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Geeks use computer power to cure cancer

Date

Anthony Agius

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Technology enthusiasts are using the power of their computers to join the fight to cure diseases such as cancer, Alzheimer's and Parkinson's.

One of OCAU's most productive folders ... Michael Russell, with his dog Skye.

One of OCAU's most productive folders ... Michael Russell, with his dog Skye.

The human race agrees cancer is awful. Nobody wants it and nobody likes it. Cancer's impact also spreads to the minds of families and friends of those with the disease, who watch their loved ones try to cope with their own bodies trying to kill them.

The same applies for diseases like Alzheimers and Parkinsons. As people are touched by the effects of these diseases, they want to help. Some become scientists, doctors or nurses, actively working in the front lines to cure, treat and assist. The majority of us contribute to charities, either directly, by volunteering, or indirectly, by giving money, or raising awareness.

Some however, choose a different way to fight these diseases, using a technology called distributed computing and a project called Folding@Home.

A person's cancer treatment can raise difficult issues for their manager and colleagues.

A person's cancer treatment can raise difficult issues for their manager and colleagues.

Let's look at how medical research occurs in the 21st century. The common ideal is a bunch of people in white coats doing a lot of stuff with beakers and test tubes and looking down microscopes. But in reality, much of it is done by computer programmers and big rooms of computers.

Those computers crunch numbers and run complex models analysing how drugs interact with the body, predicting how diseases manifest and a host of other things you need a degree in biology to understand.

Basically, the computer is a sandpit that scientists and programmers can mould as to envisage how stuff happens and how stuff works. Using theories and scientific knowledge, they can get an amazingly accurate picture of the biological mechanics and interactions that go on in nature.

This sort of research requires insane amounts of computer power. For example, the Vayu supercomputer installed at the Australian National Computational Infrastructure National Facility in Canberra, is Australia's fastest computer. It has 11,936 quad-core Intel Nehalem 2.93Ghz CPUs.

To put that into perspective, the Mac Pro sitting under my desk has one, quad-core Intel Nehalem 2.66Ghz CPU. That's effectively 12,000 of my computers, in a room, solving complex problems in the areas of biomedicine, physics, astronomy and meteorology.

12,000 computers, crunching data and doing their bit to find a cures terrible diseases is great, but to tackle big issues, like cancer, you need incredibly large amounts of data analysed. Used a traditional supercomputer would never complete the job. Even if dozens of supercomputers are utilised, it would still take decades to complete any large analysis.

But what if you have 5 million computers, theoretically 417 of Australia's fastest computer, working on the single task of analysing this data? You start getting results and achieving research never thought possible.

Harnessing five million computers sounds unachievable but that's the amount of devices currently participating in a distributed computing project called Folding@Home. It was started in 2000 by Stanford University and currently runs on over five million devices across the world, including Sony's PlayStation 3.

Folding@Home isn't the only distributed computing project, but it is the one with the most emotional ties. The aim of Folding@Home is to investigate protein folding. When proteins don't fold correctly, diseases like cancer, Alzheimer's and Parkinson's occur and research into why this happens, hopefully, can lead to cures.

The research completed by Folding@Home participants has resulted in 95 peer reviewed and published works, which benefit the entire scientific research community, inching away at cancers, Alzheimers and Parkinsons.

Most of those involved are simply nerds who want to help. It's trivial to load up the Folding@Home application and just let it sit there on your computer, doing it's work when the computer is idle. For others, there's a personal connection, be it having lost a loved one, or having a disease themselves.

Online computer enthusiast forum, Overclockers Australia has many members dedicated to Folding@Home, with a Charter and Wall of Rememberance, listing the reasons why they crunch those numbers. Some members even spend money on dedicated "folding boxes" which are computers built and set aside simply to run the Folding@Home software and nothing else.

Each month, on Overclockers Australia, an "Iron Folder" is awarded to the person who contributes the most workload to the Folding@Home project. Each winner is also interviewed, with some heartwarming insights as to why these people do what they do. Crixon, OCAU's Iron Folder for November 2011, says "My family has had a history of cancer and I'm no lab tech, so it's about all I can do to assist in helping others understanding how diseases work."

Michael Russell, who uses goes by the username OLDsniper, is one of OCAU's most productive folders. When asked why he folds, "it is personal for me, as my older brother has had Parkinson's for years, and recently our mother has been treated for a rare breast cancer." For Michael, he sees involvement with Folding@Home as going an extra mile on top of donating to charity. "It is common for people to fold, because it has a more personal involvement in doing something in the fight against cancer, Parkinson's and other diseases, rather than just giving some cash to charity."

If you are interested in using the idle power of your computer to assist research into cancer and other diseases, a great place to start is the Overclockers Australia wiki.

7 comments

  • I've been folding@home for several years now (for Team 182116: Atheists, Skeptics, & Humanists), and it does feel good to know that I can contribute a small, but significant part to understanding proteins. Until I started I had little idea just how complicated protein folding is.

    Commenter
    ginckgo
    Location
    Noble Park
    Date and time
    April 26, 2012, 9:39AM
    • Thank you to everybody who is working towards either a cure or prevention of these horrible afflictions.

      Commenter
      Lynne
      Location
      Melbourne
      Date and time
      April 26, 2012, 9:43AM
      • I think this is great stuff if your home runs on clean(er) energy.

        It doesn't seem quite as good for most people who get coal based energy.

        It's all about priorities. And as I'm currently more concerned about pollution than cancer...

        Commenter
        MattS
        Location
        Melbourne
        Date and time
        April 26, 2012, 12:58PM
        • MattS - at least 12.6 million people are diagnosed with cancer every year and 7.5 million die of the disease each year. Yes, its all about priorities. Yours seem to be a little confused.

          Commenter
          S of Melb
          Date and time
          April 26, 2012, 1:43PM
        • @S of Melb:
          I realised after posting my message that it didn't quite come out as I meant it and I apologize if I offended you.

          I was trying to explain that even though I'm very keen on folding@home, seti@home and other similar projects, I think that the increased energy consumption is a real issue as it also increases pollution.

          The cold hard truth as I see it is that pollution is among the causes of cancer and that if nothing is done about it, it will end up causing many more deaths that cancer ever will. So yes, my priorities are to fight the cause itself. For completion's sake, I'll refer you to that article that attributes 40% of all deaths to pollution: http://www.sciencedaily.com/releases/2007/08/070813162438.htm. You may also want to google pollution and cancer.

          Commenter
          MattS
          Location
          Melbourne
          Date and time
          April 26, 2012, 3:17PM
        • MattS. No offence taken. And thanks for the clarification. I see your point, however Im not sure of its relevance to this argument. Coal fired generation being of a baseload nature and due to its inherent inflexibility (with or without carbon pricing) will be running whether or not your laptop is being used for this type of research, so Im struggling to see the link. The (relatively) miniscule energy usage will have no affect on coal fired generation levels. I guess the point Im trying to make is this is a great initiative and you should not have any concerns that helping to find solutions will increase the problem.

          Commenter
          S of Melb
          Date and time
          April 26, 2012, 4:30PM
      • Dont forget folding@home is not the only distributed research project. Most of the big universities adn reserach cetnres use BOINC or World Comminuty Grid which shares a number of these medical research projects. Then you can pick and choose the project you would like to get involved in.

        Many us based ISPs and online companies give discounts to people who process at home and join their corproate processing teams (contributre their processing to the collective effort of that organisation)..

        Folding is only one option amongst many very valubale research projects requiring processing help.

        Commenter
        Andy_Syd
        Location
        Sydney
        Date and time
        April 26, 2012, 1:54PM
        Comments are now closed
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