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：
10609063
负责人：
PETER D KARP
金额：
$ 116.12万
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/10609063
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 Profiling Genes Genome Genome Mappings Grant Health Human Human Microbiome Informatics International Internet Knowledge Letters Licensing M. tuberculosis genome Maintenance 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 Training Update Vibrio cholerae Visit Visualization Work antimicrobial drug base editing 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

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.

项目概要由生物体的基因组序列定义的数据和知识的巨大广度和深度，以及生物体的大量其他实验结果需要数据库（DB）作为中央存储库有关该生物体的基因组、生化网络和调控过程的信息。 Pathway Tools 软件是一个强大且全面的系统，用于构建此类生物体特定的 Path-。工具使科学家群体能够创建、查询、可视化和分析生物体数据库，并发布该软件支持构建结合大量生物信息的生物体数据库。格式数据类型，包括基因组图谱、基因、操纵子、RNA、蛋白质、化合物、生化反应、代谢途径和调控相互作用进一步实现定性推断。根据测序的基因组进行代谢重建，并根据数据创建定量代谢流模型这些重建可以通过计算预测哪些基因和反应。代谢网络中的细菌至关重要，从而有助于设计针对致病细菌的药物。我们建议研究几种新的推理算法，这些算法可以为排序的序列导出新信息一种算法将检测交叉喂养和辅因子-包含在途径工具数据库中。交换生物群落内的关系，以促进对人类的机械理解第二种算法将实现生物体生化机制的快速通信。第三种算法将在疾病爆发期间向科学家编码。我们还建议基于新特征（包括 RNA-seq 数据）对细菌基因组内的操纵子进行解释。为 Pathway Tools 数据库实现一套基于云的编辑工具，在用户的 Web 中执行这些编辑工具将使科学家群体能够共同努力更新和共享知识。给定基因组的边缘。 Pathway Tools 是一个成熟的生产级软件环境，全世界 10,800 个研究小组都在使用 Pathway Tools world 已获得许可，并且已被引用 1,650 次我们建议维护该软件，例如通过安装。其许多组件的新版本，并通过培训、文档和支持其用户社区错误修复。