Development and Support of the Pathway Tools Software

Pathway Tools 软件的开发和支持

• 批准号: 7902995
• 负责人: PETER D KARP
• 金额: $ 47.86万
• 依托单位: SRI INTERNATIONAL
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-20 至 2011-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7902995
• 关键词: Address; Animal Model; Applications Grants; Architecture; Bacteria; Biochemical; Biochemical Pathway; Biochemical Reaction; Bioinformatics; Candidate Disease Gene; Chemicals; Choking; Collection; Communities; Complex; Computer software; Cost Savings; Custom; Data; Data Collection; Databases; Development; Disease; Documentation; Drug Delivery Systems; Environment; Enzymes; Exhibits; Experimental Models; Filler; Fostering; Future; Gene Expression; Genes; Genetic; Genome; Genome Mappings; House mice; Imagery; Individual; International; Internet; Investments; Knowledge; Laboratory mice; Lead; Letters; Licensing; Metabolic Pathway; Modeling; Mouse-ear Cress; Mus; Names; Operative Surgical Procedures; Operon; Organism; Pathway interactions; Plants; Process; Production; Proteins; Publishing; Research; Research Personnel; Saccharomyces cerevisiae; Scientist; Services; Signal Pathway; Software Tools; System; Testing; Update; Vision; base; cell growth regulation; cell type; comparative; cost; empowered; genome database; genome sequencing; model organisms databases; pathogenic bacteria; pathway tools; programs; public health relevance; quality assurance; repository; research and development; research study; software development; software systems; tool

DESCRIPTION: The completion of the genome sequence for an organism such as a disease-causing bacterium marks the start of a new era of accelerated research on that organism. The huge quantity of data and knowledge defined by the genome sequence, and by the large number of past and future experimental endings for the organism, requires the use of a database to act as a central repository for information about the genome, the biochemical network, and the regulatory processes of that organism. In the past, such organism-specific databases, also called Model-Organism Databases (MODs), were each created with custom-developed software tools. Because of the many common requirements of these projects, the cost of creating custom software, and the database incompatibility that results from using custom software, it is more effective to reuse a common software environment across many MOD projects. The Pathway Tools software is a robust and comprehensive system for the construction of MODs. Pathway Tools enables communities of scientists to create, query, visualize, analyze, and publish MODs on the Web. Pathway Tools provides support for a large number of bioinformatics data types including genome maps, genes, operons, RNAs, proteins, chemical compounds, biochemical reactions, metabolic pathways, and regulatory interactions. Pathway Tools is a mature and production-quality software environment that has been used by more than 75 groups outside SRI to create more than 250 MODs. We propose to further develop Pathway Tools to edit and display signaling pathways, to better display and interrogate cellular regulatory networks, to make its genome-scale tools for display of cellular networks more functional through the Web, and to enhance Pathway Tools representations of cellular architectures to more accurately model complex cell types. We propose to provide support services for the large and growing user community for Pathway Tools, to maintain quality documentation for the software, and to create two thoroughly tested releases of the software per year. 7 PUBLIC HEALTH RELEVANCE: will generate software tools that lead to fuller realization of the value of genome sequence data. This software enables the creation of central database repositories of genome data and data on cellular networks for disease-causing bacteria and experimental model organisms such as the laboratory mouse. The software allows researchers to access the most up-to-date information about those organisms using intuitive querying tools, and provides scientific visualization capabilities that aid scientists in more quickly understanding large complex collections of data.

产品说明：一种生物体（如致病细菌）基因组序列的完成标志着对该生物体加速研究的新时代的开始。由基因组序列以及生物体过去和未来大量实验结果所定义的大量数据和知识，需要使用数据库作为关于该生物体的基因组、生化网络和调控过程的信息的中央存储库。在过去，这种生物体特定的数据库，也称为模型生物体数据库（MOD），每个都是用定制开发的软件工具创建的。由于这些项目有许多共同的要求，创建定制软件的成本，以及使用定制软件导致的数据库不兼容性，因此在许多MOD项目中重用公共软件环境会更有效。Pathway Tools软件是构建MOD的强大而全面的系统。Pathway Tools使科学家社区能够在Web上创建、查询、可视化、分析和发布MOD。Pathway Tools为大量生物信息学数据类型提供支持，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。Pathway Tools是一个成熟的生产质量软件环境，已被SRI以外的75个团队用于创建250多个MOD。我们建议进一步开发Pathway Tools来编辑和显示信号通路，更好地显示和询问细胞调控网络，使其基因组规模的细胞网络显示工具通过Web更具功能性，并增强Pathway Tools对细胞架构的表示，以更准确地模拟复杂的细胞类型。我们建议为Pathway Tools的大型和不断增长的用户社区提供支持服务，维护软件的高质量文档，并每年创建两个经过彻底测试的软件版本。7公共卫生相关性：将产生软件工具，导致更充分地实现基因组序列数据的价值。该软件能够创建致病细菌和实验模型生物（如实验室小鼠）的基因组数据和细胞网络数据的中央数据库。该软件允许研究人员使用直观的查询工具访问有关这些生物体的最新信息，并提供科学可视化功能，帮助科学家更快地理解大型复杂数据集。