HSPH Bioinformatics Core

Location: Harvard School of Public Health, Boston Massachusetts

Name/Title: HSPH Bioinformatics Core

Links: http://www.hsph.harvard.edu/research/bioinfocore/

Group size: 6

Environment:

Embedded in the Harvard School of Public Health, the HBC supports research in public health.

Tools:

The HSPH Bioinformatics Core (HBC) offers consultations on basic questions in research computing, bioinformatics and computational biology during the initial stages of study design and grant proposals as well as for ongoing, funded studies requiring external expertise.

HBC has experience in large-scale data management, database design and software development. Staff members can provide assistance in quality assurance and analysis of gene expression arrays, genome-wise SNP arrays, CNV studies and different aspects of second-generation sequencing technologies such as ChIP-seq, RNA-Seq or re-sequencing efforts of mammalian and pathogen genomes.

Services also include provision of external information generated from public database, data curation and assistance on choosing the right data format and annotation standard to ensure best practices in data management and submission are being maintained.

Pertinent hardware info:

HBC has access to a state-of-the-art Linux computing cluster, modern desktop computers for members, and a computing laboratory for students. The Linux cluster is a 32-node (64-CPU) shared computing cluster that provides high performance, parallel processing computing and is designed for future growth. The cluster is operated by the School's Department of Information Technology (IT) by professional systems administrators, who provide considerable user support to researchers with accounts on the cluster. Each cluster node is a Dell dual CPU 3.2 Ghz Xeon 64-bit machine with 6 Gb RAM. The cluster uses ROCKS cluster scheduling software to balance usage, has 1 Tb of disk space, and has weekly tape backup. Software includes R, Matlab, and Mathematica, as well as compilers for common programming languages.

Training:

We collaborate with the Countway Library of Medicine and the Harvard Clinical and Translational Science Center to provide regular seminars and training sessions for researchers at HSPH and in the Harvard community.

Bioinformatics support model:

HBC operates as a recharge center available to researchers across the campus and affiliated hospitals.