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  • richardmitnick 8:43 pm on June 13, 2012 Permalink | Reply
    Tags: , , , , , The Baker Lab, ,   

    From Berkeley Lab: “Berkeley Lab Scientists Help Define the Healthy Human Microbiome” 

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    Berkeley Lab

    Computing, bioinformatics, and microbial ecology resources play key role in mapping our microbial make-up

    June 13, 2012
    Dan Krotz

    You’re outnumbered. There are ten times as many microbial cells in you as there are your own cells.

    The human microbiome—as scientists call the communities of microorganisms that inhabit your skin, mouth, gut, and other parts of your body by the trillions—plays a fundamental role in keeping you healthy. These communities are also thought to cause disease when they’re perturbed. But our microbiome’s exact function, good and bad, is poorly understood. That could change.

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    The bacterium, Enterococcus faecalis, which lives in the human gut, is just one type of microbe studied in NIH’s Human Microbiome Project. (Courtesy: United States Department of Agriculture)

    A National Institutes of Health (NIH)-organized consortium that includes scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has for the first time mapped the normal microbial make-up of healthy humans. [Human Microbiome Project (HMP) is a United States National Institutes of Health initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans (i.e. their microbial flora). Launched in 2008, it is a five-year project, best characterized as a feasibility study, and has a total budget of $115 million. The ultimate goal of this and similar NIH-sponsored microbiome projects is to test if changes in the human microbiome are associated with human health or disease. This topic is currently not well-understood.]

    The research will help scientists understand how our microbiome carries out vital tasks such as supporting our immune system and helping us digest food. It’ll also shed light on our microbiome’s role in diseases such as ulcerative colitis, Crohn’s disease, and psoriasis, to name a few.”

    See the full article here.

    For those interested – and you should be interested – the Human Protein Folding Project (HPF2) at the Bonneau Lab, New York University, is a participant in the HMP project. HPF2 is a project in Public Distributed Computing under the aegis of the World Community Grid (WCG), running on software from the Berkeley Open Infrastructure for Network Computing (BOINC) and using the project products of the rosetta@home project from the Baker Lab, University of Washington.

    That is a pretty long sentence. What it means is, if you visit WCG, or BOINC, and download the BOINC agent software for Windows, Linux, or Mac, you can attach to the HPF2 project and process data for HMP. While you are at it, look around at WCG website, there are about a dozen very worthwhile projects all aimed at curing illnesses and solving fundamental problems for mankind. Also, at the BOINC website the are a vast variety of projects in Biology, Chemistry, Physics, Mathematics, and Astronomy.

    Here are some pretty pictures.

    So, you know, when you see graphics, these are serious guys. Give them (us) a look.

    My BOINC stats.
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  • richardmitnick 9:32 am on December 6, 2011 Permalink | Reply
    Tags: , , , , The Baker Lab, ,   

    From the New York Times: “Computer Scientists May Have What It Takes to Help Cure Cancer” – Another Blown Opportunity to boost BOINC 

    By DAVID PATTERSON
    December 5, 2011

    This is copyright protected, so just a couple of hints.
    “The war against cancer is increasingly moving into cyberspace. Computer scientists may have the best skills to fight cancer in the next decade — and they should be signing up in droves….An inspirational example is the Foldit game — developed by the computer scientist Zoran Popovic at the University of Washington.

    Very nice, great article, but, huge gap. No mention of the roots of Dr Popovic’s successful adventure.

    Dr Popovic worked with The Baker Laboratory, the locus of rosetta@home, a project which runs on BOINC software from UC Berkeley. Rosetta@home has currently 37,456 “users” on 60162 “hosts”. The project does currently 58 TeraFLOPS of data per 24 hour period.

    On the one hand, you can certainly visit the Foldit web site to participate. If, on the other hand, you are not fond of games, you can visit the BOINC web site, download and install the small piece of software, and attach to the Rosetta project. You will receive small packs of data called “work units” or “WU’s” to “crunch”. As each WU is finished, your computer will return the results and you will receive more work.

    Rosetta software is also used by World Community Grid (WCG) project Human Proteome Folding. This project is based at New York University in the Bonneau Laboratory

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    At both the WCG and BOINC web sites you will find many other really exciting projects in which you may participate. All WCG projects run on the BOINC software, along with the many independent projects at the BOINC web site.

    Once you have installed the BOINC software and attached to your chosen projects, you can be as active or passive in this process as you wish. You can pretty much simply let the stuff happen in the background and pay it scant attention. However, each project has its own forum covering many topics, including the science involved and the operation of the software. You can also check to see how your are doing by signing on at BOINCstats.com

    There are currently 286,105 “users” (people) on 515,015 “hosts” (computers) in all of BOINC. Currently we are doing 5,337 TeraFLOPS of work in a 24 hour period. That’s over half a PetafLOP, which would put us somewhere around 14th or 15th on the TOP500 list of supercomputers in the world. Except, in that world, we don’t count. WCG currently has 94,007 users on 211,163 hosts. We are currently at 278 TeraFLOPS.

    BOINC software will run on Windows, Mac and Linux based computers. So, whatever your flavor, why don’t you visit BOINC and WCG, give us a look, and try us out? The BOINC process never interferes with anything else that you are doing on the computer. If on occasion you require huge amounts of resources, such as “storming the castle”, BOINC will instantaneously give up its resources and pause until your battle is finished. I hope to run into you in a forum.

    Mr. Patterson work is an example of why I started this blog.

     
  • richardmitnick 5:29 pm on November 25, 2011 Permalink | Reply
    Tags: , , , , , The Baker Lab, ,   

    From WCG Project Human Proteome Folding (HPF2) Exciting Updates 

    Human Proteome Folding (HPF2)., a WCG project in The Bonneau Lab at New York University has posted some very exciting news. The report is copyright protected, so I will not trespass on that.

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    Depictions of proteins

    HPF2 utilizes software developed by BOINC project Rosetta@home, in the The Baker Lab at University of Washington.
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    You can see the report here.

    But WCG crunchers can be proud of the fact that we have contributed – this from the WCG web site – 96,695 years, 223 days, 09 hours,26 minutes, 30 seconds to this effort. This is the power of Public Distributed Computing via the BOINC software on which our projects are run.

    I cannot begin to contemplate how this work would have gotten to this point without us, except at the expensive cost of processing time on some supercomputer.

    .

    You, too, dear reader, can be a part of this incredible process. Visit either WCG or BOINC, download and install the software, and attach to this and other worthy projects at the WCG web site and also at the BOINC website. You financial cost is about the same as a 100-150 watt light bulb. Your personal satisfaction at being a part of this is immeasurable.

     
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