IIBR Informatics: Integrating codon evolution and sequence-assembly error models into multiple sequence alignment

IIBR 信息学：将密码子进化和序列组装错误模型集成到多序列比对中

• 批准号: 1929850
• 负责人: Reed Cartwright
• 金额: $ 84.7万
• 依托单位: Arizona State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-15 至 2025-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1929850&HistoricalAwards=false
• 关键词: IIBR; Informatics; Integrating; codon; evolution

The information age has fundamentally changed the way most areas of science operate. Advances in genomics and informatics have radically reshaped the life sciences, producing innovations that impact multiple ares including medicine and agriculture. This project will design new computational methods and software to manage the complexities of modern genomic datasets, addressing challenges that existing approaches have overlooked. As computational training is essential for modern biology students, this project will broaden the participation in computing by training faculty and instructors at regional, community, and tribal colleges in evidence-based practices for teaching computing skills to students.This project will develop new computational methods to analyze genetic data using statistical models that are optimized for the challenges of modern datasets. First, new finite-state transducer models will be developed for aligning genetic and genomic sequences that capture the biological and technical process that shape modern datasets. Second, these models will be implemented in COATi, a new multiple-sequence alignment tool that will be free and open-sourced. Thirdly, COATi will be used to understand understudied features of molecular evolution. In addition, Software Carpentry Instructor training workshops will be held for faculty at regional, community, and tribal colleges, which will improve the quality of computational instruction at these institutions, and thus broaden the participation in computing for students from underrepresented and underserved backgrounds. The results of the project are available at https://cartwrig.ht/coati/.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

信息时代从根本上改变了大多数科学领域的运作方式。基因组学和信息学的进步从根本上重塑了生命科学，从而产生了影响多种ARE的创新，包括医学和农业。该项目将设计新的计算方法和软件来管理现代基因组数据集的复杂性，从而解决现有方法所忽略的挑战。由于计算培训对于现代生物学学生至关重要，因此该项目将扩大培训教职员工和部落学院的计算参与，以向学生讲授计算能力的循证实践。该项目将开发新的计算方法，以使用针对现代数据集的挑战进行统计模型来分析遗传数据。首先，将开发新的有限态传感器模型，以对齐捕获塑造现代数据集的生物学和技术过程的遗传和基因组序列。其次，这些模型将在Coati中实现，Coati是一种新的多序列对齐工具，将是免费和开源的。第三，Coati将用于理解分子进化的细小特征。此外，将为区域，社区和部落学院的教师举办软件木工讲师培训研讨会，这将提高这些机构的计算教学质量，从而扩大了来自代表性不足和服务不足背景的学生的计算参与。该项目的结果可在https://cartwrig.ht/coati/.This奖中获得，反映了NSF的法定任务，并且被认为是值得通过基金会的知识分子优点和更广泛的影响评估标准通过评估来获得支持的。