Computational Facilities:
The Eichler Lab computational facilities consist of three main components: The first component is an IBM cluster that includes a total of 45 execution nodes with dual Intel Xeon and dual AMD Athlon microprocessors, plus 6.2 TB of storage in GPFS (General Parallel File System) server, and another 6.5 TB of storage in NFS (Network File System) servers. Eichler lab also has access to a departmental cluster owned and operated by Department of Genome Sciences which consists of 23 dual and 14 single CPU execution nodes and a 4 TB NFS server for storage. These clusters are specifically useful in running parallel applications, such as running RepeatMasker on many sequences, or running BLAST with many queries on large databases.
The second main component is the local web and database servers where the local data is shared with the research community. These are all standalone servers, each dedicated to one genome. Each server includes different kinds of bioinformatics data mined for the specific genome it stores. These servers are all Linux nodes running MySQL database engine and Apache webserver. Their total disk space is around 2TB.
The last main component of the Eichler lab computational facilities
includes a Sun Fire V40z Server with four dual core 64-bit processors
(AMD Opteron Model 870 CPU), 32 GB of RAM and 1.2 TB of local hard disk
storage. This high memory server is used for memory-intensive
computational analysis (i.e. application of phylogenetic algorithms to
a large number of sequence taxa or graph theory analysis of multiple
pairwise alignments) that wouldn't be possible to run on a 32-bit CPU
because of the hardware limitations on addressing memory space.
Software
PARASIGHTMultiple Alignment Manipulator (MaM)
DupMasker