Week 15 – BOINC! and the search for Little Green Men

Today there are literally millions of computers sitting quietly on desks or in dark corners, doing pretty well nothing most of the time. Probably the first project to attempt to harness all this computer power was the SETI project – The Search For Extra-terrestrial Intelligence. The idea is to allow each home computer to connect to a central server, and download a small portion of the task, and then plod away until that portion is complete, and then return it to the server.

BOINC stands for the Berkeley Open Infrastructure for Network Computing, which provides all the facilities to download tasks, and collect the results. “The intent of BOINC is to make it possible for researchers in areas as diverse as molecular biology, climatology, and astrophysics to tap into the enormous but under-utilized calculating power of personal computers world-wide.” At July 2006, BOINC has approximately 735 000 users, with over 900 000 computers, spread over 249 countries. There are currently 28 separate projects.

Why am I discussing this on a blog focused on the melanoma experience? Well, one of the projects you can support via BOINC is Rosetta@home, which is attempting to solve one of the longest standing problems in molecular biology: the "protein folding" problem. Proteins are the miniature machines that carry out almost all the important functions in your body. As with any machine, understanding how proteins work requires understanding what their structures are. However, until very recently, it has seemed nearly impossible to compute the structures of proteins from their amino acid sequences, and solving this problem has been something of a scientific "Holy Grail". The major stumbling block is the very large amount of computing time required to solve the problem.

The Rosetta@home project is contributing to research into Malaria, Anthrax, HIV, other viruses, Alzheimer’s disease, and Cancer, and it was this last one that made me finally get my act together, and download the software. I would rather contribute to basic research in this area than, eg; the SETI project, as it has a more direct bearing on our current problems.

I found it quite simple to download the software and get it working on my two pcs. One pc is a rather old desktop, but it is available 24 hours a day. My notebook is more recent and much faster. Once started, BOINC automatically downloads work tasks, and grinds away whenever the machine is not busy. As soon as I press any key on the keyboard, it suspends the task and the machine is available for work as usual.

However, there is a catch, and this relates to our backward communications systems here in South Africa. At home I have a broadband connection, which I need for my consulting work. The speed of the connection is not an issue, but unfortunately bandwidth is limited in South Africa. For cost reasons I opted for the lowest bandwidth cap, which is 1 GB per month. This is quite sufficient for my normal purposes, but once I started using BOINC I quickly reached my limit, and had to switch it off about half way through the month.

So, what is the bottom line on this? Well, I can still contribute to some extent, but there is no way I can just leave BOINC running all the time … Well, not until the cost of bandwidth drops in South Africa!

So, another good idea bites the dust. Pity!

Some useful references if you want to explore further:

Rosetta@home: http://boinc.bakerlab.org/rosetta/
BOINC: http://boinc.berkeley.edu/
SETI@home: http://setiathome.berkeley.edu/
There are also good articles on BOINC, SETI@home and Rosetta@home on wikipedia.