Taking Control of the Cluster

When Gernot Stocker noticed that the biologists in his lab were not using the department's brand-new, 24-node computer cluster, he started taking notes. Running sequences on a desktop computer could take days, yet these scientists preferred that to the cluster for a simple reason. "Biologists don't like command-line software," says Stocker, a graduate student at the Institute for Genomics and Bioinformatics at Graz University of Technology in Austria. "They're used to using Web browsers."So Stoc

Sam Jaffe
May 9, 2004

When Gernot Stocker noticed that the biologists in his lab were not using the department's brand-new, 24-node computer cluster, he started taking notes. Running sequences on a desktop computer could take days, yet these scientists preferred that to the cluster for a simple reason. "Biologists don't like command-line software," says Stocker, a graduate student at the Institute for Genomics and Bioinformatics at Graz University of Technology in Austria. "They're used to using Web browsers."

So Stocker programmed a simple solution: a Web browser-based interface that will run most sequence-crunching algorithms on the master PC that controls a Linux cluster. Called ClusterControl http://genome.tugraz.at/Software/ClusterControl, this queuing program uses any Microsoft, Netscape, or Mozilla-based browser.1 It requires installation of PHP (a server-side scripting language), Apache (a Web server), and OpenPBS (a queuing system).

In just three steps, a user can have the cluster run a sequence using NCBI BLAST, FASTA, or...

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