Mega2: Manipulation Environment for Genetic Analyses

描述(由申请人提供)：项目摘要/摘要Mega2，遗传分析操纵环境，是一个独特的开源计算机程序，用于促进从作为遗传研究一部分收集的数据创建可用于分析的数据集。Mega2透明地允许用户准确和高效地处理基于家庭或病例/对照研究的基因数据。除了数据验证检查之外，Mega2还为各种常用的基因分析程序提供了分析设置功能。它在世界各地的遗传学研究界发挥了重要作用。根据这一提议，我们计划增强Mega2的能力，同时应用软件工程中的最佳实践来满足开放源码项目的这些关键需求：跨操作系统平台的可移植性、随着遗传学研究的需求而发展的能力、广泛的文档、最大限度地实现代码重用以及系统测试、调试和维护。具体地说，我们计划通过简化Mega2并将其重组为面向对象的应用程序，实现应用程序编程接口和图形用户界面，以及创建用于添加新输入格式、过滤器和输出格式的动态机制，从而使Mega2更易于扩展、修复和维护。我们计划通过增加快速交互模式，实现对原始数据的修改和过滤的调整层，以及支持中间预验证的数据格式，来改进Mega2的S大规模数据处理，以满足研究界的需求。我们计划通过支持更多的输入格式和分析程序，改善与现有数据库的连接，并将Mega2整合到Galaxy工作流管道中，来扩展Mega2的S互操作性。我们计划继续保持Mega2作为公共资源，不断修订它以支持所支持的分析程序的最新版本，执行严格和广泛的质量控制测试，并维护和改进文档。这些目标的实现将显著提高兆丰S的可用性、数据输入处理能力、目标分析设置能力、可扩展性、可维护性和互操作性，从而确保这一广泛使用的软件的持续可用性和可用性。Mega2已被用于加速对一大批复杂人类疾病的基因发现研究。改进这一关键资源将对加快基因发现进程产生重大影响，这反过来将减轻美国和世界范围内复杂遗传病造成的医疗负担。 公共卫生相关性：Mega2项目被用于复杂人类疾病遗传学的许多不同研究，使研究人员能够迅速改变文件格式，准备用于统计分析的文件，并以透明的方式准确和有效地处理遗传数据。因此，Mega2已经并将继续显著加快绘制和识别复杂人类疾病的遗传风险因素。Mega2的用户已经使用Mega2促进和加速了大量重要人类疾病的基因研究中的统计分析，包括阿尔茨海默病、精神分裂症、冠状动脉疾病、1型糖尿病、2型糖尿病、肺癌、前列腺癌、双相情感障碍、严重抑郁障碍、骨关节炎、癫痫、肥胖症、疼痛、类风湿性关节炎等等。

DESCRIPTION (provided by applicant): Project Summary/Abstract Mega2, the Manipulation Environment for Genetic Analysis, is a unique open-source computer program for facilitating the creation of analysis-ready datasets from data gathered as part of a genetic study. Mega2 transparently allows users to process genetic data for family-based or case/control studies accurately and efficiently. In addition to data validation checks, Mega2 provides analysis setup capabilities for a broad choice of commonly-used genetic analysis programs. It has served an important role in the genetics research community worldwide. Under this proposal, we plan to enhance the capabilities of Mega2, while applying best practices in software engineering to meet these critical needs of an open-source project: portability across OS platforms, ability to evolve with the needs of genetics research, extensive documentation, maximizing code reuse, as well as systematic testing, debugging and maintenance. Specifically, we plan to make Mega2 much easier to extend, repair, and maintain by streamlining it and restructuring it as an object-oriented application, implementing an application programming interface and a graphical user interface, and creating a dynamic mechanism for adding new input formats, filters, and output formats. We plan to improve Mega2's large-scale data handling in order to meet the needs of the research community by adding a fast interactive mode, implementing adjustment layers for modifying and filtering original data, and supporting an intermediate pre- validated data format. We plan to extend Mega2's interoperability by supporting more input formats and analysis programs, improving connections to existing databases, and integrating Mega2 within the Galaxy workflow pipeline. We plan to continue to maintain Mega2 as a public resource, constantly revising it to support the very latest versions of the supported analysis programs, carrying out rigorous and extensive quality-control testing, and maintaining and improving the documentation. Accomplishment of these aims will significantly improve Mega2's usability, data input handling capabilities, abilities to set up target analyses, extensibility, maintainability, and interoperability, thus ensuring continuing usefulness and availability of this widely-used software. Mega2 has been used to accelerate gene discovery studies for a large list of complex human diseases. Improving this crucial resource will have a significant impact on speeding up the gene-discovery process, which in turn will ease the healthcare burden due to complex genetic disease in the US and world-wide. PUBLIC HEALTH RELEVANCE: Project Narrative Mega2 is used in many different studies of the genetics of complex human diseases, enabling researchers to swiftly change file formats and prepare files for statistical analysis and transparently processing genetic data accurately and efficiently. As such, Mega2 has and will continue to markedly accelerate the mapping and identification of genetic risk factors for complex human diseases. Already, Mega2 users have used Mega2 to facilitate and accelerate statistical analyses in genetic studies of a large range of important human diseases, including Alzheimer disease, schizophrenia, coronary artery disease, type 1 diabetes, type 2 diabetes, lung cancer, prostate cancer, bipolar affective disorder, major depressive disorder, osteoarthritis, epilepsy, obesity, pain, rheumatoid arthritis, and many more.