Development and Support of the Pathway Tools Software

描述：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。基因组序列定义的海量数据和知识，以及生物体过去和未来的大量实验结果，需要使用数据库作为关于基因组、生化网络和生物体调控过程的信息的中央储存库。在过去，这样的生物体特定数据库，也被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常见需求、创建自定义软件的成本以及使用自定义软件导致的数据库不兼容，跨多个MOD项目重用一个通用软件环境会更有效。Path Tools软件是一个用于构建MODS的强大而全面的系统。路径工具使科学家社区能够在Web上创建、查询、可视化、分析和发布MOD。途径工具支持大量的生物信息学数据类型，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。Path Tools是一个成熟的生产质量软件环境，已被SRI以外的75个组织使用，创建了250多个MOD。我们建议进一步开发Path工具来编辑和显示信号通路，更好地显示和询问细胞调控网络，使其基因组规模的工具通过Web显示细胞网络的功能更强，并增强Path工具对细胞结构的表示以更准确地模拟复杂的细胞类型。我们建议为不断增长的庞大的Path Tools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全面测试的软件版本。7公共卫生相关性：将生成软件工具，从而更充分地实现基因组序列数据的价值。该软件能够为致病细菌和实验模型生物(如实验室小鼠)创建基因组数据和细胞网络数据的中央数据库存储库。该软件允许研究人员使用直观的查询工具获取有关这些生物体的最新信息，并提供科学可视化功能，帮助科学家更快地了解大量复杂的数据集合。

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.