Computational Biology

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The CFAR Molecular Diversity Core was initiated in 1995 to provide a DNA sequencing service to support the AIDS research community. It evolved into the current Genomics Core with a new focus on providing assistance in assuring HIV sequence quality control and in performing detailed phylogenetic and bioinformatic analyses. Since its inception, the Core has contributed to ten or more collaborative, peerreviewed publications per year. Going forward, we will continue to develop, refine, implement, support and teach methods for the study of HIV gene sequences. However, we will also broaden the scope of the core in ways that together make Computational Biology, rather than Genomics, the most apt description of our new Core. First, we will create an open-source bioinformatics toolkit that includes incorporation of existing analytical tools together with emerging techniques. This toolkit is being developed in collaboration with the local CFAR Biostatistics Core, the Los Alamos National Laboratory (LANL) and investigators at the UCSD CFAR. Second, we will expand our efforts at training and research community outreach. To this end we will develop a unified web-based interface to access our analysis tools, using questionnaires to determine need for tool development and training sessions. We will develop an easier mechanism for users to ask specific questions or request specific support for both existing tool usage and possibly additional novel analyses. Lastly, we will produce a regular Newsletter to inform the CFAR community of the availability and functionality of our computational tools and similar programs from other sources. Third, our CFAR efforts will link and assist parallel and separately funded efforts to develop a database to acquire, retain and mine clinical, laboratory and genetic data derived from HIV and infected human hosts. These database and mining tools are being developed, implemented and will be spread to investigators throughout the international CFAR community and other AIDS researchers. Development is proceeding through collaboration with all of the major laboratories gathering viral gene sequence data, leaders of those gathering AIDS-related clinical, therapy, host genetics and viral immunology data, as well as those leading in the area of integrated data analysis. These include investigators at the UW, LANL, six CFARs that focus on a combination of these areas, as well as the Multicenter AIDS Cohort Study (MACS), the Center for HIV-AIDS Vaccine Immunology (CHAVI), and the Collaborative AIDS Vaccine Discovery (CAVD) and Partners in Prevention (PIP) programs funded by the Bill and Melinda Gates foundation.