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  • richardmitnick 3:22 pm on November 18, 2014 Permalink | Reply
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    From NOVA: “Why There’s No HIV Cure Yet” 

    [After the NOVA article, I tell you how you and your family, friends, and colleagues can help to find a cure for AIDS and other diseases]

    PBS NOVA

    NOVA

    27 Aug 2014
    Alison Hill

    Over the past two years, the phrase “HIV cure” has flashed repeatedly across newspaper headlines. In March 2013, doctors from Mississippi reported that the disease had vanished in a toddler who was infected at birth. Four months later, researchers in Boston reported a similar finding in two previously HIV-positive men. All three were no longer required to take any drug treatments. The media heralded the breakthrough, and there was anxious optimism among HIV researchers. Millions of dollars of grant funds were earmarked to bring this work to more patients.

    But in December 2013, the optimism evaporated. HIV had returned in both of the Boston men. Then, just this summer, researchers announced the same grim results for the child from Mississippi. The inevitable questions mounted from the baffled public. Will there ever be a cure for this disease? As a scientist researching HIV/AIDS, I can tell you there’s no straightforward answer. HIV is a notoriously tricky virus, one that’s eluded promising treatments before. But perhaps just as problematic is the word “cure” itself.

    Science has its fair share of trigger words. Biologists prickle at the words “vegetable” and “fruit”—culinary terms which are used without a botanical basis—chemists wrinkle their noses at “chemical free,” and physicists dislike calling “centrifugal” a force—it’s not; it only feels like one. If you ask an HIV researcher about a cure for the disease, you’ll almost certainly be chastised. What makes “cure” such a heated word?

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    HIV hijacks the body’s immune system by attacking T cells.

    It all started with a promise. In the early 1980s, doctors and public health officials noticed large clusters of previously healthy people whose immune systems were completely failing. The new condition became known as AIDS, for “acquired immunodeficiency syndrome.” A few years later, in 1984, researchers discovered the cause—the human immunodeficiency virus, now known commonly as HIV. On the day this breakthrough was announced, health officials assured the public that a vaccine to protect against the dreaded infection was only two years away. Yet here we are, 30 years later, and there’s still no vaccine. This turned out to be the first of many overzealous predictions about controlling the HIV epidemic or curing infected patients.

    The progression from HIV infection to AIDS and eventual death occurs in over 99% of untreated cases—making it more deadly than Ebola or the plague. Despite being identified only a few decades ago, AIDS has already killed 25 million people and currently infects another 35 million, and the World Health Organization lists it as the sixth leading cause of death worldwide.

    HIV disrupts the body’s natural disease-fighting mechanisms, which makes it particularly deadly and complicates efforts to develop a vaccine against it. Like all viruses, HIV gets inside individual cells in the body and highjacks their machinery to make thousands of copies of itself. HIV replication is especially hard for the body to control because the white blood cells it infects, and eventually kills, are a critical part of the immune system. Additionally, when HIV copies its genes, it does so sloppily. This causes it to quickly mutate into many different strains. As a result, the virus easily outwits the body’s immune defenses, eventually throwing the immune system into disarray. That gives other obscure or otherwise innocuous infections a chance to flourish in the body—a defining feature of AIDS.

    Early Hope

    In 1987, the FDA approved AZT as the first drug to treat HIV. With only two years between when the drug was identified in the lab and when it was available for doctors to prescribe, it was—and remains—the fastest approval process in the history of the FDA. AZT was widely heralded as a breakthrough. But as the movie The Dallas Buyer’s Club poignantly retells, AZT was not the miracle drug many hoped. Early prescriptions often elicited toxic side-effects and only offered a temporary benefit, as the virus quickly mutated to become resistant to the treatment. (Today, the toxicity problems have been significantly reduced, thanks to lower doses.) AZT remains a shining example of scientific bravura and is still an important tool to slow the infection, but it is far from the cure the world had hoped for.

    In three decades, over 25 highly-potent drugs have been developed and FDA-approved to treat HIV.

    Then, in the mid-1990s, some mathematicians began probing the data. Together with HIV scientists, they suggested that by taking three drugs together, we could avoid the problem of drug resistance. The chance that the virus would have enough mutations to allow it to avoid all drugs at once, they calculated, would simply be too low to worry about. When the first clinical trials of these “drug cocktails” began, both mathematical and laboratory researchers watched the levels of virus drop steadily in patients until they were undetectable. They extrapolated this decline downwards and calculated that, after two to three years of treatment, all traces of the virus should be gone from a patient’s body. When that happened, scientists believed, drugs could be withdrawn, and finally, a cure achieved. But when the time came for the first patients to stop their drugs, the virus again seemed to outwit modern medicine. Within a few weeks of the last pill, virus levels in patients’ blood sprang up to pre-treatment levels—and stayed there.

    In the three decades since, over 25 more highly-potent drugs have been developed and FDA-approved to treat HIV. When two to five of them are combined into a drug cocktail, the mixture can shut down the virus’s replication, prevent the onset of AIDS, and return life expectancy to a normal level. However, patients must continue taking these treatments for their entire lives. Though better than the alternative, drug regimens are still inconvenient and expensive, especially for patients living in the developing world.

    Given modern medicine’s success in curing other diseases, what makes HIV different? By definition, an infection is cured if treatment can be stopped without the risk of it resurfacing. When you take a week-long course of antibiotics for strep throat, for example, you can rest assured that the infection is on track to be cleared out of your body. But not with HIV.

    A Bad Memory

    The secret to why HIV is so hard to cure lies in a quirk of the type of cell it infects. Our immune system is designed to store information about infections we have had in the past; this property is called “immunologic memory.” That’s why you’re unlikely to be infected with chickenpox a second time or catch a disease you were vaccinated against. When an infection grows in the body, the white blood cells that are best able to fight it multiply repeatedly, perfecting their infection-fighting properties with each new generation. After the infection is cleared, most of these cells will die off, since they are no longer needed. However, to speed the counter-attack if the same infection returns, some white blood cells will transition to a hibernation state. They don’t do much in this state but can live for an extremely long time, thereby storing the “memory” of past infections. If provoked by a recurrence, these dormant cells will reactivate quickly.

    This near-immortal, sleep-like state allows HIV to persist in white blood cells in a patient’s body for decades. White blood cells infected with HIV will occasionally transition to the dormant state before the virus kills them. In the process, the virus also goes temporarily inactive. By the time drugs are started, a typical infected person contains millions of these cells with this “latent” HIV in them. Drug cocktails can prevent the virus from replicating, but they do nothing to the latent virus. Every day, some of the dormant white blood cells wake up. If drug treatment is halted, the latent virus particles can restart the infection.

    Latent HIV’s near-immortal, sleep-like state allows it to persist in white blood cells in a patient’s body for decades.

    HIV researchers call this huge pool of latent virus the “barrier to a cure.” Everyone’s looking for ways to get rid of it. It’s a daunting task, because although a million HIV-infected cells may seem like a lot, there are around a million times that many dormant white blood cells in the whole body. Finding the ones that contain HIV is a true needle-in-a-haystack problem. All that remains of a latent virus is its DNA, which is extremely tiny compared to the entire human genome inside every cell (about 0.001% of the size).
    Defining a Cure

    Around a decade ago, scientists began to talk amongst themselves about what a hypothetical cure could look like. They settled on two approaches. The first would involve purging the body of latent virus so that if drugs were stopped, there would be nothing left to restart the infection. This was often called a “sterilizing cure.” It would have to be done in a more targeted and less toxic way than previous attempts of the late 1990s, which, because they attempted to “wake up” all of the body’s dormant white blood cells, pushed the immune system into a self-destructive overdrive. The second approach would instead equip the body with the ability to control the virus on its own. In this case, even if treatment was stopped and latent virus reemerged, it would be unable to produce a self-sustaining, high-level infection. This approach was referred to as a “functional cure.”

    The functional cure approach acknowledged that latency alone was not the barrier to a cure for HIV. There are other common viruses that have a long-lived latent state, such as the Epstein-Barr virus that causes infectious mononucleosis (“mono”), but they rarely cause full-blown disease when reactivated. HIV is, of course, different because the immune system in most people is unable to control the infection.

    The first hint that a cure for HIV might be more than a pipe-dream came in 2008 in a fortuitous human experiment later known as the “Berlin patient.” The Berlin patient was an HIV-positive man who had also developed leukemia, a blood cancer to which HIV patients are susceptible. His cancer was advanced, so in a last-ditch effort, doctors completely cleared his bone marrow of all cells, cancerous and healthy. They then transplanted new bone marrow cells from a donor.

    Fortunately for the Berlin patient, doctors were able to find a compatible bone marrow donor who carried a unique HIV-resistance mutation in a gene known as CCR5. They completed the transplant with these cells and waited.

    For the last five years, the Berlin patient has remained off treatment without any sign of infection. Doctors still cannot detect any HIV in his body. While the Berlin patient may be cured, this approach cannot be used for most HIV-infected patients. Bone marrow transplants are extremely risky and expensive, and they would never be conducted in someone who wasn’t terminally ill—especially since current anti-HIV drugs are so good at keeping the infection in check.

    Still, the Berlin patient was an important proof-of-principle case. Most of the latent virus was likely cleared out during the transplant, and even if the virus remained, most strains couldn’t replicate efficiently given the new cells with the CCR5 mutation. The Berlin patient case provides evidence that at least one of the two cure methods (sterilizing or functional), or perhaps a combination of them, is effective.

    Researchers have continued to try to find more practical ways to rid patients of the latent virus in safe and targeted ways. In the past five years, they have identified multiple anti-latency drug candidates in the lab. Many have already begun clinical trials. Each time, people grow optimistic that a cure will be found. But so far, the results have been disappointing. None of the drugs have been able to significantly lower levels of latent virus.

    In the meantime, doctors in Boston have attempted to tease out which of the two cure methods was at work in the Berlin patient. They conducted bone marrow transplants on two HIV-infected men with cancer—but this time, since HIV-resistant donor cells were not available, they just used typical cells. Both patients continued their drug cocktails during and after the transplant in the hopes that the new cells would remain HIV-free. After the transplants, no HIV was detectable, but the real test came when these patients volunteered to stop their drug regimens. When they remained HIV-free a few months later, the results were presented at the International AIDS Society meeting in July 2013. News outlets around the world declared that two more individuals had been cured of HIV.

    Latent virus had likely escaped the detection methods available.

    It quickly became clear that everyone had spoken too soon. Six months later, researchers reported that the virus had suddenly and rapidly returned in both individuals. Latent virus had likely escaped the detection methods available—which are not sensitive enough—and persisted at low, but significant levels. Disappointment was widespread. The findings showed that even very small amounts of latent virus could restart an infection. It also meant meant that the anti-latency drugs in development would need to be extremely potent to give any hope of a cure.

    But there was one more hope—the “Mississippi baby.” A baby was born to an HIV-infected mother who had not received any routine prenatal testing or treatment. Tests revealed high levels of HIV in the baby’s blood, so doctors immediately started the infant on a drug cocktail, to be continued for life.

    The mother and child soon lost touch with their health care providers. When they were relocated a few years later, doctors learned that the mother had stopped giving drugs to the child several months prior. The doctors administered all possible tests to look for signs of the virus, both latent and active, but they didn’t find any evidence. They chose not to re-administer drugs, and a year later, when the virus was still nowhere to be found, they presented the findings to the public. It was once again heralded as a cure.

    Again, it was not to be. Just last month, the child’s doctors announced that the virus had sprung back unexpectedly. It seemed that even starting drugs as soon as infection was detected in the newborn could not prevent the infection from returning over two years later.
    Hope Remains

    Despite our grim track record with the disease, HIV is probably not incurable. Although we don’t have a cure yet, we’ve learned many lessons along the way. Most importantly, we should be extremely careful about using the word “cure,” because for now, we’ll never know if a person is cured until they’re not cured.

    Clearing out latent virus may still be a feasible approach to a cure, but the purge will have to be extremely thorough. We need drugs that can carefully reactivate or remove latent HIV, leaving minimal surviving virus while avoiding the problems that befell earlier tests that reactivated the entire immune system. Scientists have proposed multiple, cutting-edge techniques to engineer “smart” drugs for this purpose, but we don’t yet know how to deliver this type of treatment safely or effectively.

    As a result, most investigations focus on traditional types of drugs. Researchers have developed ways to rapidly scan huge repositories of existing medicines for their ability to target latent HIV. These methods have already identified compounds that were previously used to treat alcoholism, cancer, and epilepsy, and researchers are repurposing them to be tested in HIV-infected patients.
    The less latent virus that remains, the less chance there is that the virus will win the game of chance.

    Mathematicians are also helping HIV researchers evaluate new treatments. My colleagues and I use math to take data collected from just a few individuals and fill in the gaps. One question we’re focusing on is exactly how much latent virus must be removed to cure a patient, or at least to let them stop their drug cocktails for a few years. Each cell harboring latent virus is a potential spark that could restart the infection. But we don’t know when the virus will reactivate. Even once a single latent virus awakens, there are still many barriers it must overcome to restart a full-blown infection. The less latent virus that remains, the less chance there is that the virus will win this game of chance. Math allows us to work out these odds very precisely.

    Our calculations show that “apparent cures”—where patients with latent virus levels low enough to escape detection for months or years without treatment—are not a medical anomaly. In fact, math tells us that they are an expected result of these chance dynamics. It can also help researchers determine how good an anti-latency drug should be before it’s worth testing in a clinical trial.

    Many researchers are working to augment the body’s ability to control the infection, providing a functional cure rather than a sterilizing one. Studies are underway to render anyone’s immune cells resistant to HIV, mimicking the CCR5 mutation that gives some people natural resistance. Vaccines that could be given after infection, to boost the immune response or protect the body from the virus’s ill effects, are also in development.

    In the meantime, treating all HIV-infected individuals—which has the added benefit of preventing new transmissions—remains the best way to control the epidemic and reduce mortality. But the promise of “universal treatment” has also not materialized. Currently, even in the U.S., only 25% of HIV-positive people have their viral levels adequately suppressed by treatment. Worldwide, for every two individuals starting treatment, three are newly infected. While there’s no doubt that we’ve made tremendous progress in fighting the virus, we have a long way to go before the word “cure” is not taboo when it comes to HIV/AIDS.

    See the full article here.

    Did you know that you can help in the fight against AIDS? By donating time on your computer to the Fight Aids at Home project of World Community Grid, you can become a part of the solution. The work is called “crunching” because you are crunching computational data the results of which will then be fed back into the necessary lab work. We save researchers literally millions of hours of lab time in this process.
    Vsit World Community Grid (WCG) or Berkeley Open infrastructure for Network Computing (BOINC). Download the BOINC software and install it on your computer. Then visit WCG and attach to the FAAH project. The project will send you computational work units. Your computer will process them and send the results back to the project, the project will then send you more work units. It is that simple. You do nothing, unless you want to get into the nuts and bolts of the BOINC software. If you take up this work, and if you see it as valuable, please tell your family, friends and colleagues, anyone with a computer, even an Android tablet. We found out that my wife’s oncologist’s father in Brazil is a cruncher on two projects from WCG.

    This is the projects web site. Take a look.

    While you are visiting BOINC and WCG, look around at all of the very valuable projects being conducted at some of the worlds most distinguished universities and scientific institutions. You can attach to as many as you like, on one or a number of computers. You can only be a help here, particpating in Citizen Science.

    This is a look at the present and past projects at WCG:

    Please visit the project pages-

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    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
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    Please help promote STEM in your local schools.

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    NOVA is the highest rated science series on television and the most watched documentary series on public television. It is also one of television’s most acclaimed series, having won every major television award, most of them many times over.

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  • richardmitnick 1:47 pm on November 11, 2014 Permalink | Reply
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    From DDDT at WCG: “Discovering Dengue Drugs – Together” 

    New WCG Logo

    10 Nov 2014
    By: Dr. Stan Watowich, PhD
    University of Texas Medical Branch (UTMB) in Galveston, Texas

    Summary
    For week five of our decade of discovery celebrations we’re looking back at the Discovering Dengue Drugs – Together project, which helped researchers at the University of Texas Medical Branch at Galveston search for drugs to help combat dengue – a debilitating tropical disease that threatens 40% of the world’s population. Thanks to World Community Grid volunteers, researchers have identified a drug lead that has the potential to stop the virus in its tracks.

    mic

    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 the World 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.

    The disease is a mosquito-borne infection found in tropical and sub-tropical regions – primarily in the developing world. It belongs to the flavivirus family of viruses, together with Hepatitis C, West Nile and Yellow Fever.

    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.

    In the first phase of the project, we aimed to identify compounds that could be used to develop dengue drugs. Thanks to the computing power donated by World Community Grid volunteers, my fellow researchers and I at the University of Texas Medical Branch in Galveston, Texas, screened around three million chemical compounds to determine which ones would bind to the dengue virus and disable it.

    By 2009 we had found several thousand promising compounds to take to the next stage of testing. We began identifying the strongest compounds from the thousands of potentials, with the goal of turning these into molecules that could be suitable for human clinical trials.

    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. Importantly, our newly discovered drug lead also demonstrates no negative side effects such as adverse toxicity, carcinogenicity or mutagenicity risks, making it a promising antiviral drug candidate for dengue and potentially other flavivirues. We are working with medicinal chemists to synthesize variants of this exciting candidate molecule with the goal of improving its activity for planned pre-clinical and clinical trials.

    I’d like to express my gratitude for the dedication of World Community Grid volunteers. The advances we are making, and our improved understanding of drug discovery software and its current limitations, would not have been possible without your donated computing power.

    If you’d like to help researchers make more ground-breaking discoveries like this – and have the chance of winning some fantastic prizes – take part in our decade of discovery competition by encouraging your friends to sign up to World Community Grid today. There’s a week left and the field is wide open – get started today!

    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-

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    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 November 7, 2014 Permalink | Reply
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    From WCG: “Decade of discovery: New precision tools to diagnose and treat cancer” 

    New WCG Logo

    3 Nov 2014
    By: Dr. David J. Foran, PhD
    Rutgers Cancer Institute of New Jersey

    Summary
    It’s week four of our 10th anniversary celebrations, and we’re following up last week’s childhood cancer feature by spotlighting another cancer project that’s helped researchers develop powerful new tools to diagnose cancer and tailor treatments to individual patients, using big data and analytics.

    no

    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.

    A key tool for precision medicine is tissue microarray analysis. This enables investigators to analyze large batches of tissue sample images simultaneously, so they can look for patterns and identify cancer signatures. It also provides them with a deeper understanding of cancer biology and uncovers new sub-classifications of cancer and likely patient responses – all of which influence new courses of treatment and future drug design.

    Tissue microarray analysis shows great promise, but it is not without its limitations. Pathologists typically examine the specimens visually, resulting in subjective interpretations and variations in diagnoses.

    We realized that if this method of analysis could be automated using digital pattern recognition algorithms, we could improve accuracy and reveal new patterns across large sets of data. This would make it possible for researchers to determine a patient’s type and stage of cancer more precisely, meaning they can prescribe therapies or combinations of treatments that are most likely to be effective.

    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.

    Access to this vast computing power enabled our team to rapidly conduct this research under a much wider range of environmental conditions and to perform specimen analysis at much greater degrees of sensitivity.

    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.

    Leveraging these experimental results, our team secured competitive funding from the National Institutes of Health (NIH) to build a clinical decision support system to automatically analyze and classify cancer specimens with improved diagnostic and prognostic accuracy. We used the core reference library of expression signatures generated through the Help Defeat Cancer project to demonstrate the proof-of-concept for the system.

    These decision support tools are now being tested and refined by investigators from the Rutgers Cancer Institute of New Jersey, Stony Brook University School of Medicine, University of Pittsburgh Medical Center and Emory University. They are exploring how the tools can aid clinical decision-making, plus are pursuing further investigative research. Together, our ultimate aim is to refine these tools sufficiently so they can be certified for routine clinical use in diagnosing and treating patients.

    Although the Help Defeat Cancer project has completed its research on World Community Grid, we continue to investigate the findings and they have contributed to some significant new beginnings. At Rutgers Cancer Institute of New Jersey, physicians and scientists – aided by high-performance computing resources – are analyzing genomes and human tissues, and identifying cancer patterns, faster than ever before.

    In collaboration with our research partners at the Rutgers Discovery Informatics Institute (RDI2) and RUCDR Infinite Biologics (the world’s largest university-based biorepository, located within the Human Genetics Institute of New Jersey), the Rutgers Cancer Institute is shaping a revolution in how best to determine cancer therapy for patients – a vast improvement from the time-intensive, trial-and-error approach that doctors have faced for years. To date, only a fraction of known cancer biomarkers have been examined. The long-term goal is to create a library of biomarkers and their expression patterns so that, in the future, physicians can consult the library to help diagnose cancer patients and provide them with the most effective treatment.

    I would like to express my gratitude to Stanley Litow, Robin Willner, and Jen Crozier from IBM and to World Community Grid’s Advisory Board for supporting the Help Defeat Cancer project. I’d also like to extend my special thanks to the IBM World Community Grid team members who contributed to the success of the project – I hope to have the opportunity to work with them again in the near future.

    Additionally, I would like to acknowledge the NIH, Department of Defense and IBM for supporting this research – and give credit to those individuals from my laboratory and partnering institutions who were involved in the early experiments and the initial design and development of the imaging and computational tools, which we then used throughout the project. And, of course, a very big thank you to all the World Community Grid volunteers – without their support, our accomplishments with Help Defeat Cancer would not have been possible.

    The Help Defeat Cancer project has completed its analysis on World Community Grid – but another innovative project, Mapping Cancer Markers, is currently running and needs your help. Help us celebrate a decade of discovery on World Community Grid by sharing this story and encouraging your friends to donate their unused computing power to cutting-edge cancer research.

    Here’s to another decade of discovery.

    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-

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    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 4:52 pm on November 6, 2014 Permalink | Reply
    Tags: , BOINC, , ,   

    From FAAH at WCG: “Teamwork yields experimental support for FightAIDS@Home calculations” 

    New WCG Logo

    By: The FightAIDS@Home research team
    6 Nov 2014

    Summary
    Imaging studies have now confirmed some of the computational predictions made during FightAIDS@Home, providing important confirmation of our methodology and the value of your computational results. This work is ongoing, but promises to increase our understanding of how HIV protease can be disrupted.

    site
    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 of FightAIDS@Home.

    We’re excited to announce that our collaborators at Scripps Florida have now optimized their NMR experiments and have been able to characterize the binding of promising ligands with the prospective allosteric sites on the HIV protease. These sites represent new footholds in the search for therapies that defeat viral drug resistance. The NMR experiment allows us to detect the location of the interactions between the candidate inhibitors and the protein, but unlike X-ray crystallography experiments, these interactions are measured in solution, which better represents the biological environment.

    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.

    There are many more NMR experiments still to run, but another advantage of NMR over crystallography is that it does not require the lengthy step of growing diffraction-quality crystals. This allows higher experimental throughput, so we look forward to experimental confirmation of many more compounds in much shorter time. So far we have shipped 15 compounds to test and another batch is going to be sent this week. The new compounds will help to validate another potential interaction site on one of HIV protease’s two movable “flaps”.

    Once the validation is completed, we will proceed to test a number of compounds that we identified in different FightAIDS@Home experiments for all of the target protease allosteric sites.

    As always, thank you for your support! This research would not be possible without your valuable computing time.

    The Scripps research team needs your help to continue making progress on developing new treatments for AIDS! Take part in our decade of discovery competition by encouraging your friends to sign up to World Community Grid today to start donating their computer or mobile device’s computing power to FightAIDS@Home. There’s just over a week left and some great prizes are up for grabs – get started today!

    Here’s to another decade of discovery.

    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-

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    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: , , BOINC, ,   

    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: , , BOINC,   

    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 5:38 am on July 26, 2014 Permalink | Reply
    Tags: , BOINC, OProject@home,   

    OProject@home
    OProject@home

    OProject@Home is a research project that uses Internet-connected computers. You can participate by downloading and running a free program on your computer.

    The main idea of this project is the analysis of algorithms.

    project
    The sub-project Shor’s Algorithm is slowly going to an end

    The sub-project Shor’s Algorithm is slowly going to an end. Tasks will be still available for some time, so it will be possible to download them, calculate and return for the validation.

    Many users have complained about the lack of apps for Windows. Therefore, at the end we decided to add an Shor’s Algorithm application for Windows. The application is not yet available for this platform (because of some technical problems), but this should change soon.

    Thank you all for your help in the calculation. Also, thanks to your support we were able to create a paper: Simulation of a functional quantum system on parallel, classical IV generation computers (English title).

    Bachelor of Science thesis
    It was published my Bachelor of Science thesis: “Symulacja funkcjonalnego systemu kwantowego na równoległych komputerach klasycznych IV generacji”.

    English title: “Simulation of a functional quantum system on parallel, classical IV generation computers”.

    The thesis can be downloaded from the CEON repository – URL:
    https://depot.ceon.pl/handle/123456789/1923

    Thesis available only in Polish. 22 Jun 2013 | 10:52:01 UTC · Comment

    OProject@Home based at OLib Library. The library is open and available in the code.google.com SVN repository.

    If you are interested in helping with this project, visit BOINC, download and install the software on which the project is running. While you are at BOINC, look over some of the other projects to see what else you might find of interest.

    BOINC


    ScienceSprings is powered by MAINGEAR computers

     
  • richardmitnick 10:16 pm on July 21, 2014 Permalink | Reply
    Tags: , , BOINC, , , ,   

    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: , , BOINC, , , ,   

    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 8:17 pm on July 20, 2014 Permalink | Reply
    Tags: , , BOINC, CAS@home,   

    From CAS@home 

    CAS@home
    CAS@home is hosted by the Computing Centre of the Institute of High Energy Physics (IHEP), Chinese Academy of Sciences. CAS@home is a volunteer computing platform for Chinese scientists based on the BOINC volunteer computing software. CAS@home collects the volunteer contributions to computing resources for scientists at the Chinese Academy of Sciences and other Chinese research institutions, to provide massive free computing resources that help the scientists complete major scientific computing tasks. Therefore, CAS@home supports multiple applications. The first application to be launched on CAS@home was developed by scientists at the Institute of Computing Technology (ICT), Chinese Academy of Sciences. It focused on protein structure prediction application (software called SCThread). In addition, Tsinghua University’s Centre for Micro and Nano Mechanics (CNMM) an interdisciplinary innovation research center, has prepared an application for simulating flow of fluids and motion of solids on the nanoscale. Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, is preparing an application for gene sequencing for applications in cancer research. And physicists of the Institute of High Energy Physics (IHEP), Chinese Academy of Sciences, are preparing an application for simulating particle collisions at the Beijing Electron Positron Collider, based on software called BOSS.

    If you wish to participate in this project, download and install the BOINC software upon which it runs. Then attach to the project. While you are at BOINC, look over some of the other projects. You might find them to be of interest.

    BOINC


    ScienceSprings is powered by MAINGEAR computers

     
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