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AMD64 Cluster

 Caton is a AMD64 cluster. It consists in a 32 nodes with 4 processors and 3 GB of ram memory each of them. As a storage solution, caton has a iSCSI RAID with 4 terabytes of space.

AMD's High Performance Computing (HPC) solution stack delivers powerful performance advantages through a software ecosystem tuned for the hardware that it runs on. The solution stack includes a hardware platform based on the AMD Opteron processor and a software ecosystem that encompasses HPC-targeted compilers tuned for AMD platforms and the AMD Core Math Library (ACML).


 Caton is mainly used for sequence analysis projects, genotypyng analysys and some HPC projects. High Performance Computing can be defined as the combination of  high performance computers with high performance networks. Hence, a large part of the HPC story  comes from the underlying networking infrastructure; the network backbone and interconnect fabrics,  that tie the independent computing resources together. AMD partners like Mellanox, Myricom, and  others create these network technologies. This infrastructure in turn is leveraged by application-facing software middleware such as Platform's MPI and SGE that support the programming and scheduling of  HPC applications on top of this infrastructure.

On caton you can find the following software :

hmmer: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models .

hex : Hex is an interactive protein docking and molecular superposition program. Hex understands protein and DNA structures in PDB format, and it can also read small-molecule SDF files.

PennCNV : Welcome! PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.

T-coffee : A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures .

psipred : The PSIPRED Protein Structure Prediction method aggregates several of our structure prediction methods into one location.

: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

Plink : is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.