Use of the Core is initiated by email to Eric Hoffman, with a short description of the desired services. For services requiring a small amount of time (e.g. providing access to software tools for bioinformatics), no fee and no formal collaboration is required. For projects requiring extensive computer coding or statistical assistance, then collaboration and/or fee-for-service may be requested.

The Bioinformatics and Computing Core is integrated with a series of additional NIH-funded Core facilities in the Research Center for Genetic Medicine, and additional assistance and pilot funding may be available through these other sources. These include a NICHD National Center for Medical Rehabilitation Research Core (see http://www.ncmrr.org ), a NICHD Mental Retardation and Developmental Disabilities Genetics and Proteomics Core, and a Department of Defense funded Murine Functional Testing Core. All efforts will be made to ensure that the potential Core user will have access to all available resources from the ensemble Cores.

Brief description of services or resources (a paragraph or two)

A. Public access data resources. The Core maintains a series of public access web sites that permit download and interactive query of microarray data sets generated by the Center. These include muscle regeneration time series, muscular dystrophy data, and many additional human and rodent muscle data sets. Access is through the PEPR site ( http://pepr.cnmcresearch.org ), and a public access SAS server ( http://sas.cnmcresearch.org ). The Center is the largest single contributor of microarray data in the public domain (12% of NCBI GEO), and much of this is relevant to muscle and muscular dystrophy.

B. Public access software. The Core provides access to both the HCE (Hierarchical Clustering Explorer) (see Seo et al. 2004), and Interactive Power Analysis Tool (see Seo et al. 2006) ( http://www.cnmcresearch.org/bioinformatics ).

C. Statistical analysis. The Core includes PhD-level personnel with extensive experience in statistical genetics, higher order multi-dimensional data analysis, neural networks, and human/computer interfaces. The Core can assist with SNP association studies, linkage analyses, microarray data interpretation, and proteomics data interpretation.

D. Database design and coding. The Core houses expertise in a variety of computer languages, with a specific focus on internet-accessible large-scale datasets including genomics and/or proteomics data. The Center can provide consultation on database design, and can assist with coding if needed.

Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP. Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics . 2004; 20: 2534-44.

Seo J, Gordish-Dressman H, Hoffman EP. An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics . 2006; 22: 808-14.