Supporting Integrative Genomic Analysis Users with GenePattern

描述(由申请者提供)：项目摘要：大量的基因组数据正在彻底改变我们理解正常细胞过程和疾病机制的方法。这推动了复杂计算方法的发展，使这些数据的分析成为可能，并重新强调综合技术。让科学家直接接触这些新技术和技术以进行分析和解释，从而赋予他们领域专业知识，这一点至关重要。然而，复杂的计算方法可能很难理解和正确使用。它们可能不容易在一起工作或复制。自2004年以来，我们一直在一个用户友好的、免费提供的软件包GenePattern中与研究社区共享用于基因组分析的先进数学方法和计算算法。GenePattern的强大之处在于它可供广大用户访问，能够访问和互操作分析和可视化模块的库，环境支持新方法的快速开发和传播的简便性，以及计算研究的重现性。我们此次更新的目标是发展和增强GenePattern平台，以支持新数据获取平台、新方法和新基因组学项目带来的现代生物医学研究不断变化的面貌。我们建议扩大模块存储库的内容，以应对这些新的科学挑战，并通过提供一个强大的、可扩展的数据处理平台来服务于社区的项目。此外，我们将继续提供和增强我们的用户支持、培训和文档。目标1.扩展GenePattern的模块存储库，并提供与我们的集成基因组学查看器的互操作性，以更好地支持用户及其研究。目标2.扩展GenePattern用于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.培训、文件编制、持续维护和支持GenePattern成套软件。我们在前一个资助期取得的进展、在软件工程方面的广泛经验、庞大的用户基础、庞大的基因组分析工具库、文件和对用户的培训，使我们能够很好地实现这项提案的目标。

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.