CD: Bioinformatics Core

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The University of Texas SPORE in Lung Cancer has Projects and Cores at both the University of Texas Southwestern Medical Center (UTSW, Dallas, TX) and the University of Texas M.D. Anderson Cancer Center (UTMDACC, Houston, TX) sites that involve multiple clinical and basic investigators. These Projects and Cores and the reagents and large datasets generated need to be analyzed by, and shared between SPORE investigators, Projects, and Cores and also need to be shared with investigators at other institutions and with other Lung Cancer SPOREs. In addition, bioinformatics tools are needed to help store, extract, manipulate and interpret this data. Also this data needs to have reliable backup. Finally, there is a large amount of new data being reported in the literature and deposited into accessible databases to which our SPORE investigators need access. These needs led to the creation and development of this Bioinformatics Core (Core D). The goal of this Core is to develop and maintain database integration and a data sharing website of information developed in the Projects and Cores that is important to many SPORE investigators as well as aid in the development and use of data analysis mining tools in support of the projects of this SPORE. This Core must deploy these enabling technologies to meet the needs of all of the SPORE Projects and Cores. After de-identification of patient information in SPORE Pathology Core B, this Core will help SPORE investigators gather complete data sets on SPORE laboratory and clinical samples, as well as publicly available datasets, interface these datasets with the SPORE Biostatistics Core (Core C), and then assist SPORE investigators and CORE C in the interpretation of these data using data mining techniques. This includes interaction with other Lung Cancer SPOREs and institutions. Other facilities include educational modules/classes, identification/testing of new technologies/methods of potential value to all SPORE researchers, and the large complement of computational codes and databases made available on our servers at http://spore.swmed.edu. Software, available over the web or via downloadable modules for the analysis of expression data, genomics experimental design, text mining and DMA sequence analysis was produced and is used by SPORE researchers. This Core has 4 specific aims: 1. Development of internet accessible databases for data sharing and analysis, and development of computational biology, resources; 2. Development of a distributed computational infrastructure for integrated data management and analysis; 3. Develop and perform data quality and assurance procedures. 4. Enhance and maintain the SPORE web site. This Core is led by Dr. Garner (with aid from Dr. Ahn for clinical data sharing issues) and Dr. Almeida that are both area experts and have each developed important components for this system and have been pioneering in data-sharing efforts at their respective institutions.