Supporting Integrative Genomic Analysis Users with GenePattern

基因组数据的洪流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，从而能够分析这些数据，并重新强调综合技术。通过让科学家直接获得这些分析和解释的新技术和技术，使他们具备领域专业知识是至关重要的。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被复制。自2004年以来，我们一直在一个用户友好的免费软件包geneppattern中与研究界分享用于基因组分析的先进数学方法和计算算法。geneppattern的强大之处在于它对广大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，环境支持新方法的快速开发和传播的便利性，以及计算研究的可再现性。我们此次更新的目标是发展和增强geneppattern平台，以支持由新的数据采集平台、新方法和新的基因组学项目带来的现代生物医学研究的变化。我们建议扩展模块存储库的内容，以应对这些新的科学挑战，并通过提供一个健壮的、可扩展的数据处理平台来服务于社区的项目。此外，我们将继续提供并加强我们的用户支持、培训和文档。目的1。扩展geneppattern的模块库，并提供与我们的整合基因组查看器的互操作性，以更好地支持用户和他们的研究。目标2。扩展geneppattern用于一般生产和下一代测序数据处理，用于广泛的基因组学项目。目标3。培训，文档，持续维护和支持geneppattern包。我们在之前的融资期间取得的进展，在软件工程方面的丰富经验，重要的用户基础，庞大的基因组分析工具库，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. PUBLIC HEALTH RELEVANCE: The GenePattern genomic analysis environment puts sophisticated computational methods within the reach of all biomedical researchers. Through the analysis of the increasing amount of available genomic data, GenePattern is used to address a variety of problems at the forefront of biomedical research including patient diagnosis and prognosis, identification of new drug targets, and understanding biological mechanisms. The work in this project will improve the GenePattern software by expanding the tools and methods it contains and enhance its capabilities to make it even better able to support the broadest range of biomedical researchers and large genomics projects tackling the important questions facing them today.