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  • richardmitnick 4:28 pm on October 16, 2014 Permalink | Reply
    Tags: , , World Community Grid   

    From WCG: “Project Launch: Uncovering Genome Mysteries” 

    16 Oct 2014
    Summary
    To kick off World Community Grid’s 10th anniversary celebrations, we’re launching Uncovering Genome Mysteries to compare hundreds of millions of genes from many organisms that have never been studied before, helping scientists unearth some of the hidden superpowers of the natural world.

    From the realization that the Penicillium fungus kills germs, to the discovery of bacteria that eat oil spills and the identification of aspirin in the willow tree bark – a better understanding of the natural world has resulted in many improvements to human health, welfare, agriculture and industry.

    diver
    Diver collecting microbial samples from Australian seaweeds for Uncovering Genome Mysteries

    Our understanding of life on earth has grown enormously since the advent of genetic research. But the vast majority of life on this planet remains unstudied or unknown, because it’s microscopic, easy to overlook, and hard to study. Nevertheless, we know that tiny, diverse organisms are continually evolving in order to survive and thrive in the most extreme conditions. The study of these organisms can provide valuable insights on how to deal with some of the most pressing problems that human society faces, such as drug-resistant pathogens, pollution, and energy shortages.

    Inexpensive, rapid DNA sequencing technologies have enabled scientists to decode the genes of many organisms that previously received little attention, or were entirely unknown to science. However, making sense of all that genomic information is an enormous task. The first step is to compare unstudied genes to others that are already better understood. Similarities between genes point to similarities in function, and by making a large number of these comparisons, scientists can begin to sort out what each organism is and what it can do.

    In Uncovering Genome Mysteries, World Community Grid volunteers will run approximately 20 quadrillion comparisons to identify similarities between genes in a wide variety of organisms, including microorganisms found on seaweeds from Australian coastlines and in the Amazon River. This database of similarities will help researchers understand the diversity and capabilities that are hidden in the world all around us. For more on the project’s aims and methods, see here.

    Once published, these results should help scientists with the following goals:

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

    In addition, a better understanding of these organisms will likely be useful in developing new medicines, harnessing new sources of renewable energy, improving nutrition, cleaning the environment, creating green industrial processes and many other advances.

    The timing of this project launch is a perfect way to kick off celebrations of another important achievement – World Community Grid’s 10th anniversary. There’s much to celebrate and reflect upon from the past decade’s work, but it’s equally important to continue pushing forward and making new scientific discoveries. With your help – and the help of your colleagues and friends – we can continue to expand our global network of volunteers and achieve another 10 years of success. Here’s to another decade of discovery!

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

    Please visit the following pages to learn more:

    Uncovering Genome Mysteries project overview
    Frequently Asked Questions

    See the full article here.

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 7:38 pm on October 2, 2014 Permalink | Reply
    Tags: , , , , World Community Grid   

    From WCG: “Global PC network gives researchers supercomputer power” 

    star

    Sep 21 2014
    Joseph Hall

    Igor Jurisica wants you to help him conquer cancer.

    Oh, don’t worry, the Princess Margaret Cancer Centre scientist is not looking for money.

    But he would like to borrow your computer.

    In the age of molecular medicine, with its staggering genetic complexity, much cutting-edge cancer research has become a game of brute computational number crunching.

    And with access to laboratory supercomputers scarce and expensive, Jurisica has turned to a massive network of home and business PCs to run his research algorithms.

    “It’s basically a network of workstations around the globe,” says Jurisica, a computational biologist at the hospital and a University of Toronto professor.

    “When you’re not using your machine (it) can be donated for the project.”

    Known as the World Community Grid, the IBM-run network has gathered some 676,000 businesses and individuals globally who have volunteered about 2.9 million computers of varying capacities to help run scientific studies.

    Some 13,000 Canadian volunteers are currently donating time on about 67,000 devices.

    Begun last November, Jurisica’s Mapping Cancer Markers project has been granted access to about one-third of the machines worldwide, which gives him some 258 computer processing unit (CPU) years worth of power to run his data each day.

    jm
    Igor Jurisica is using global network of computers to discover more precise cancer treatments. Andrew Francis Wallace / Toronto Star

    That means a typical computer would have to run continuously for 258 years to process the data the network can work through in 24 hours.

    In aggregate, the full grid can generate more than 400 CPU years each day, which would rank it among the world’s 15 largest supercomputers, said Viktors Berstis, the senior IBM software engineer who runs the network.

    “When you have these big data problems, you have big processing problems to go with them,” Berstis said.

    “And so these kinds of projects that take many tens of thousands of years of CPU time are so massive that only the biggest supercomputers can handle them.”

    Again the problem, Berstis said, is that an institution with a supercomputer must typically divvy up access to it among hundreds or thousands of competing researchers.

    “So no one researcher gets that supercomputer 24/7 for several years on end which is the equivalent of what we’re giving (them),” he said.

    “They are getting something extremely rare and they are getting it for free.”

    The grid, which is eager for more volunteers, is run through a Toronto-based central processor that accesses home and business computers when the donors are not using them, Berstis said.

    It’s available for downloading to anyone who has a computer or Android device running Windows, Mac or Linux systems by going to the grid site and clicking the join link.

    That downloads a program to the home or business computer which will run in the device’s background at the lowest priority, Berstis said.

    “The instant your computer has nothing else left to do for you, then it can work a piece of this big research problem,” he said.

    “We try to make this software very unobtrusive so it doesn’t bother anything else.”

    Volunteers can donate their unused capacity in a number of ways, even allowing project computing to be done in the microseconds between key strokes.

    Member machines contact the central Toronto processor when they’re ready for work and are sent a tiny portion of a project problem.

    The worked information is then sent back to the server where it is checked for accuracy and cobbled together with all the other incoming data.

    Berstis said the grid code has been scoured line by line by IBM programmers for potential security problems and is likely to be the safest piece of software on any machine.

    He said the network also boasts environmental benefits.

    “When you have a supercomputer centre you have to have an air conditioning system that is almost as powerful as the computer to cool it back down so that the building doesn’t melt,” he said.

    The IBM grid is similar to one used by the earlier SETI — or Search for Extraterrestrial Intelligence — project, which linked millions of home computers to help scan the heavens for alien signals.

    Grid volunteers can also download screensavers that relate to the science project — there are currently three — that their computers are helping to crunch.

    Jurisica’s cancer marker project is the largest of these and is looking to discover the genetic and molecular signatures of lung, prostate, ovarian and sarcoma cancers — a search of stupefying complexity.

    When the Human Genome Project released its map of our species’ DNA more than a decade ago, it opened the door to the possibility of personalized medicine, where an individual’s cancer or heart disease could be diagnosed and treated according to its specific genetic signatures.

    Unfortunately, the genome project also opened a Pandora’s box of complexity in medicine with the realization that any single gene could be run or influenced by a mesmerizing array of other genetic materials and their protein products.

    And an individual’s complex cancer signatures, for example, would determine whether their disease could be detected early or would respond to given therapies.

    Jurisica said, however, that one cancer biopsy may now generate some 40,000 potentially involved variables. That means finding a set of signatures for any particular cancer — and there may be dozens across the patient population — could be a daunting exercise.

    In its search for such signatures — or markers — the Princess Margaret project has so far used up more than 81,000 CPU years of computation.

    Berstis said IBM began building the service a decade ago as one of its “Good Citizen’s Projects” and that researchers are selected on the scientific value of their proposals.

    [Correct certain inaccuracies: First, SETI@home is still running. Second, no mention was made that all of WCG runs on BOINC software from the Space Science Lab at U.C. Berkeley. Most important, long past is the day when WCG ran only when a computer was idle or took last position in what was running. All of that was true when BOINC and WCG were much younger and home computers had little of today's power. While you can calibrate down how much CPU and memory are used, there is little need to with quad core and hyper threaded dual-core processors. Just know that the BOINC process develops a great deal of heat which must be dissipated.]

    See the full article here.

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.


    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 4:19 pm on September 18, 2014 Permalink | Reply
    Tags: , , , World Community Grid   

    From WCG: New Team 

    September 18, 2014

    World Community Grid is pleased to welcome Vivere Ateneo, as a new partner! Vivere Ateneo is associated with the Polytechnic School at the University of Palermo, Italy and is committed to supporting World Community Grid as one of their philanthropic projects. You can learn more about their team here: http://ow.ly/BEArd

    Team Information
    Name: BOINC – Vivere Ateneo – Scuola Politecnica
    Created: 08/24/2014
    Captain: Ivan Marchese
    Country: ITALY
    Type: University or department
    Description: The project BOINC – Living University is a collaboration between Living University, the Polytechnic School of the University of Palermo and the IBM Foundation Italy to support the design of distributed computing platform WCG. The Team BOINC – Living University, wants to be a clear structure for anyone who wants to start a volunteer computing project dedicated to the development of treatments against AIDS, Cancer and energy innovation of the future (Clean Energy).

    BOINC Team Id: 31488

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 2:44 pm on September 4, 2014 Permalink | Reply
    Tags: , , World Community Grid   

    From WCG: Please welcome World Community Grid’s newest partner 

    Please welcome World Community Grid’s newest partner – ANEPF (Association Nationale des Etudiants en Pharmacie de France)! ANEPF represent the interests of French pharmacy students, with health policy and education being key focus areas. You can check out their team here: http://ow.ly/B63fB

    anepf

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.


    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 8:53 am on September 3, 2014 Permalink | Reply
    Tags: , , World Community Grid   

    From WCG: Last Month’s Activity 

    Last month, #WCGrid volunteers donated over 12,000 years of computing time & over 30 million results to our humanitarian projects!

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 3:13 pm on August 4, 2014 Permalink | Reply
    Tags: , , World Community Grid   

    From World Community Grid: A Banner Month 

    Last month, World Community Grid volunteers donated almost 13,000 years of computer run time and over 37 million results were returned towards our humanitarian projects! Thank you all for your continued support, and please, recruit a friend or two to join this great cause!

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 2:28 pm on July 29, 2014 Permalink | Reply
    Tags: , , , World Community Grid   

    From WCG: “Calling all climate change scientists” 

    29 Jul 2014

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

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

    To date, over 300,000 World Community Grid volunteers have already provided sustainability scientists with the equivalent of almost 100,000 years of computing power to support researchers in numerous fields, including energy, water and agricultural science:

    The University of Virginia’s Computing for Sustainable Water project is shedding new light on the effects of human activity on the Chesapeake Bay watershed. Organizations and policymakers will be able to use this data-driven insight to guide their efforts to support the restoration and health of the area.

    water

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

    rice

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

    We invite sustainability researchers who could benefit from massive supercomputing power to advance their work to submit a project proposal. In addition, anyone can contribute to understanding climate change and mitigating its impacts by joining World Community Grid and supporting our current research projects. Take a minute right now to start supporting cutting-edge climate science.

    See the full article here.

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp


    ScienceSprings is powered by MAINGEAR computers

     
  • richardmitnick 10:16 pm on July 21, 2014 Permalink | Reply
    Tags: , , , , , , World Community Grid   

    From WCG: “Pioneering a Molecular Approach to Fighting AIDS” 

    World Community Grid

    Dr. Arthur Olson
    Professor, The Scripps Research Institute
    21 Jul 2014

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

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

    FightAidsOlsonLab@home

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

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

    World Community Grid has enabled our research to progress well beyond what we could have dreamed of when we started our HIV research in the early 1990s. Through our FightAIDS@Home project, we can screen millions of chemical compounds to evaluate their effectiveness against HIV target proteins – including those known to be drug-resistant. By deploying these and other methods, we have significantly increased our understanding of HIV and its ability to evolve to resist treatment. Using these computational capabilities, we have just begun working with an HIV Cure researcher to help us move beyond treatment in search of a cure.

    See the full article here.

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    Computing for Sustainable Water

    Mapping Cancer Markers
    Mapping Cancer Markers Banner

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp


    ScienceSprings is powered by MAINGEAR computers

     
  • richardmitnick 8:57 pm on July 20, 2014 Permalink | Reply
    Tags: , , , , , , World Community Grid   

    From Mapping Cancer Markers at WCG: “Project roadmap and first phase results from the Mapping Cancer Markers team” 

    Mapping Cancer Markers

    Mapping Cancer Markers Banner

    Mapping Cancer Markers

    By: The Mapping Cancer Markers research team
    10 Jul 2014

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

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

    Project roadmap

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

    Currently, the Mapping Cancer Markers project has two phases:

    In the first phase we have been attempting to set a benchmark for further experiments.
    The second phase will be geared towards finding clinically useful molecular signatures, initially focusing on gene signatures that can predict the occurrence of various types of cancer.

    We expect a smooth transition between the two phases, with no interruption in work. The “benchmarking” phase of our project is important not only for our own research, but for other researchers around the world. Every year, numerous groups worldwide develop and publish interesting molecular signatures for various diseases, including multiple cancers. One of the challenges of interpreting these findings is that many of the reports are not directly comparable to each other. The benchmarking phase of our project is designed to set a standard benchmark so that we and other groups can estimate how well individual signatures perform.

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

    Benchmarking

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

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

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

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

    Funding & Fundraising

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

    Finally, if you will be in Ontario between 15-17 August, please consider donating to, or cheering on the Team Ian Ride from Kingston to Montreal, which raises money for the Ian Lawson Van Toch Cancer Informatics Fund at the Princess Margaret Cancer Centre (if you are interested, please contact us about joining the Team Ian ride this or next year). If you can join us, it will give you the chance to meet some of the research team, as well as raise money for a worthy cause and participate in an outstanding event. For more details visit:http://www.team-ian.org/

    Cancers, one of the leading causes of death worldwide, come in many different types and forms in which uncontrolled cell growth can spread to other parts of the body. Unchecked and untreated, cancer can spread from an initial site to other parts of the body and ultimately lead to death. The disease is caused by genetic or environmental changes that interfere with biological mechanisms that control cell growth. These changes, as well as normal cell activities, can be detected in tissue samples through the presence of their unique chemical indicators, such as DNA and proteins, which together are known as “markers.” Specific combinations of these markers may be associated with a given type of cancer.

    The pattern of markers can determine whether an individual is susceptible to developing a specific form of cancer, and may also predict the progression of the disease, helping to suggest the best treatment for a given individual. For example, two patients with the same form of cancer may have different outcomes and react differently to the same treatment due to a different genetic profile. While several markers are already known to be associated with certain cancers, there are many more to be discovered, as cancer is highly heterogeneous.

    Mapping Cancer Markers on World Community Grid aims to identify the markers associated with various types of cancer. The project is analyzing millions of data points collected from thousands of healthy and cancerous patient tissue samples. These include tissues with lung, ovarian, prostate, pancreatic and breast cancers. By comparing these different data points, researchers aim to identify patterns of markers for different cancers and correlate them with different outcomes, including responsiveness to various treatment options.

    This project runs on BOINC software. Visit BOINC or WCG, download and install the software and attach to the project. While you are at BOINC and WCG, look over the other projects for some that you might find of interest.

    WCG

    BOINC


    ScienceSprings is powered by MAINGEAR computers

     
  • richardmitnick 11:18 am on July 19, 2014 Permalink | Reply
    Tags: , , , , , , , , World Community Grid   

    Mapping Cancer Markers From WCG 

    Mapping Cancer Markers

    Mapping Cancer Markers Banner

    Mapping Cancer Markers

    Cancers, one of the leading causes of death worldwide, come in many different types and forms in which uncontrolled cell growth can spread to other parts of the body. Unchecked and untreated, cancer can spread from an initial site to other parts of the body and ultimately lead to death. The disease is caused by genetic or environmental changes that interfere with biological mechanisms that control cell growth. These changes, as well as normal cell activities, can be detected in tissue samples through the presence of their unique chemical indicators, such as DNA and proteins, which together are known as “markers.” Specific combinations of these markers may be associated with a given type of cancer.

    The pattern of markers can determine whether an individual is susceptible to developing a specific form of cancer, and may also predict the progression of the disease, helping to suggest the best treatment for a given individual. For example, two patients with the same form of cancer may have different outcomes and react differently to the same treatment due to a different genetic profile. While several markers are already known to be associated with certain cancers, there are many more to be discovered, as cancer is highly heterogeneous.

    Mapping Cancer Markers on World Community Grid aims to identify the markers associated with various types of cancer. The project is analyzing millions of data points collected from thousands of healthy and cancerous patient tissue samples. These include tissues with lung, ovarian, prostate, pancreatic and breast cancers. By comparing these different data points, researchers aim to identify patterns of markers for different cancers and correlate them with different outcomes, including responsiveness to various treatment options.

    This project runs on BOINC software. Visit BOINC or WCG, download and install the software and attach to the project. While you are at BOINC and WCG, look over the other projects for some that you might find of interest.

    WCG

    BOINC


    ScienceSprings is powered by MAINGEAR computers

     
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