Bioinformatics Core

Neeley Bioinformatics Core

The Bioinformatics Core provides High-Performance Computing services to SKCC faculty, as well as web-based services to Internet users.

For computational power, the Bioinformatics Core relies on a custom-built Linux Cluster comprised of 36 CPUs, 122 GB of RAM memory, and 3400 GB of RAID disk storage. The Linux Cluster provides massively-parallel computing services to the Genomics, Proteomics, and other cores. Tasks that would normally require years of computational time can now be finished in just a few days, and tasks that would normally take days can be finished in minutes.

Besides providing a large suite of commonly-used Bioinformatics Software (BLAST, BLAT, MUMmer, MEME/MAST, AMOS, EMBOSS, Primer3, MAFFT, FirstEF, etc.), the Bioinformatics Core also provides custom programming services to help SKCC scientists process data, design experiments, and visualize results. For example, a comparative sequence assembler was written for the Genomics Core in order to build genomes for new bacteria strains. This software will be included in a later release of the AMOS suite of assembly tools, and is currently being used in a collaborative genome-assembly effort with Washington University.

Also, custom software was written for the Proteomics department to allow their Sequest and DTASelect programs to be run on the Linux Cluster instead of a PC, greatly reducing the time needed to compute experimental results.

In collaboration with the Genomics Core, the Bioinformatics Core also hosts a number of web applications for Internet users, most notably the WebArray service, which provides storage and statistical analysis of microarray data.