Saturday, August 01, 2009

Karen Completes Babel (Aug 02 09)

Equipped with a PHP75,000.00 budget to buy a desktop computer for the Protein Structure and Immunology laboratory at the National Institute of Molecular Biology and Biotechnology (NIMBB) at the University of the Philippines, my daughter Karen decided to make the most of this money, and buy a compute cluster instead. With that amount, she got four nodes: a master front end and three compute nodes. Each node had an Intel Core2 Duo processor, 2GB memory, 320GB disk, and a gigabit network card. She also got a Samsung LCD monitor, keyboard, and mouse, shared by all four nodes via a KVM switch. She was left with enough money to get a 16 port 10/100MB network switch, although a gigabyte switch would have been better but more expensive option. She got the 16 port switch, so that when their laboratory get more money in the future, they can add more compute nodes. She installed Rocksclusters v5.2, and the installation process took her several days, because this is her first cluster installation job. She had no one to consult, because there are not too many molecular biology people who know how to install compute clusters.

When her boss, Dr. Bascos, saw the contraption, she called it Babel because it reminded her of the biblical tower of Babel. This name might actually be an appropriate name, since the cluster speaks many computer languages like C, C++, Java, Perl, Python, and PHP, and in addition, many BIO packages/languages like TIGR, BioPython, ClustalW, NCBI Blast, T_Coffee, Fasta, Gromacs, and Phylip.

Her next problem is learning to use these BIO packages to help in her work. The search for knowledge never ends.

No comments: