roll:
 
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#16
Decade of Discovery: A new drug lead to combat dengue fever


10 Nov 2014

Dengue fever, also known as “breakbone fever”, causes excruciating joint and muscle pain, high fever and headaches. Severe dengue, known as “dengue hemorrhagic fever”, has become a leading cause of hospitalization and death among children in many Asian and Latin American countries. According to theWorld Health Organization (WHO), over 40% of the world’s population is at risk from dengue; another study estimated there were 390 million cases in 2010 alone.
Despite the fact dengue represents a critical global health concern, it has received limited attention from affluent countries until recently and is widely considered to be a neglected tropical disease. Currently, no approved vaccines or treatments exist for the disease. We launched Discovering Dengue Drugs - Together on World Community Grid in 2007 to search for drugs to treat dengue infections using a computer-based discovery approach.
We have recently made an exciting discovery using insights from Discovering Dengue Drugs - Together to guide additional calculations on our web portal for advanced computer-based drug discovery, DrugDiscovery@TACC. A molecule has demonstrated success in binding to and disabling a key dengue enzyme that is necessary for the virus to replicate.
Furthermore, it also shows signs of being able to effectively disable related flaviviruses, such as the West Nile virus.
BONUS!!! :toast:

The Rest of the Story

The Discovering Dengue Drugs research team has published a paper describing a new drug candidate that was discovered with the help of World Community Grid volunteers.
 
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#17
Decades of Discovery: Here’s to the next 10 years of humanitarian science


16 Nov 2014

We’ve reached the end of our six-week decade of discovery celebrations - marking 10 years of scientific success. Since October, we’ve been revisiting key projects from the last decade and highlighting some of the fantastic achievements that you’ve helped make possible. We’ve also been running a competition to encourage more people to join World Community Grid. We’d like to thank you again for your support and remind you why it’s so important to keep spreading the word...
All these cutting-edge projects would not have been possible without the computing power donated by volunteers like you. In order to power more humanitarian research projects like these, it’s vitally important that we continue to raise awareness and get more people to join World Community Grid.
Thank you again for your continued support and stay tuned for the launch of another significant project on World Community Grid in the coming weeks.
I can't wait!! I can't WAIT!!! :laugh:

The full Story, Here.
 
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#18
From simulation to prediction: advances in understanding proteins


26 Nov 2014

Summary
The Help Cure Muscular Dystrophy project finished its grid calculations last year. Team leader Dr. Alessandra Carbone has posted an update explaining her colleagues’ ongoing work on understanding and modeling the complex protein-protein interactions that lie behind diseases such as muscular dystrophy.
Dr. Carbone’s post gives another great example of how the work done on World Community Grid continues to have value for researchers long after the grid phase of the project is complete.

For further details, read Dr. Carbone’s update on her project website.
https://secure.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=137
Dr.Carbone's Link to her project site.

More from Dr. Carbone's report....

COEVOLUTION ANALYSIS AND PROTEIN-PROTEIN INTERACTIONS
We planned to obtain extra evidence of protein-protein interactions, and a better understanding of their nature, by exploiting information coming from co-evolution of residues at the interface of the two proteins. Novel kinds of interaction between potential partners, identified on interaction surfaces by coevolution analysis, are currently under investigation. We also developed a very fast version of the algorithm for the analysis of co-evolution "Blocks In Sequences" (BIS) [Dib & Carbone 2012]. Today, this implementation allows us to analyse long genomic sequences, such as complete viral genomes and to study the interaction of sets of proteins. This was previously impossible and it allows us to identify contacts among multiple proteins for which no interaction information was available. Using this approach, we considered the entire coding portion of the genome of hepatitis C virus (HCV) and identified, with BIS, all potential points of contact between the 10 proteins of this virus. In collaboration with F. Penin we are currently analyzing the interaction data.
Emphasis, mine. This IS exciting!! :rockout:
 
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#19
Finding new solutions for a neglected tropical disease


28 Nov 2014

The last year of work really helps emphasize the tremendous scale of our project. World Community Grid volunteers generated approximately 4TB of data, consisting of more than 1.5 billion records, which store information about interaction energies between a set of Leishmania proteins and a library of 600,000 compounds.
1.5 BILLION, Billion people, Billion!! :toast:

Based on the preliminary results, we are optimistic about finding a good candidate to treat leishmaniasis, which can be improved with further computational and experimental validations. We are preparing for a second phase of the project, which involves an extra selection filter using an adapted MD protocol to avoid false positives and consequently detect molecular hits that can behave similarly to real life. With the help of all the volunteers we hope to identify at least one new molecule capable of fighting against a neglected disease that urgently needs more effective and non-toxic chemical treatments.
Could this be the "NEW" project being rumored about? BTW, I'm all in on this one!!

Working with World Community Grid for over three years has been a fantastic experience. Since the beginning of the project in September 2011, we have maintained a tight relationship with the team at World Community Grid. And of course, the volunteers who donated their computing time made this entire project possible—we can’t say thank you enough for that generosity.
Finally, we started communication with Dr. Olson´s Lab at The Scripps Research Institute in La Jolla, California. They have a lot of experience in drug discovery, and are the developers of AutoDock Vina, the program we use in the DSFL project. Their BEDAM program may allow us to filter our results further based on thermodynamic parameters.
WCG Collaboration, Nice! :D

The rest of the Story, with more detail, Here!
 
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#20
Cool. Thanks @Arjai. Even if they aren't the current beta, it means they're going to be another project coming soon hopefully.
 

manofthem

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#21
This is very cool. I don't know how I've missed this thread until just this second, but I'm lovin' it!
Great Work @Arjai :toast:
 
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#22
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#23
Help researchers find an Ebola cure


3 Dec 2014

The current outbreak of the Ebola virus is the largest in history, and has been described by the World Health Organization as "the most severe acute public health emergency seen in modern times”.
Currently, there are no approved treatments or vaccines for this deadly disease. In response to this urgent need, I reached out to my colleagues around the world to create the Viral Hemorrhagic Fever Immunotherapeutic Consortium, a collaborative effort of the world’s top Ebola experts to pool our knowledge and skills to find a cure as quickly as possible.
Today, we’re launching Outsmart Ebola Together to accelerate the search for a cure. Outsmart Ebola Together is a collaboration between The Scripps Research Institute and IBM’s World Community Grid to screen millions of chemical compounds, searching for ones that can disable the Ebola virus.
World Community Grid volunteers are critical to the success of Outsmart Ebola Together. If you have a computer or Android device, you can help too. Join World Community Grid today to donate your spare computing power to searching for Ebola treatments with our team.

Let's DO THIS!!! :toast:
 
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#24
Anybody sporting these Ebola WU's yet? Is it still in Beta? I seem to have very limited success getting Beta's...
 

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#25
I checked my two computers and no Ebola is tasked.