Mega2: Manipulation Environment for Genetic Analyses

Mega2：遗传分析的操作环境

• 批准号: 8015837
• 负责人: Daniel E Weeks
• 金额: $ 29.81万
• 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/8015837
• 关键词: Amendment; Back; Case-Control Studies; Chromosome Mapping; Code; Communities; Complex; Computational Biology; Computer software; Country; Data; Data Set; Databases; Development; Documentation; Ensure; Environment; Family; Galaxy; Genetic; Genetic Processes; Genetic Research; Genome Scan; Graph; Hand; Healthcare; Hereditary Disease; Institution; Maintenance; Output; Process; Quality Control; Research; Research Personnel; Resources; Role; Running; Software Engineering; Speed; Testing; Validation; abstracting; base; biomedical informatics; computer program; data format; evaluation/testing; gene discovery; genetic analysis; graphical user interface; human disease; improved; interoperability; meetings; open source; portability; programs; 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.

描述（由申请人提供）：遗传分析的操纵环境项目摘要/摘要MEGA2是一个独特的开源计算机程序，用于促进作为基因研究的一部分收集的数据创建可分析的数据集。 MEGA2透明地允许用户准确有效地处理基于家庭或病例/控制研究的遗传数据。除了数据验证检查外，MEGA2还提供了分析设置功能，可为常用的遗传分析程序提供广泛的选择。它在全球遗传学研究界发挥了重要作用。根据该提案，我们计划增强MEGA2的功能，同时应用软件工程中的最佳实践来满足开源项目的这些关键需求：跨OS平台的可移植性，随着遗传学研究的需求，广泛的文档，最大化代码重用的需求，最大化代码重复使用，以及系统的测试，调试，调试和维护。具体而言，我们计划通过简化，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，并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更容易扩展，维修和维护。我们计划通过添加快速交互模式，实施调整层来修改和过滤原始数据并支持中间的预验证的数据格式，以改善MEGA2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，改善与现有数据库的连接并将MEGA2集成在Galaxy Workflow Pipeline中，以扩展MEGA2的互操作性。我们计划继续将MEGA2保持为公共资源，不断对其进行修改，以支持最新版本的受支持的分析程序，进行严格且广泛的质量控制测试，并维护和改进文档。这些目标的完成将显着提高MEGA2的可用性，数据输入处理能力，设置目标分析的能力，可扩展性，可维护性和互操作性，从而确保此通用软件的持续有用性和可用性。 MEGA2已被用来加速基因发现研究，以供大量复杂的人类疾病。改善这种关键资源将对加速基因发现过程产生重大影响，这反过来又将缓解由于美国和全球范围内复杂的遗传疾病而导致的医疗保健负担。 公共卫生相关性：项目叙事MEGA2用于对复杂人类疾病的遗传学的许多不同研究，使研究人员能够迅速更改文件格式并准备文件进行统计分析，并透明地处理遗传数据。因此，MEGA2拥有并将继续显着加速对复杂人类疾病的遗传危险因素的映射和鉴定。 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,类风湿关节炎等等。