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Bioinformatics & Information Technologies (BIT)

The CFAR BIT Core Provides Bioinformatics and Information Technology Expertise


OCCAMS: OCCAMS is an open source biomedical data management platform designed to support clinical research studies with complex and custom data needs. With OCCAMS, our experienced staff currently supports five research cohorts consisting of +3,000 participant enrollments in +10 studies at both domestic and international locations.

HyPhy/Datamonkey: HyPhy is a scriptable package for evolutionary analysis. It can fit statistical evolutionary models to alignment of homologous sequences using maximum likelihood; estimate various parameters that have biological meaning, e.g., branch lengths, substitution rates, dN/dS ratios, recombination breakpoints; and test hypotheses about how sequences have evolved. We also host Datamonkey, a public web-server that implements some of the most popular HyPhy functions (e.g., recombination, positive selection detection).

NGS data analysis services: Our analytic services cover both traditional and NGS (all major platforms) data. We specialize in custom analysis for virological, immunomics, and molecular epidemiology research applications.

High performace computing (HPC): We provide private access to our 700+ processor compute cluster on per project basis.

Information Technologies

Mobile data collection services: We custom develop iPad-based survey instruments for computer-assisted self-interview (CASI) and other clinical research applications. These surveys meet HIPAA/FISMA security requirements and can be collected in the field or in the clinic, in the presence or absence of a continuous Internet connection.

Collaborative web-based tools: We offer web-based tools to our users to facilitate communication and meeting of project goals in a timely fashion. These tools include secure access to private, locally-hosted collaborative wikis, Dropbox-like file sharing, team online chat, as well as agile project management planning and training services.

Website development and hosting: We are continually developing and maintaining websites for numerous research projects and organizations. Please see the following sites for examples of our work:

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AntiViral Research Center
220 Dickinson St.
San Diego, CA 92103