We use BLAT mostly - it's much much faster than BLAST, and can cope with introns. You can run multiple programs on a cluster. The job scheduler - LSF, SGE, PBS, Parasol or whatever gives the jobs to the machines one at a time typically. Jim Kent Genome Bioinformatics Group University of California at Santa Cruz http://www.soe.ucsc.edu/~kent/ ----- Original Message ----- From: "Sylvain Foisy" <foisys@mac.com> To: <bioclusters@bioinformatics.org> Sent: Thursday, May 02, 2002 10:57 AM Subject: [Bioclusters] Request for discussions-How to build a biocluster Part 6 (Misc.) > Hi, > > A reminder: this is coming from a total newbie at this BioCluster stuff. > it is also to serve as the seed of a tutorial/history-of-building site > for our creation. I am a total newbie in UNIX administration and > installation. This is why we will get a system administrator to help us > out. But I still have to figure out the right questions to ask!! > > OTHER SOFTWARES > > Besides BLAST, what other bioinfo software are known to work in cluster > config? I would imagine that FASTA, the HMMER suite and any software > that work in embarrassingly parallel fashion will. Anybody has > experience running multi-softwarer clusters? > > Also, can a cluster do let's say, BLAST and RNA folding together? or > BLAST and molecular modelling? At 8 nodes, we will concentrate on BLAST > but we are planning a 32 nodes stage soon afterward and the demand is > there. > > CLUSTERS HELPING CLUSTERS > > Another point that has been raised in our group is the fact that if some > clusters might be less busy than others, is it possible for the head of > the busy one to get help from the nodes of a less busy cluster? I ask > because our projected cluster is to be a public-access resource. Another > cluster is also planned for philogeny analysis by a group in the same > department. In exchange for maintaining a mirror of GenBank, they are > offering some of their horsepower to us. Is this feasible? > > Am I missing something? > > This is open for helpful and constructive discussion > > I know that lots of my questions have been asked before but I found some > of the answers to be very cryptic. By pooling my questions in this > multipost, I invite discussion on the hows of putting a BioCluster > together for the less technically inclined among us! > > Sylvain > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Sylvain Foisy, Ph. D. > Manager > BIONEQ - Le Reseau quebecois de bioinformatique > Genome-Quebec > Tel.: (514) 343-6111 poste 5188 > E-mail: foisys@medcn.umontreal.ca > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bioclusters >