Tagged: BOINC Toggle Comment Threads | Keyboard Shortcuts

  • richardmitnick 4:14 pm on May 24, 2017 Permalink | Reply
    Tags: BOINC, , ,   

    From The Atlantic via SETI@home: “A Brief History of SETI@Home” 

    SETI@home
    SETI@home

    The Atlantic

    1
    Frank Drake, (Left) president of the SETI (Search for Extraterrestrial Intelligence) reviews data from radiotelescopes used to scan the universe for intelligent life.

    How astronomers deputized early internet users to help find alien civilizations.

    The year was 1999, and the people were going online. AOL, Compuserve, mp3.com, and AltaVista loaded bit by bit after dial-up chirps, on screens across the world. Watching the internet extend its reach, a small group of scientists thought a more extensive digital leap was in order, one that encompassed the galaxy itself. And so it was that before the new millennium dawned, researchers at the University of California released a citizen-science program called SETI@Home.

    The idea went like this: When internet-farers abandoned their computers long enough that a screen saver popped up, that saver wouldn’t be WordArt bouncing around, 3-D neon-metallic pipes installing themselves inch by inch, or a self-satisfied flying Windows logo. No. Their screens would be saved by displays of data analysis, showing which and how much data from elsewhere their CPUs were churning through during down-time. The data would come from observations of distant stars, conducted by astronomers searching for evidence of an extraterrestrial intelligence. Each participating computer would dig through SETI data for suspicious signals, possibly containing a “Hello, World” or two from aliens. Anyone with 28 kbps could be the person to discover another civilization.

    When the researchers launched SETI@Home, in May of ’99, they thought maybe 1,000 people might sign up. That number—and the bleaker view from outsiders, who said perhaps no one would join the crew—informed a poor decision: to set up a single desktop to farm out the data and take back the analysis.

    But the problem was, people really liked the idea of letting their computers find aliens while they did nothing except not touch the mouse. And for SETI@Home’s launch, a million people signed up. Of course, the lone data-serving desktop staggered. SETI@Home fell down as soon as it started walking. Luckily, now-defunct Sun Microsystems donated computers to help the program get back on its feet. In the years since, more than 4 million people have tried SETI@Home. Together, they make up a collective computing power that exceeds 2008’s premier supercomputer.

    But they have yet to find any aliens.

    SETI is a middle-aged science, with 57 years under its sagging belt. It began in 1960, when an astronomer named Frank Drake used an 85-foot radio telescope in Green Bank, West Virginia, to scan two Sun-like stars for signs of intelligent life—radio emissions the systems couldn’t produce on their own, like the thin-frequency broadcasts of our radio stations, or blips that repeated in a purposeful-looking way.

    Green Bank today



    GBO radio telescope, Green Bank, West Virginia, USA

    Since then, scientists and engineers have used radio and optical telescopes to search much more of the sky—for those “narrowband” broadcasts, for fast pings, for long drones, for patterns distinguishing themselves from the chaotic background static and natural signals from stars and supernovae.

    But the hardest part about SETI is that scientists don’t know where ET may live, or how ET’s civilization might choose to communicate. And so they have to look for a rainbow of possible missives from other solar systems, all of which move and spin at their own special-snowflake speeds through the universe. There’s only one way to do that, says Dan Werthimer, the chief SETI scientist at Berkeley and a co-founder of SETI@Home: “We need a lot of computing power.”

    In the 1970s, when Werthimer’s Berkeley colleagues launched a SETI project called SERENDIP, they sucked power from all the computers in their building, then the neighboring building. In a way, it was a SETI@Home prototype. In the decades that followed, they turned to supercomputers. And then, they came for your CPUs.

    The idea for SETI@Home originated at a cocktail party in Seattle, when computer scientist David Gedye asked a friend what it might take to excite the public about science. Could computers somehow do something similar to what the Apollo program had done? Gedye dreamed up the idea of “volunteer computing,” in which people gave up their hard drives for the greater good when those drives were idle, much like people give up their idle cars, for periods of time, to Turo (if Turo didn’t make money and also served the greater good). What might people volunteer to help with? His mind wandered to The X-Files, UFOs, hit headlines fronting the National Enquirer. People were so interested in all that. “It’s a slightly misguided interest, but still,” says David Anderson, Gedye’s graduate-school advisor at Berkeley. Interest is interest is interest, misguided or guided perfectly.

    But Gedye wasn’t a SETI guy—he was a computer guy—so he didn’t know if or how a citizen-computing project would work. He got in touch with astronomer Woody Sullivan, who worked at the University of Washington in Seattle. Sullivan turned him over to Werthimer. And Gedye looped in Anderson. They had a quorum, of sorts.

    Anderson, who worked in industry at the time, dedicated evenings to writing software that could take data from the Arecibo radio telescope, mother-bird it into digestible bits, send it to your desktop, command it to hunt for aliens, and then send the results back to the Berkeley home base. No small task.

    They raised some money—notably, $50,000 from the Planetary Society and $10,000 from a Paul Allen-backed company. But most of the work-hours, like the computer-hours they were soliciting, were volunteer labor. Out of necessity, they did hire a few people with operating-system expertise, to deal with the wonky screensaver behavior of both Windows and Macintosh. “It’s difficult trying to develop a program that’s intended to run on every computer in the world,” says Anderson.

    __________________________________________________________________
    Today, you can use BOINC to serve up your computer’s free time to develop malaria drugs, cancer drugs, HIV drugs.

    __________________________________________________________________

    And yet, by May 17, 1999, they were up, and soon after, they were running. And those million people in this world were looking for not-people on other worlds.

    One morning, early in the new millennium, the team came into the office and surveyed the record of what those million had done so far. In the previous 24 hours, the volunteers had done what would have taken a single desktop one thousand years to do. “Suppose you’re a scientist, and you have some idea, and it’s going to take 1,000 years,” says Anderson. “You’re going to discard it. But we did it.”

    After being noses-down to their keyboards since the start, it was their first feeling of triumph. “It was really a battle for survival,” says Anderson. “We didn’t really have time to look up and realize what an amazing thing we were doing.”

    Then, when they looked up again, at the SETI@Home forums, they saw something else: “It was probably less than a year after we started that we started getting notices about the weddings of people who met through SETI@Home,” says Eric Korpela, a SETI@Home project scientist and astronomer at Berkeley.

    The SETI astronomers began to collect more and different types of data, from the likes of the Arecibo radio telescope. Operating systems evolved. There were new signal types to search for, like pulses so rapid they would have seemed like notes held at pianissimo to previous processors. With all that change, they needed to update the software frequently. But they couldn’t put out a new version every few months and expect people to download it.

    Anderson wanted to create a self-updating infrastructure that would solve that problem—and be flexible enough that other, non-SETI projects could bring their work onboard and benefit from distributed computing. And so BOINC—Berkeley Open Infrastructure for Network Computing—was born.

    Today, you can use BOINC to serve up your computer’s free time to develop malaria drugs, cancer drugs, HIV drugs. You can fold proteins or help predict the climate. You can search for gravitational waves or run simulations of the heart’s electrical activity, or any of 30 projects. And you can now run BOINC on GPUs—graphical processing units, brought to you by gamers—and on Android smartphones Nearly half a million people use the infrastructure now, making the système totale a 19 petaflop supercomputer, the third-largest megacalculator on the planet.

    Home computers have gotten about 100 times faster since 1999, thank God, and on the data distribution side, Berkeley has gotten about 10 times faster. They’re adding BOINC as a bandwidth-increasing option to the Texas Advanced Computing Center and nanoHUB, and also letting people sign up for volunteer computing, tell the system what they think are the most important scientific goals, and then have their computers be automatically matched to projects as those projects need time. It’s like OkCupid dating, for scientific research. BOINC, and SETI@Home can do more work than ever.

    The thing is, though, they’ve already done a lot of work—so much work they can’t keep up with themselves. Sitting in a database are 7 billion possible alien signals that citizen scientists and their idle computers have already uncovered.

    Most of these are probably human-made interference: short-circuiting electric fences, airport radar, XM satellite radio, or a microwave opened a second too soon. Others are likely random noise that added up to a masquerade of significance. As Anderson says, “Random noise has the property that whatever you’re looking for, it eventually occurs. If you generate random letters. You eventually get the complete works of Shakespeare.” Or the emissions are just miscategorized natural signals.

    Anderson has been working on a program called Nebula that will trawl that billions-and-billions-strong database, reject the interference, and upvote the best candidates that might—just might—be actual alien signals. Four thousand computers at the Max Planck Institute for Gravitational Physics in Germany help him narrow down the digital location of that holiest of grails. Once something alien in appearance pops up—say from around the star Vega—the software automatically searches the rest of the data. It finds all the other times, in the 18 years of SETI@Home history, that Arecibo or the recently added telescopes from a $100 milion initiative called Breakthrough Listen have looked at Vega. Was the signal there then too? “We’re kind of hoping that the aliens are sending a constant beacon,” says Korpela, “and that every time a telescope passes over a point in the sky, we see it.”

    If no old data exists—or if the old data is particularly promising—the researchers request new telescope time and ask SETI colleagues to verify the signal with their own telescopes, to see if they can intercept that beacon, that siren, that unequivocal statement of what SETI scientists and SETI@Home participants hope is true: That we are not alone.

    So far, that’s a no-go. “We’ve never had a candidate so exciting that we call the director and say, ‘Throw everybody off the telescope,’” says Werthimer. “We’ve never had anything that resembles ET.”

    And partly for that reason, the SETI@Homers are now working on detecting “wideband” signals—ones that come at a spread spectrum of frequencies, like the beam-downs from DIRECTV. Humans (and by extension, extraterrestrials) can embed more information more efficiently in these spread-spectrum emissions. If the goal is to disseminate information, rather than just graffiti “We’re here!” on the fabric of spacetime, wideband is the way to go. And SETI scientists’ thinking goes like this: We’ve been looking mostly for purposeful, obvious transmissions, ones wrapped neatly for us. But we haven’t found any—which might mean they just aren’t there. Extraterrestrial communications might be aimed at members of their own civilizations, in which case they’re more likely to go the DIRECTV route, and we’re likely to find only the “leakage” of those communication lines.

    “If there really are these advanced civilizations, it’d be trivial to contact us,” says Werthimer. “They’d be landing on the White House—well, maybe not this White House. But they’d be shining a laser in Frank Drake’s eyes. I don’t see why they would make it so difficult that we would have to do all this hard stuff.”

    And so humans, and our sleeping computers, may have to eavesdrop on messages not addressed to us—the ones the aliens send to their own (for lack of a better word) people, and then insert ourselves into the chatter. “I don’t mean to interrupt,” we might someday say, “but I couldn’t help overhearing…” And because of SETI@Home and BOINC, it might be your laptop that gets that awkward conversation started.

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The science of SETI@home
    SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

    Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

    Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.

    SETI@home is not a part of the SETI Institute

    The SETI@home screensaver image
    SETI@home screensaver

    To participate in this project, download and install the BOINC software on which it runs. Then attach to the project. While you are at BOINC, look at some of the other projects which you might find of interest.

    MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

    SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

    Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

    Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”


    SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

    seti
    The famous SET@home screen saver, a beauteous thing to behold.

    einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

    MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

    Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

    World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

    Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

    GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

    gif

    These projects are just the oldest and most prominent projects. There are many others from which you can choose.

    There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

    My BOINC

    graph

     
  • richardmitnick 1:52 pm on May 12, 2017 Permalink | Reply
    Tags: BOINC, , ,   

    From WCG: Ebola outbreak 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    The World Health Organization just announced three recent deaths from Ebola in the Democratic Republic of Congo, which may grown into a new outbreak of the disease. Please support the Outsmart Ebola Together project and help scientists find better treatments for this deadly virus.

    Outsmart Ebola Together

    You can help researchers at The Scripps Research Institute find a cure for Ebola by donating your computing power to this project and encouraging others to join.

    You can also support the research team by contributing to The Scripps Research Institute’s crowdfunding campaign. The team will use these funds to analyze the enormous volume of data generated by Outsmart Ebola Together and study the most promising drug candidates.

    The Ebola virus is a significant global health threat and is a growing humanitarian crisis in Africa, killing thousands of victims in 2014.

    2
    http://www.webmd.com/a-to-z-guides/ebola-fever-virus-infection

    If not handled properly, an Ebola outbreak can turn into an epidemic, overwhelming regional health services and disrupting trade and the delivery of social services, causing the welfare and economy of a region to deteriorate. The ongoing viral load in the human population increases the likelihood of further mutation. Additionally, the virus’s long incubation period and our highly connected modern world could allow the virus to spread to new geographies and across oceans.

    Currently, there are no approved treatments or vaccines for this deadly disease, and the search for an effective antiviral drug to treat the disease is a high priority. While previous outbreaks have ended when the disease disappeared from the human population, the scope of the 2014 outbreak raises the possibility that the virus, rather than disappearing again, could become endemic – permanently persisting in human populations in one or more areas.

    Outsmart Ebola Together on World Community Grid aims to help researchers at The Scripps Research Institute develop a treatment for Ebola virus. The computational power donated by World Community Grid volunteers is being used to screen millions of candidate drug molecules to identify ones that can disable the Ebola virus.

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “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-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 2:03 pm on April 6, 2017 Permalink | Reply
    Tags: BOINC, , ,   

    From Mapping Cancer Markers at WCG: “Mapping Cancer Markers Team Analyzes Lung Cancer Data” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    By: The Mapping Cancer Markers research team
    6 Apr 2017

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

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

    Patterns of gene-family signatures in lung cancer

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

    1
    Illustration 1: Summary of the analysis workflow

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

    Next, we divided all genes in the lung cancer dataset into 180 clusters (gene families), where genes in each family show similar activity in the lung cancer dataset. We then labelled those top signatures with the gene families into which the genes were assigned. This gave us a set of high-performing signatures expressed as gene families instead of genes. This allowed us to treat two different gene signatures as the same gene-family signature, as long as the corresponding genes in each signature are members of the same family.

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

    From there, we looked for patterns in these gene-family signatures: which families appear unusually frequently (or rarely) in high-performing signatures, or families that tend to appear multiple times in the same signature. We used Frequent-Itemset mining algorithm to discover specific patterns that occur unusually frequently in good signatures.

    2
    Illustration 2: Some gene families occur multiple times in a single signature with surprising frequency (high or low). Family 109 rarely appears multiple times. Family 12 appears surprisingly often in 9x multiples.

    3
    Illustration 3: Several important gene families, characterized by word clouds describing the genes’ molecular function annotations from the Gene Ontology database. Circles group families into common patterns found in high-performing signatures. Patterns often overlap, as in this example: one pattern containing families 3, 5, and 18 intersects with another containing families 12, 18, and 57.

    Using databases such as IID or pathDIP, we can take these patterns and examine the relationships between the gene-families they contain, so we can start to understand why certain combinations of such families carry so much information about lung cancer. We use NAViGaTOR to visualize and explore these complex sets of relationships.

    4
    Illustration 4: Relationship between 11 significant gene families (large circles) within a protein interaction network. Only the most important genes (dots, colour-coded by biological function) in each family are shown.

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

    Some of the additional, related results have been presented in other publications, including:

    Pinheiro, M., Drigo, S.A., Tonhosolo, R., Andrade, S.C.S., Marchi, F.A., Jurisica, I., Kowalski, L.P., Achatz, M.I., Rogatto, S.R., HABP2 p.G534E variant in patients with family history of thyroid and breast cancer, Oncotarget, In press.
    Citron, F., Armenia, J., Barzan, L., Franchin, G., Polesel, J., Talamini, R., Sulfaro, S., Croce, C.M., Klement, W., Pastrello, C., Jurisica, I., Vecchione, A., Belletti, B., Baldassarre, G., A microRNA signature identifies SP1 and TGFbeta pathways as potential mediators of local recurrences in head and neck squamous carcinomas, Clin Cancer Res, In press.
    Sokolina K, Kittanakom S, Snider J, Kotlyar M, Maurice P, Gandía J, Benleulmi-Chaachoua A, Tadagaki K, Wong V, Malty RH, Deineko V, Aoki H, Amin S, Riley L, Yao Z, Morató X, Otasek D, Kobayashi H, Menendez J, Auerbach D, Angers S, Pržulj N, Bouvier M, Babu M, Ciruela F, Jockers R, Jurisica I, and Stagljar I. Systematic protein-protein interaction mapping for clinically-relevant human GPCRs, Mol Sys Biol, In press.
    Yao Z, Darowski K, St-Denis N, Wong V, Offensperger F, Villedieu A, Amin S, Malty R, Aoki H, Guo H, Xu Y, Iorio C, Kotlyar M, Emili A, Jurisica I, Babu M, Neel B, Gingras AC, and Stagljar I, A global analysis of the protein phosphatase interactome, Mol Cell, in press.
    Petschnigg J, Kotlyar M, Blair L, Jurisica I, Stagljar I, and Ketteler R, Systematic identification of oncogenic EGFR interaction partners, J Mol Biol, in press.
    Rahmati, S., Abovsky, M., Pastrello, C., Jurisica, I. pathDIP: An annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. Nucl Acids Res, 45(D1): D419-D426, 2016.
    Chehade, R., R. Pettapiece-Phillips, Salmena, L., Kotlyar, M., Jurisica, I., Narod, S. A., Akbari, M. R., Kotsopoulos, J. Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific, Breast Cancer Res, 18(1): 87, 2016.
    Cierna, Z., Mego, M., Jurisica, I., Machalekova, K., Chovanec, M., Miskovska, V., Svetlovska, D., Hainova, K., Kajo, K., Mardiak, J., Babal, P. Fibrillin-1 (FBN-1) a new marker of germ cell neoplasia in situ, BMC Cancer, 16: 597, 2016.

    Thank you to members

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

    See the full article here.

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “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-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    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

    faah-1-new-screen-saver

    faah-1-new

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

    IBM – Smarter Planet
    sp

     
  • richardmitnick 1:12 pm on February 26, 2017 Permalink | Reply
    Tags: , , BOINC,   

    From Nature: “[International] supercomputer, BOINC, needs more people power” 

    Nature Mag
    Nature

    22 February 2017
    Ivy Shih

    1
    Xinhua / Alamy Stock Photo

    A citizen science initiative that encourages public donations of idle computer processing power to run complex calculations is struggling to increase participation.

    Berkeley Open Infrastructure for Network Computing (BOINC), a large grid that harnesses volunteered power for scientific computing, has been running for 15 years to support research projects in medicine, mathematics, climate change, linguistics and astrophysics.

    boinclarge

    boinc-wallpaper

    But, despite strong demand by scientists for supercomputers or computer networks that can rapidly analyse high volumes of data, the volunteer run BOINC has struggled to maintain and grow its network of users donating their spare computer power. Of its 4 million-plus registered users, only 6% are active, a number that has been falling since 2014.

    “I’m constantly looking for ways to expose sectors of the general population to BOINC and it’s a struggle,” says David Anderson, a co-founder and computer scientist at the University of California Berkeley.

    How many people use BOINC?

    Many more people have registered with BOINC than actually donate their computer power (active users).
    Anderson says BOINC, which is [no longer] funded by the National Science Foundation, currently hosts 56 scientific projects that span an international network of more than 760,000 computers. [current: 24-hour average: 17.367 PetaFLOPS. Active: 267,932 volunteers, 680,893 computers.]The platform’s combined processing power simulates a supercomputer whose performance is among the world’s top 10.

    Access to such supercomputers can be expensive and require lengthy waits, so BOINC offers research groups access to processing power at a fraction of the prohibitive cost.

    “A typical BOINC project uses a petaflop of computing — which typically costs maybe USD $100,000 a year. If you were to go to buy the same amount of computing power on the Amazon cloud, it would cost around $40 million,” says Anderson.

    Kevin Vinsen, a scientist at the International Centre for Radio Astronomy Research, Australia, leads a project that analyses photos of galaxies. BOINC’s helps analyse the SkyNet’s huge dataset, which is especially valuable given the project’s shoestring budget.

    “In BOINC I can have 20,000 people working on it at the same time. Each one is doing a small portion of the galaxy,” he says.

    Anderson wants to connect BOINC to major supercomputer facilities in the United States, to reduce the lengthy wait researchers have to process their data. He is working to add the network to the Texas Advanced Computing Center as an additional resource for researchers.

    Access to such supercomputers can be expensive and require lengthy waits, so BOINC offers research groups access to processing power at a fraction of the prohibitive cost.

    “A typical BOINC project uses a petaflop of computing — which typically costs maybe USD $100,000 a year. If you were to go to buy the same amount of computing power on the Amazon cloud, it would cost around $40 million,” says Anderson.

    Kevin Vinsen, a scientist at the International Centre for Radio Astronomy Research, Australia, leads a project that analyses photos of galaxies. BOINC’s helps analyse the SkyNet’s huge dataset, which is especially valuable given the project’s shoestring budget.

    “In BOINC I can have 20,000 people working on it at the same time. Each one is doing a small portion of the galaxy,” he says.

    Anderson wants to connect BOINC to major supercomputer facilities in the United States, to reduce the lengthy wait researchers have to process their data. He is working to add the network to the Texas Advanced Computing Center as an additional resource for researchers.

    boincstatsimage-new

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology on the basis of its originality, importance, interdisciplinary interest, timeliness, accessibility, elegance and surprising conclusions. Nature also provides rapid, authoritative, insightful and arresting news and interpretation of topical and coming trends affecting science, scientists and the wider public.

     
  • richardmitnick 1:49 pm on December 27, 2016 Permalink | Reply
    Tags: , , BOINC, Community Achievements in 2016,   

    From WCG: “Community Achievements in 2016” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

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

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

    Helping Stop a Global Killer

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

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

    Searching for Potential Treatments for Zika

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

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

    1

    Winning Awards

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

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

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

    Thank You

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

    See the full article here.

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “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-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    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

     
  • richardmitnick 3:04 pm on December 6, 2016 Permalink | Reply
    Tags: , , BOINC, Meet Keith Uplinger,   

    From WCG: “Meet a World Community Grid Team Member: Keith Uplinger” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    6 Dec 2016
    No writer credit

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

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

    1
    Earlier this year, Keith co-starred in a video of our acceptance speech for the People’s Voice Webby Award.

    Keith grew up in a technology-oriented family in Austin, Texas, where his father worked for IBM. Always drawn to math and technology, Keith began programming while still in grade school. Once his family installed a dedicated internet connection, he became even more focused. “I was online almost 24/7, programming and researching computer components,” he says.

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

    Since then, he has touched nearly all parts of World Community Grid’s platform, including developing project screensavers, server management, running the testing environment, website development, and working closely with the BOINC group to help with the open source platform on which World Community Grid runs. “I’ve stayed with World Community Grid for the challenges,” Keith says. “Many people work on a single product, but our scope is broader. Every few months we have a new project that needs to go out to large groups of people all over the world.”

    Keith is currently World Community Grid’s technical lead. His latest work-related challenge is leading World Community Grid’s work on asynchronous replica exchange, a new sampling protocol being developed by the research team for FightAIDS@Home – Phase 2. He explains, “When World Community Grid receives completed work units (research tasks) back from volunteers’ devices, we don’t send the results back to the researchers until the entire batch of work units is complete. This isn’t always ideal for researchers like the Fight AIDS@Home team, who need to process their results more quickly. With asynchronous replica exchange, these researchers will get their data back more quickly, which will help them analyze their data more quickly.”

    “We have not done anything like this with our work units before. Asynchronous replica exchange has the potential to expand the scientific capabilities of World Community Grid,” says Keith. “It not only helps the science, but also could be beneficial for the technology side of the other projects.”

    When he’s not solving complex problems for World Community Grid, Keith’s pastimes center around his family, which includes wife Erica and their two young children. He enjoys coaching his kids’ soccer, basketball, football, and baseball teams. At a height of 6’4″ (193 cm), he’s a formidable basketball opponent and likes to play whenever he can. His family also enjoys traveling in the United States (by car whenever possible) and throughout the world. Recently, he and his wife participated in the Baatan Death Memorial March, a challenging hike through the New Mexico desert that honors the military personnel who defended the Philippine Islands during World War II.

    To the many volunteers that he has served over the years, Keith says, “Thanks for your ongoing efforts to help find answers to science’s toughest questions. I hope we can grow to millions of volunteers, and someday I’d like to see us cure cancer.”

    See the full article here.

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “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-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    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

     
  • richardmitnick 2:38 pm on December 2, 2016 Permalink | Reply
    Tags: , , , BOINC, , Einstein@Home Finds a Double Neutron Star   

    From AAS NOVA: ” Einstein@Home Finds a Double Neutron Star” 

    AASNOVA

    American Astronomical Society

    2 December 2016
    Susanna Kohler

    2
    Artist’s impression of a double-pulsar system. A new double-neutron-star system was recently discovered using Einstein@Home, a program that analyzes data on home computers. [John Rowe Animations]

    Have you been contributing your computer idle time to the Einstein@Home project? If so, you’re partly responsible for the program’s recent discovery of a new double-neutron-star system that will be key to learning about general relativity and stellar evolution.

    3
    The 305-m Arecibo Radio Telescope, built into the landscape at Arecibo, Puerto Rico. [NOAO/AURA/NSF/H. Schweiker/WIYN]

    The Hunt for Pulsars

    Observing binary systems containing two neutron stars — and in particular, measuring the timing of the pulses when one or both companions is a pulsar — can provide highly useful tests of general relativity and binary stellar evolution. Unfortunately, these systems are quite rare: of ~2500 known radio pulsars, only 14 of them are in double-neutron-star binaries.

    To find more systems like these, we perform large-scale, untargeted radio-pulsar surveys — like the ongoing Pulsar-ALFA survey conducted with the enormous 305-m radio telescope at Arecibo Observatory in Puerto Rico. But combing through these data for the signature of a highly accelerated pulsar (the acceleration is a clue that it’s in a compact binary) is very computationally expensive.

    4
    PSR J1913+1102’s L-band pulse profile, created by phase-aligning and summing all observations. [Adapted from Lazarus et al. 2016]

    To combat this problem, the Einstein@Home project was developed.

    Einstein@home

    Einstein@home

    My BOINC results:
    boincstatsimage-new

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Einstein@Home is a World Year of Physics 2005 and an International Year of Astronomy 2009 project supported by the American Physical Society (APS) and by a number of international organizations.

    Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than three dozens new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.

    To join this project go to BOINC, download the software and attach to the project. While you are at BOINC, review all of the projects and see what else might be of interest.

    boinclarge

    boinc-wallpaper

    Einstein@Home allows anyone to volunteer their personal computer’s idle time to help run the analysis of survey data in the search for pulsars. In a recent publication led by Patrick Lazarus (Max Planck Institute for Radio Astronomy), the Einstein@Home team announced the discovery of the pulsar PSR J1913+1102 — a member of what seems to be a brand new double-neutron-star system.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

     
  • richardmitnick 8:00 am on October 1, 2016 Permalink | Reply
    Tags: , BOINC, , ,   

    From FightAIDS@ WCG: “FightAIDS@Home Team Expands Techniques, Refines Phase 1 Results, and Collaborates on a New Study” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    30 Sep 2016
    By: The FightAIDS@Home research team

    Summary
    The FightAIDS@Home team is working with the World Community Grid technical team to create a new sampling protocol, which will more closely predict the binding strengths of potential drugs to their HIV protein targets as determined in real-life experiments. Read about this work, and other news, in this extensive update.

    1
    (Left to right) World Community Grid program manager Juan Hindo with some of the members of the Ron Levy group at Temple University: Ron Levy, Bill Flynn, Junchao Xia, Peng He, Nanjie Deng

    Creating a New Sampling Protocol

    Background

    The simulations running under FightAIDS@Home – Phase 2 have been using two new simulation methods (independent sampling and lambda scheduling) that we tailored for the unique computing environment of World Community Grid.

    faah-phase-ii

    While volunteers have been crunching away, we have been diligently analyzing the results returned to us to determine whether these new protocols are sufficient to both meet our scientific goals and provide the volunteers with efficient, worthwhile computing tasks. The results for the first 106 batches show qualitative agreement with prior benchmarks run on high-performance computing clusters, but some results demonstrate the new simulation protocols are not satisfactory for all types of analysis.

    With the support of our collaborators at the HIV Interaction and Viral Evolution Center (HIVE) and the World Community Grid team, we have been working closely with the World Community Grid software developers to implement a more rigorous simulation scheme that closely mimics the more algorithmically efficient simulations run on non-grid computing resources.

    faah-hive
    Scripps/HIVE

    This new sampling protocol is called asynchronous replica exchange.

    How Asynchronous Replica Exchange Works

    Our Current Process: Currently, multiple copies of a protein-ligand complex (the structure consisting of a drug candidate compound docked with a protein receptor) are sent out to many volunteers and are simulated with no interaction with one another. The collective information from all those simulations are combined during analysis at the very end.

    The New Process: Asynchronous replica exchange allows information from the different copies to be shared and exchanged among all copies dynamically after short periods of simulations, and this process yields the correct equilibrium statistical physics needed for our analysis.

    Benefits of the New Process: Replica exchange drastically increases the efficiency of the computations. This means that, in addition to being more valuable in terms of analysis, (a) future work units will have shorter runtimes, making Phase 2 computations accessible to more volunteers; (b) the number of batches running simultaneously can be increased; and (c) each batch will have shorter total simulation times.

    This new technique was first prototyped and then put to use on our local BOINC-powered grid at Temple University. Now, the World Community Grid software developers are working hard to implement the same technique on the World Community Grid platform. This effort would allow the largest replica exchange simulations (by two orders of magnitude) ever performed, and we anticipate testing to begin in the next few weeks. In the meantime, we will continue to run and extract valuable information from simulations using our current algorithms.

    For more information about this work, see these two articles:

    http://onlinelibrary.wiley.com/doi/10.1002/jcc.23996/abstract

    http://www.sciencedirect.com/science/article/pii/S0010465515002556

    Refining Results from FightAIDS@Home – Phase 1

    We are moving away from benchmarking simulations, and we are working closely with our collaborators and long-time FightAIDS@Home – Phase 1 research scientists at The Scripps Research Institute to collect the best hits from the many virtual screens performed over the last decade. We are in the process of preparing the input files for the top candidates from over 35 million compounds screened in Phase 1 from the ZINC library, a free database of commercially available compounds for virtual screening. Over the next set of batches, volunteers can expect to see research tasks that are geared toward refining the Phase 1 results.

    FAAH

    New Study on Computational Modeling of HIV

    3
    Figure: (Left) ALLINI KF116 (green) bound at the interface of two Catalytic Core Domain (CCD) subunits of HIV-integrase. (Right) ALLINI-2 (green) facilitating interactions between the CCD dimer and the C-Terminal Domain (CTD) of another HIV integrase molecule. Due to the presence of the ALLINI, the interaction between the CTD of one Integrase dimer and the CCD-CCD interface of another Integrase dimer is stabilized; chains of these inter-subunit interactions lead to aggregates.

    An exciting study regarding computational modeling of HIV has come out of a collaboration with our lab and experimentalists at the HIVE Center.

    HIV Integrase is a viral protein which plays a critical role in the replication of the HIV virus. A class of compounds, called allosteric Integrase inhibitors, or ALLINIs, has a unique inhibition mechanism targeting HIV Integrase. ALLINIs act like a glue that causes many Integrase molecules to become tangled together and make it difficult for them to complete their normal job, which is to incorporate HIV viral DNA into the cell’s own DNA.

    Research scientist Nanjie Deng, an associate research professor with the Ron Levy Group at Temple University, has demonstrated with molecular dynamics simulations of HIV Integrase dimers how this process, which is called multimerization, is promoted by the ALLINIs. Deng’s predictions appear to be confirmed by a high resolution crystal structure which will be available later this year. An accelerated publication of his work can be found here.

    We appreciate the support this project has received from World Community Grid volunteers around the globe.

    See the full article here.

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    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.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

    “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-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    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

     
  • richardmitnick 11:19 am on September 16, 2016 Permalink | Reply
    Tags: , , BOINC, , Hyperstable peptides, Institute for Protein Design,   

    From U Washington: “Super-stable peptides might be used to create ‘on-demand’ drugs” 

    U Washington

    University of Washington

    09.14.2016
    Michael McCarthy

    1
    An artist’s conception of a peptide created at the UW Medicine Institute for Protein Design. The backbone structure is shown in pink, and the molecular surface is blue. White indicates the crossbonds that stabilize the peptide’s shape. Vikram Mulligan

    2

    Scientists at the University of Washington’s Institute for Protein Design have shown it is possible to create small, hyperstable peptides that could provide the basis for developing powerful new drugs and diagnostic tests.

    “These super stable peptides provide an ideal molecular scaffold on which it should be possible to design ‘on demand’ a new generation of peptide-based drugs,” said UW Medicine protein engineering pioneer David Baker, who oversaw the research project. He is a UW professor of biochemistry.

    David Baker
    David Baker

    In a study, which appears in the journal Nature, the researchers demonstrate that not only is it possible to design peptides that fold into a wide variety of different conformations, but also that it is possible to incorporate functional groups of chemicals not normally found in peptides.

    3
    Illustrations of designed peptides with different configurations of two structures: tightly wound ribbons and flat, arrow-shaped ribbons.

    Both of these abilities could give designers even greater flexibility to create drugs that act on their molecular targets with high precision. Such drugs should not only be more potent but would also be less likely to have harmful side effects.

    Most drugs work by binding to a key section of a protein in a way that alters how the protein functions, typically by stimulating or inhibiting the protein’s activity. For the binding to occur, the drug must fit into the target site on the protein as a key fits into a lock. How close the lock-and-key fit is can often determine how well the medication works.

    Currently, most prescription drugs are either made of small molecules or much larger proteins. Both classes of drugs have advantages and disadvantages.

    Small molecule drugs, for example, tend to be easy to manufacture, tend to have a long shelf life, and are often easily absorbed. But they often don’t fit the targeted “lock” as selectively as could be hoped. This imperfect fit can result in off-target binding and side-effects that diminish their effectiveness. Protein drugs, on the other hand, often fit their target receptors very well but they are difficult to manufacture, are more unstable, and lose their potency if they are not kept refrigerated. Because of their size and instability, they need to be injected into patients.

    Peptide drugs fall in between these two classes. They are small, so they have many of advantages of small molecule drugs. But they are made of a chain of amino acids, the same components that make up proteins, so they have the potential to achieve the precision of larger protein drugs.

    The power of some tiny peptides can be observed in venomous creatures. A number of poisonous insects and sea creatures produce small peptide toxins. Those are some of the most potent pharmacologically active compounds known. Their potency is among the reasons why medical scientists are interested in tapping into beneficial uses of peptides.

    In the new study, Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, senior fellows in the Baker lab, and their colleagues, developed computational methods that are now incorporated in the computer program called Rosetta.

    rosetta-screensaver
    rosettahome
    Rosetta@home, a project running on BOINC software from UC Berkeley
    BOINC WallPaper

    These methods are being used to design peptides ranging from 18 to 47 amino acids in length in 16 different conformations, called topologies.

    Originally developed by Baker and his earlier team, Rosetta uses advanced modelling algorithms to design new proteins by calculating the energies of the biochemical interactions within a protein, and between the protein and its surroundings. Because a protein will assume the shape in which the sum of these interaction energies is at its minimum, the program can calculate which shape a protein will most likely assume in nature.

    The peptides were made hyperstable by designing them to have interior crosslinking structures, called disulfide bonds, which staple together different sections of the peptide. Additional stabilization was secured by tying the two ends of the peptide chain together, a process called cyclization. The resulting constrained peptides were so stable that they were able to survive temperatures to 95 °C, nearly boiling. This survival feat would be impossible for antibody drugs.

    The researchers also showed that the design of these peptides could include amino acids not normally found in proteins. Amino acids have a property called handedness or chirality. Two amino acids can be made of the same atoms but have different arrangements, just as our hands have the same number of fingers but have two mirror-image configurations, right and left. This handedness keeps the right hand from fitting properly into a left-handed glove and vice versa.

    In nature, perhaps due to a chance event billions of years ago, amino acids in living cells are all left-handed. Right-handed amino acids are very rare in naturally occurring proteins. Nevetheless, the researchers were able to insert right-handed amino acids in their designed peptides.

    “Being able to include other types of amino acids allows us to create peptides with a much wider variety of conformations,” said Baker, “and being able to use right-handed amino acids essentially doubles your palette.”

    “By making it possible to create peptides that include ‘unnatural’ amino acids, this approach will allow researchers to explore peptide structures and function that have not been explored by nature through evolution,” Baker said.

    Today’s edition of Nature also has a special supplement, Insight The Protein World. Baker, Po-Ssu, and Scott E. Boyken authored the review article, The coming of age of de novo protein design.

    Also see coverage of the Nature hyperstable peptide design paper in Hutch News by the Fred Hutchinson Cancer Research Center.

    The National Institutes of Health provided partial support for this work through grants P50 AG005136, T32-H600035., GM094597, GM090205, and HHSN272201200025C. Additional funding was provided by The Three Dreamers.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    u-washington-campus
    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 9:57 am on September 9, 2016 Permalink | Reply
    Tags: , BOINC, , , , ,   

    From Vanderbilt: “Investigators create ‘Trojan Horse’ to fight Ebola” 

    Vanderbilt U Bloc

    Vanderbilt University

    Sep. 8, 2016
    Bill Snyder
    william.snyder@Vanderbilt.Edu
    (615) 322-4747

    A multi-center research team including scientists from the Vanderbilt Vaccine Center has come up with a clever “Trojan Horse” strategy for thwarting the highly lethal Ebola virus.

    Using “bispecific” antibodies — two monoclonal antibodies combined into a single package — they first tricked the virus into revealing a normally hidden binding site required for infection. Then in a mouse model, they blocked the site, fully protecting the animals from Ebola infection.

    Their findings, reported in this week’s Science magazine, suggest that this two-step, “deliver-and-block” strategy can provide broad protection against Ebola and other members of its hemorrhagic filovirus family, including the Marburg virus.

    We were intrigued to find this remarkable antibody that has the capacity to inhibit both Marburg and Ebola viruses,” said James Crowe Jr., M.D., Ann Scott Carell Professor in the Vanderbilt University School of Medicine and director of the Vanderbilt Vaccine Center at Vanderbilt University Medical Center.

    “The team’s feat of delivering the antibody into cells using creative engineering tricks so that it can kill Ebola inside cells is very exciting,” Crowe said.

    This advance is only the latest in a string of fundamental discoveries made during the past decade by a far-flung group of researchers including Crowe and four other corresponding authors of the paper.

    The four are Kartik Chandran, Ph.D., and Jonathan Lai, Ph.D., of Albert Einstein College of Medicine in New York, John Dye, Ph.D., of the U.S. Army Medical Research Institute of Infectious Diseases in Fort Detrick, Maryland, and Javad Aman, Ph.D., of Integrated Biotherapeutics in Gaithersburg, Maryland.

    Like other viruses, Ebola must “hijack” factors in the cells it infects to make copies of itself. As a first step, the virus enters a vesicle called an endosome inside the cell. There it commandeers two cellular enzymes called proteases to cut a sugar-bearing glycoprotein on its surface in two.

    Cleavage of the glycoprotein reveals a previously hidden receptor-binding site that attaches to another cellular factor, a cholesterol transporter protein called Niemann–Pick C1 or NPC1. This step is essential for infection to occur.

    Mutations in the NPC1 gene result in an abnormal protein that causes the rare lipid storage disorder Niemann-Pick type C disease. While patients with this disease are often quite ill, their abnormal NPC1 protein also renders them resistant to infection by Ebola and the related Marburg virus.

    Last year, Crowe, Vanderbilt graduate student Andrew Flyak and colleagues at The Scripps Research Institute in La Jolla, California, reported that a human survivor of a severe Marburg infection had neutralizing antibodies that recognized and blocked the NPC1 binding site in Marburg virus

    These antibodies also could bind to the Ebola virus, but only to the form of the virus inside cells.

    Crowe and Flyak followed up that finding by generating a “monoclonal” antibody, called MR72, which specifically recognized and could block the NPC1 binding site. To actually prevent Ebola virus infection, however, they’d have to get the antibody into the endosome inside the cell where the action is taking place.

    To do that, the researchers fused MR72 to another antibody, called FVM09, which recognizes and attaches to the Ebola glycoprotein before it is cut in two. The result was an immunological “Trojan horse.” Once the virus brought its antibody cargo into the endosome, MR72 went to work, and blocked infection.

    “This Trojan horse bispecific antibody approach may also find utility against other viral pathogens known to use intracellular receptors,” they concluded.

    Other contributors to the current study were Erica Ollmann Saphire, Ph.D., at Scripps and Zachary Bornholdt, Ph.D., now at Mapp Pharmaceutical in San Diego. The study was supported in part by National Institutes of Health grants AI109762, AI088027 and AI122403.

    See the full article here .

    You can Help Stamp Out EBOLA.

    This WCG project runs at Scripps Institute

    Outsmart Ebola Together

    Visit World Community Grid (WCG). Download and install the BOINC software on which it runs. Attach to the Outsmart Ebola Together project. This will allow WCG to use your computer’s free CPU cycles to process computational data for the project.

    WCGLarge
    WCG Logo New

    BOINCLarge
    BOINC WallPaper

    While you are at WCG and BOINC, check out the other very worthwhile projects running on this software. All project results are “open source”, free for the use of scientists world while to advance health and other issues of mankind.

    MyBOINC

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Vanderbilt Campus

     
c
Compose new post
j
Next post/Next comment
k
Previous post/Previous comment
r
Reply
e
Edit
o
Show/Hide comments
t
Go to top
l
Go to login
h
Show/Hide help
shift + esc
Cancel
%d bloggers like this: