The Bioinformatics Resource for Computational Applications (BRCA) at the Computational Laboratory in Translational Bioinformatics is a bioinformatics computer cluster that was established with funds provided by the NFGC and is located in the University of South Florida Research-Oriented Computing Services department. The bioinformatics cluster was established for collaboration, experimentation, and evaluation of bioinformatics methods, and is currently focused on gene expression microarrays. The name of the cluster was chosen to signify the close connection between biology and the computational sciences, as “BRCA” also refers to genes that are frequently mutated in persons with breast cancer.
Several projects have generated preliminary data using this resource. In collaboration with faculty in the USF Computer Science department, NFGC personnel are developing a technique for evaluating the classification complexity of gene expression datasets. This information is crucial in understanding where additional methodological research is required, a key goal of this laboratory. It is also important for the development of unsupervised learning and visualization techniques in complex datasets. A second project was developed in collaboration with researchers at Moffitt using the NCI panel of 60 cancer cell lines. This project involves a novel technique for integrating prior biological knowledge and extracting classes of genes that respond similarly with similar biological context.
In the upcoming year, there are plans to further develop the evaluation framework for methods in microarray analysis through expanded datasets and additional software. In addition, two specific projects that directly evaluate techniques within this framework will be pursued.