Mega2: Manipulation Environment for Genetic Analyses

Mega2：遗传分析的操作环境

• 批准号: 8206493
• 负责人: Daniel E Weeks
• 金额: $ 29.79万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-03-01 至 2014-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8206493
• 关键词: Alzheimer' s Disease; Amendment; Back; Bipolar Disorder; Case-Control Studies; Chromosome Mapping; Code; Communities; Complex; Computational Biology; Computer software; Coronary Arteriosclerosis; Country; Data; Data Set; Databases; Degenerative polyarthritis; Development; Documentation; Ensure; Environment; Epilepsy; Family; Galaxy; Genetic; Genetic Processes; Genetic Research; Genome Scan; Graph; Hand; Healthcare; Hereditary Disease; Institution; Insulin-Dependent Diabetes Mellitus; Maintenance; Major Depressive Disorder; Malignant neoplasm of lung; Malignant neoplasm of prostate; Maps; Non-Insulin-Dependent Diabetes Mellitus; Obesity; Output; Pain; Process; Quality Control; Research; Research Personnel; Resources; Rheumatoid Arthritis; Role; Running; Schizophrenia; Software Engineering; Speed; Testing; Validation; abstracting; base; biomedical informatics; computer program; data format; evaluation/testing; file format; gene discovery; genetic analysis; genetic risk factor; graphical user interface; human disease; improved; interoperability; meetings; open source; portability; programs; public health relevance; repaired; task analysis; tool; usability

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.

Mega 2，遗传分析的操作环境，是一个独特的开源计算机程序，用于促进从作为遗传研究的一部分收集的数据中创建分析就绪的数据集。Mega 2透明地允许用户准确有效地处理基于家族或病例/对照研究的遗传数据。除了数据验证检查外，Mega 2还为广泛的常用遗传分析程序提供分析设置功能。它在全球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Mega 2的功能，同时应用软件工程的最佳实践来满足开源项目的这些关键需求：跨操作系统平台的可移植性，随着遗传学研究需求而发展的能力，广泛的文档，最大限度地提高代码重用，以及系统测试，调试和维护。具体来说，我们计划通过精简Mega 2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，使Mega 2更易于扩展、修复和维护。我们计划通过添加快速交互模式、实现用于修改和过滤原始数据的调整层以及支持中间预验证数据格式来改进Mega 2的大规模数据处理，以满足研究社区的需求。我们计划通过支持更多的输入格式和分析程序，改进与现有数据库的连接，并将Mega 2集成到Galaxy工作流程管道中，来扩展Mega 2的互操作性。我们计划继续将Mega 2作为公共资源进行维护，不断对其进行修订以支持最新版本的支持分析程序，进行严格和广泛的质量控制测试，并维护和改进文档。这些目标的实现将大大提高Mega 2的可用性、数据输入处理能力、建立目标分析的能力、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有用性和可用性。 Mega 2已被用于加速一系列复杂人类疾病的基因发现研究。改善这一关键资源将对加快基因发现过程产生重大影响，这反过来又将减轻美国和世界范围内复杂遗传疾病造成的医疗负担。 公共卫生相关性：Project Narrative Mega 2被用于复杂人类疾病遗传学的许多不同研究中，使研究人员能够快速更改文件格式并准备用于统计分析的文件，并准确有效地透明处理遗传数据。因此，Mega 2已经并将继续显著加快复杂人类疾病遗传风险因素的绘图和识别。Mega 2用户已经使用Mega 2来促进和加速大量重要人类疾病的遗传研究中的统计分析，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、重度抑郁症、骨关节炎、癫痫、肥胖、疼痛、类风湿性关节炎等等。