Tagged: Crunching Toggle Comment Threads | Keyboard Shortcuts

  • richardmitnick 8:23 pm on June 14, 2012 Permalink | Reply
    Tags: , , , , Crunching, ,   

    From WCG’s Say No to Schistosoma Project, Rosangela Hickson Writes About the Disease and the Project 

    Schistosomiasis – a tropical disease caused by the parasitic worms transmitted by freshwater snails – affects more than 200 million people each year, killing 200,000 of them. Schistosomiasis is second only to malaria in its devastating effects on the world’s population.

    To find a treatment for this deadly disease, researchers at Inforium University in Belo Horizonte and Fiocruz Minas, Brazil are using World Community Grid to run computer simulations that map the interactions of millions of chemical compounds with selected target proteins. Powered by the unused computing capacity of more than two million World Community Grid member computers, Brazil’s Say No to Schistosoma project is leading the charge to wipe out this deadly disease.

    June, 14th 2012
    Dr. Rosangela Hickson

    [Rosangela Hickson, Ph.D., is the principal investigator of Brazil’s “Say No to Schistosoma” Project, powered by World Community Grid.]

    “The story of a disease that infects nearly 200 million people today begins in the ancient remains of mummies from the Upper Nile River Delta. Analyses of mummies from Nubia – the former Nile River kingdom located in present-day southern Egypt and northern Sudan – reveal that ancient populations suffered and died from infections that caused anemia and chronic illnesses which impaired their growth and cognitive development, damaged their organs, and weakened their immune systems.

    Schistosoma mansoni

    A child gathers contaminated water.

    The Say No to Schistosoma project is using bioinformatics tools to engineer new drug therapies to fight schistomiasis.

    Progression of the disease

    We plan to make public the results of our research so other scientists may build upon it. The Fiocruz Minas team is planning on conducting additional laboratory work to develop better drugs to fight schistosomiasis – using the best candidate compounds identified by the computer simulations. We thank the many people who have volunteered their computers to make this research possible.”

    See the full blog post 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 Public 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


    Computing for Sustainable Water

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

    IBM – Smarter Planet

    My BOINC

  • richardmitnick 1:03 pm on April 30, 2012 Permalink | Reply
    Tags: , , , , Crunching, , ,   

    From David Baker at Rosetta@home: Rosetta Chosen for the BOINC Pentathlon 

    This is a post from Dr. David Baker, The Baker Lab at the University of Washington, the site of rosetta@home.

    Dr. David Baker

    “I have just been told the very good news that Rosetta@home will be the first project of the BOINC pentathlon, and would like to thank all of the participating teams. I also just learned from the discussion thread that Rosetta@home will be the project of the month for BOINC synergy-this is more excellent news!!

    Your increased contributions to rosetta@home could not come at a better time! We’ve been testing our improved structure prediction methodology in a recently started challenge called CAMEO. For most of the targets, the Rosetta@home models are extremely good, but for a minority of targets the predictions are not good at all. We’ve now tracked down the source of these failures and it is what we are calling “workunit starvation”; in the limited amount of time the Rosetta server has to produce models (2-3 days) in these cases very few models were made-this happens because many targets are being run on the server so that only a fraction of your cpu power is focused on any one target. while we are working to fix this internally, by far the best solution is to have more total CPU throughput so each target gets more models.

    You can follow how we are doing at http://www.cameo3d.org/. You will see that Rosetta is one of the few servers whose name is not kept secret-this is because Rosetta is a public project. Our server receives targets from CAMEO and soon CASP, sends the required calculations out to your computers through Rosetta@home, and then processes the returned results and submits the lowest energy models.

    We are excited that the workunit starvation problem may go away through your increased efforts for Rosetta@home. Thanks!!!”

    David’s post is here.


    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, developed at UC Berkeley.

    Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.


    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.

    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.

    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


  • richardmitnick 2:55 pm on October 13, 2011 Permalink | Reply
    Tags: , , , Crunching, , , , , , ,   

    Citizen Scientists, Unite!! Around two LHC@home Projects 

    Join your colleagues at the LHC in two Public Distributed Computing projects working for the Large Hadron Collider at CERN.

    LHC@home/Sixtrack works on magnet tuning so that there is less lost effort in the beam line.


    LHC@home 2.0 simulates collision events


    So, what do you do? First, if you are not already “crunching” for other worthwhile scientific projects, you go to the BOINC UC Berkeley Space Science Lab web site for a wee bit of software, which you install on your computer(s). Then, you visit the above two web sites, and attach to the two projects. For LHC@home 2.0 you might need to register and await an invitation. This project is very new and is in “beta”. LHC@home/Sixtrack is a mature project, so no waiting. At each project web site, you can find explanations of what is happening, the science. You can find forums in which you can participate.

    Historically, projects running on BOINC software used the idle CPU cycles of your computer. In fact, the grand daddy of all projects, SETI@home , actually ran in a screen saver. Today, with greater power, protected memory, “sandboxed” technology, projects run all the time and in no way interfere with whatever else you are doing on your computer.

    We need your help. There are over 1 billion computers in the world. BOINC counts all of its current users at about 295,000. The LHC is the largest and most complex basic scientific research experiment ever mounted by Modern Man. It ranks with the pyramids, penicillin, and Starbucks.

    SET@home, the largest and oldest project, based at the birthplace of BOINC, currently has 147,000 crunchers on 222,000 computers. To paraphrase Seth Shostak of the SETI Institute (no relation to SETI@home) they haven’t found pond scum. Not even dead pond scum. But, they are processing 423 TeraFLOPS per second. That’s half a PetaFLOP. That would put them at about #15 in the TOP500 world supercomputers list, except, of course, they are distributed.

    We deserve to be that big. We need to scale up and vie with our friends at SETI@home (I crunch for SETI@home on four of my six computers.)

    So, please, visit the sites. Take a look. Tell your colleagues. Be part of something great.

    [If you are at any school, university, institution of any sort, never ever install BOINC software on their computers without written permission of an authority.]

    Meet CERN in a variety of places:

    Cern Courier








  • richardmitnick 1:02 pm on August 8, 2011 Permalink | Reply
    Tags: , , Crunching, , , , , ,   

    From CERN and interactions.org: “CERN supports European Year of Volunteering through Citizen Cyberscience Centre” 

    Geneva, 8 August 2011

    Today, researchers at CERN began public testing of a new version of the popular volunteer computing project LHC@home [2.0]. This version allows volunteers to participate for the first time in simulating high-energy collisions of protons in CERN’s Large Hadron Collider (LHC). Thus, volunteers can now actively help physicists in the search for new fundamental particles that will provide insights into the origin of our Universe, by contributing spare computing power from their personal computers and laptops.

    LHC@home 2.0

    [LHC@home and many other very worthwhile projects run on software from Berkeley Open Infrastructure for Network Computing from UC Berkeley, and famous for its SETI@home project, in which the BOINC software was born.]

    This is just one example of a series of projects and events organized by the Citizen Cyberscience Centre, a partnership between CERN, UNITAR (the UN Institute for Training and Research) and the University of Geneva, to promote volunteer-based science in this, the European Year of Volunteering 2011.

    Other projects the Citizen Cyberscience Centre has initiated focus on promoting volunteer science in the developing world, for humanitarian purposes. For example, in collaboration with IBM’s philanthropic World Community Grid and Tsinghua University in Beijing, the Citizen Cyberscience Centre launched the Computing for Clean Water project (5). The project uses the supercomputer-like strength of World Community Grid to enable scientists to design efficient low-cost water filters for clean water.”

    Center for Nano and Molecular Mechanics at Tsinghua University

    See the full article interactions.org article here. This is a huge and important article, with fuller explanations of everything and every organization involved.

    Meet CERN in a variety of places:

    Cern Courier









  • richardmitnick 2:34 pm on July 28, 2011 Permalink | Reply
    Tags: , , Crunching, , , , , ,   

    From isgtw: “Virtual atom smasher in LHC@Home 2.0” 

    Wonderful article about a new project being birthed from the ground up.

    Here is a beginning to entice the scientifically inclined:

    Jacqui Hayes
    July 27, 2011

    ““When I learned that if successful, LHC@home 2.0 would allow BOINC users to participate in physics experiments being done at CERN – and ultimately perhaps even the search for the Higgs Boson itself – I jumped at the chance to be a part of it,” said Tony De Bari.


    De Bari, who is from New Jersey, USA, joined the project in February 2011, after finding out about it from forum posts online and emailing the developers to ask for an invitation code.

    Dr Bari now has three computers, at work and at home, contributing time to the LHC@Home 2.0 project. “Even though I do not have a formal physics background, I am a self-proclaimed ‘science geek’ with a particular interest in physics. While pursuing my computer science degree, I took as many elective physics courses as time would permit, and I try to read as much about the subject as I can.”

    The developers hope LHC@Home 2.0 will be used for several research projects in the future. The first project, called Test4Theory, has been in the alpha testing phase since October 2010, and now has more than 100 volunteers just like De Bari. Even at this early stage, volunteers have already provided about 10% of the total computing resources currently available to theoretical physicists at CERN according to Anton Karneyeu, one of the developers on the project who also works on the CMS experiment.”

    My personal story is close to Dr De Bari’s, even to my location in New Jersey. I have six machines on the project. I have been on the original lhc@home project for quite some time. I asked for the invitation and was allowed to participate.

    What is BOINC?

    BOINC (Berkeley Open Infrastructures for Network Computing) is an open-source software platform for computing with volunteered resources. It was first developed at the University of California Berkeley to manage the SETI@Home project, and uses the unused CPU and GPU cycles on a computer for scientific computing.

    Please see the full articled here. There is a lot to read and to stimulate the curious toward this incredible project.

  • richardmitnick 9:25 pm on April 25, 2011 Permalink | Reply
    Tags: , , , Crunching, ,   

    From Sandia Labs: “Sandia and UNM lead effort to destroy cancers” 

    Boosting medicine with nanotechnology strengthens drug cocktail many times over

    “Melding nanotechnology and medical research, Sandia National Laboratories, the University of New Mexico, and the UNM Cancer Research and Treatment Center have produced an effective strategy that uses nanoparticles to blast cancerous cells with a mélange of killer drugs.

    In the cover article of the May issue of Nature Materials, available online April 17 , the researchers describe silica nanoparticles about 150 nanometers in diameter as honeycombed with cavities that can store large amounts and varieties of drugs.

    ‘ The enormous capacity of the nanoporous core, with its high surface area, combined with the improved targeting of an encapsulating lipid bilayer [called a liposome], permit a single ‘protocell’ loaded with a drug cocktail to kill a drug-resistant cancer cell,’ says Sandia researcher and UNM professor Jeff Brinker, the principal investigator. ‘That’s a millionfold increase in efficiency over comparable methods employing liposomes alone — without nanoparticles — as drug carriers.’

    The nanoparticles and the surrounding cell-like membranes formed from liposomes together become the combination referred to as a protocell: the membrane seals in the deadly cargo and is modified with molecules (peptides) that bind specifically to receptors overexpressed on the cancer cell’s surface. (Too many receptors is one signal the cell is cancererous.) The nanoparticles provide stability to the supported membrane and contain and release the therapeutic cargo within the cell. ”

    The figure on the left (Hep3B) shows a greenly fluoresced cancerous liver cell penetrated by protocells. The small red dots are lipid bilayer wrappings. Their cargo — drug-filled nanoparticles, their pores here filled with white fluorescent dyes for imaging purposes — penetrate the cancerous cell. (Penetration is more clearly seen in the second image.) The normal cell on the right (hepatocyte) shows no penetration. (Images courtesy of Carlee Ashley)

    Sandia post-doctoral fellow Carlee Ashley introduces a buffer into a protocell solution to dilute it as Sandia researcher and University of New Mexico professor Jeff Brinker watches. (Photo by Randy Montoya)

    R$ead the full article here.

    And, don’t forget, at World Community Grid we have two Cancer projects,
    Help Conquer Cancer

    Help Fight Childhood Cancer

    You can join the 98,000 WCG crunchers in these two projects. Visit WCG, download and install the little piece of BOINC software. Then attch to these two projects and look at the rest of what we are doing. You will be amazed.

Compose new post
Next post/Next comment
Previous post/Previous comment
Show/Hide comments
Go to top
Go to login
Show/Hide help
shift + esc
%d bloggers like this: