Supporting Integrative Genomic Analysis Users with GenePattern

描述（由申请人提供）：项目摘要基因组数据的洪水正在彻底改变我们的方法来理解正常的细胞过程和疾病的机制。这推动了复杂的计算方法的发展，使这些数据的分析，以及对综合技术的新的重视。至关重要的是，通过让科学家直接获得这些新技术和分析和解释技巧，使他们拥有领域专业知识。然而，复杂的计算方法可能难以理解和正确使用。它们可能不容易一起工作或复制。自2004年以来，我们一直在与研究界分享先进的数学方法和计算算法，用于基因组分析，这是一个用户友好的，免费提供的软件包，GenePattern。GenePattern的强大之处在于它对广泛的用户社区的可访问性，访问和互操作分析和可视化模块库的能力，环境支持新方法快速开发和传播的便利性，以及计算研究的可重复性。我们此次更新的目标是发展和增强GenePattern平台，以支持新数据采集平台、新方法和新基因组学项目所带来的现代生物医学研究的变化。我们建议扩大模块库的内容，以满足这些新的科学挑战，并通过提供一个强大的，可扩展的数据处理平台服务于社区的项目。此外，我们将继续提供和加强我们的用户支持，培训和文档。 目标1。扩展GenePattern的模块库，并提供与我们的Integrative Genomics Viewer的互操作性，以更好地支持用户及其研究。 目标二。将GenePattern扩展到一般生产和下一代测序数据处理，以供广泛的基因组学项目使用。 目标3。GenePattern软件包的培训、文档编制、持续维护和支持。我们在上一个资助期取得的进展，在软件工程方面的丰富经验，重要的用户基础，基因组分析工具的大型库，文档和用户培训使我们能够很好地实现本提案的目标。

DESCRIPTION (provided by applicant): Project Summary The flood of genomic data is revolutionizing our approach to understanding normal cellular processes and the mechanisms of disease. This has driven the development of sophisticated computational methods to enable the analysis of this data, and a new emphasis on integrative techniques. It is critical to empower scientists with domain expertise by giving them direct access to these new technologies and techniques for analysis and interpretation. However, complex computational methods can be difficult to understand and use correctly. They may not easily work together or be reproduced. Since 2004 we have been sharing advanced mathematical methods and computational algorithms for genomic analysis with the research community in a user-friendly, freely available software package, GenePattern. The power of GenePattern is its accessibility to a broad community of users, the ability to access and interoperate a library of analytic and visualization modules, the ease with which the environment supports the rapid development and dissemination of new methods, and the reproducibility of computational research. Our goal for this renewal is to evolve and enhance the GenePattern platform to support the changing face of modern biomedical research brought on by new data acquisition platforms, new methods, and new genomics projects. We propose to broaden the content of the module repository to meet these new scientific challenges, and to serve the community's projects by providing a robust, scalable data processing platform. In addition, we will continue to provide and enhance our user support, training, and documentation. Aim 1. Expanding GenePattern's module repository and providing interoperability with our Integrative Genomics Viewer to better support users and their research. Aim 2. Extending GenePattern for general production and next-generation sequencing data processing for use by a wide range of genomics projects. Aim 3. Training, documentation, continuing maintenance and support for the GenePattern package. Our progress over our previous funding period, extensive experience in software engineering, significant user base, large repository of genomic analysis tools, documentation and training for users make us well poised to carry out the aims of this proposal.