CIBR: New Methods for Multi-Omics Data Analysis and Genome Analysis

今天的科学家面临着大量的单一和多组学数据，以及已测序的基因组。尽管这些数据前景看好，但它们带来了相当大的分析挑战：数据分析是从多组学技术和基因组测序中发现的主要瓶颈。多组学数据的例子包括转录组数据加代谢组学数据、反应通量测量加转录组数据和转录组数据加蛋白质组学数据。Path Tools是一个广泛的生物信息学软件系统，其功能包括基因组信息学、途径信息学、组学数据分析和代谢建模。PTools加速了成千上万下载它的科学家和学生的研究和教育，以及成千上万访问PTools网站的科学家和学生的研究和教育。由于基因组是现代生物学的基础，改进的基因组分析和数据管理对社会的好处是广泛的，包括农业土壤微生物的研究；动物病原体的研究；绿色燃料和化学品的微生物代谢工程；微生物改善人类食品的研究；入侵微生物物种的研究；废水处理的研究；以及参与全球化学循环的微生物的研究，包括那些将受到气候变化影响的微生物的研究。有了这笔资金，将开发用于单组学和多组学数据分析的PTools的重大扩展。该项目的目标是为多组学数据分析提供工具，使多达四种类型的组学数据能够在三个不同的路径相关图上同时可视化。这些基于可视化的分析工具将使人们能够比目前的工具更快、更深入地理解组学数据集。后一种工具的一个关键见解是创建软件，将多个输入组学数据维度映射到与多组学评分工具紧密耦合的直观导航路径图和全代谢网络图，使科学家能够在功能上下文中解释这些数据。在获奖期间，每年将发布两个强大的软件新版本，并通过用户拓展和培训、回答问题和修复错误来支持其用户社区。为了使用P-Tools，访问http://bioinformatics.ai.sri.com/ptools/.This奖反映了国家科学基金会的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Scientists today are faced with a deluge of single- and multi-omics data, and of sequenced genomes. Although these data hold great promise, they present sizable analysis challenges: data analysis is a major bottleneck to discovery from multi-omics technologies and genome sequencing. Examples of multi-omics data include transcriptomics data plus metabolomics data, reaction flux measurements plus transcriptomics data, and transcriptomics data plus proteomics data. Pathway Tools (PTools) is an extensive bioinformatics software system whose capabilities include genome informatics, pathway informatics, omics data analysis, and metabolic modeling. PTools accelerates the research and education of the thousands of scientists and students who have downloaded it, and for the thousands of scientists and students who access PTools-powered websites. As genomes are the foundation of modern biology, the benefits to society of improved genome analysis and data management are extensive, including studies of soil microbes for agriculture; studies of animal pathogens for animal health; metabolic engineering of microbes for greener fuels and chemicals; studies of microbes to enhance human foods; studies of invasive microbial species; studies of wastewater treatment; and studies of microbes involved in global chemical cycles, including those that will be affected by climate change.With this funding, significant extensions to PTools for both single-omics and multi-omics data analysis will be developed. The goal of the project is to provide tools for multi-omics data analysis that will enable simultaneous visualization of up to four types of omics data on three different pathway-related diagrams. These visualization-based analysis tools will enable faster, deeper understanding of omics datasets than is possible with current tools. A key insight for the latter tool is to create software that maps multiple input omics data dimensions to intuitively navigable pathway and whole-metabolic network diagrams that are tightly coupled to multi-omics scoring tools, enabling scientists to interpret these data in a functional context. During the award period, two robust new versions of the software will be release per year, and its user community supported through user outreach and training, answering questions, and fixing bugs. To access P-tools, visit http://bioinformatics.ai.sri.com/ptools/.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.