Computational Biology

CFAR分子多样性核心于1995年启动，旨在提供DNA测序服务 支持艾滋病研究界。它演变成了目前的基因组学核心，并将新的重点放在 在确保艾滋病毒序列质量控制和执行详细的系统进化和 生物信息学分析。自成立以来，核心已经促成了十个或更多的协作、同行评审 每年出版一次。展望未来，我们将继续开发、完善、实施、支持和 讲授研究艾滋病毒基因序列的方法。然而，我们也将扩大核心的范围在 这些共同作用使得计算生物学而不是基因组学成为对我们新的 核心。 首先，我们将创建一个开源的生物信息学工具包，其中包括整合现有的 分析工具与新兴技术相结合。此工具包是与 当地CFAR生物统计核心、洛斯阿拉莫斯国家实验室(LANL)和加州大学圣地亚哥分校的调查人员 CFAR。 第二，我们将扩大在培训和研究社区推广方面的努力。为此，我们将 开发统一的基于Web的界面来访问我们的分析工具，使用问卷来确定需求 用于工具开发和培训课程。我们将为用户开发一种更容易的机制来询问特定的 对现有工具的使用以及可能的其他新颖分析提出问题或请求具体支持。 最后，我们将制作一份定期通讯，通知CFAR社区可用和 我们的计算工具和来自其他来源的类似程序的功能。 第三，我们的CFAR努力将联系和协助平行和单独资助的努力，以制定 获取、保留和挖掘源自艾滋病毒和受感染的临床、实验室和基因数据的数据库 人类的主人。正在开发、实施这些数据库和挖掘工具，并将推广到 整个国际CFAR社区的调查人员和其他艾滋病研究人员。发展是 通过与所有主要实验室合作收集病毒基因序列数据， 收集与艾滋病相关的临床、治疗、宿主遗传学和病毒免疫学数据的领导人，以及 在综合数据分析领域处于领先地位的公司。这些人包括UW，LANL，Six的调查人员 关注这些领域组合的CFAR，以及多中心艾滋病队列研究(MACS)， 艾滋病疫苗免疫学中心(CHAVI)与艾滋病疫苗合作发现 (CAVD)和由比尔和梅琳达·盖茨基金会资助的预防伙伴(PIP)计划。

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.