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Development and Support of the Pathway Tools Software

Pathway Tools 软件的开发和支持

基本信息

批准号：
10220624
负责人：
PETER D KARP
金额：
$ 117.25万
依托单位：
SRI INTERNATIONAL
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-05-12 至 2025-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10220624
关键词：
Algorithmic Analysis Algorithms Bacteria Bacterial Genome Bacterial Infections Biochemical Biochemical Pathway Biochemical Reaction Bioinformatics Biological Biology Chemicals Choking Communication Communities Computer software Data Data Analyses Databases Development Disease Disease Outbreaks Documentation Drug Design Drug Targeting Environment Essential Genes Filler Genbank Gene Expression Genes Genome Grant Health Human Human Microbiome Informatics International Internet Knowledge Letters M. tuberculosis genome Maintenance Maps Metabolic Metabolic Pathway Mission Modeling Mycobacterium tuberculosis National Institute of Allergy and Infectious Disease Online Systems Operon Organism Pathogenicity Pathway Analysis Pathway interactions Procedures Process Production Proteins Publishing RNA Reaction Research Research Personnel Running Scientist Services Software Tools Speed Structure System Systems Biology Time Training Update Vibrio cholerae Visit Work antimicrobial drug base cell growth regulation central database chronic inflammatory disease cloud based cofactor comparative dashboard experimental study feeding gene product genome database genome-wide gut microbiome improved interest member metabolomics metagenome microbial community microbial genome microbiome next generation operation pathogen pathogen genome pathogenic Escherichia coli pathogenic bacteria pathway tools reconstruction repository research and development response software systems tool transcriptome sequencing web site web-enabled

项目摘要

Project Summary The huge breadth and depth of data and knowledge deﬁned by the genome sequence of an organism, and by large numbers of other experimental ﬁndings for the organism, requires a database (DB) as a central repository for information about the genome, the biochemical network, and the regulatory processes of that organism. The Pathway Tools software is a robust and comprehensive system for constructing such organism-speciﬁc DBs. Path- way Tools enables communities of scientists to create, query, visualize, and analyze organism DBs, and to publish such DBs on the web. The software supports construction of organism DBs that combine a large number of bioin- formatics datatypes, including genome maps, genes, operons, RNAs, proteins, chemical compounds, biochemical reactions, metabolic pathways, and regulatory interactions. Pathway Tools further enables inference of qualitative metabolic reconstructions from sequenced genomes, and the creation of quantitative metabolic ﬂux models from those reconstructions. Such metabolic models enable computational predictions of which genes and reactions within the metabolic network are essential, thus facilitating the design of drugs against disease-causing bacteria. We propose to research several new inference algorithms that derive new information for a sequenced pathogen genome for inclusion in Pathway Tools DBs. One algorithm will detect cross-feeding and cofactor- exchange relationships within a community of organisms to advance mechanistic understanding of the human microbiome. A second algorithm will enable rapid communication of the biochemical machinery of an organism encoded in its genome to scientists, such as during a disease outbreak. A third algorithm will improve the pre- diction of operons within bacterial genomes based on new features including RNA-seq data. We also propose to implement a suite of cloud-based editing tools for Pathway Tools databases that execute within the user's web browser. These editing tools will enable communities of scientists to work together to update and share knowl- edge about a given genome. Pathway Tools is a mature and production-grade software environment that 10,800 research groups around the world have licensed, and it has been cited 1,650 times. We propose to maintain the software, such as by installing new versions of its many components, and to support its user community through training, documentation, and bug ﬁxing.

项目总结