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

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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.