PathCase-SB architecture and database design
PathCase-SB architecture and database design
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DOI：
10.1186/1752-0509-5-188
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发表时间：
2011-11-09
影响因子：
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通讯作者：
Ozsoyoglu, Z. Meral
中科院分区：
文献类型：
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作者：
Cakmak, Ali;Qi, Xinjian;Ozsoyoglu, Z. Meral
背景资料：整合代谢途径资源和调节代谢网络模型，并在集成平台上部署新工具，可以帮助进行更有效、更高效的系统生物学研究，了解代谢网络的调节。因此，（a）在单一数据库环境下整合调控代谢网络和现有模型，以及（B）构建工具以帮助建模和分析的任务是理想的和智力上具有挑战性的计算任务。描述：PathCase系统生物学（PathCase-SB）构建并发布。PathCase-SB数据库为多个用户界面和软件工具提供数据和API。目前的PathCase-SB系统提供了一个数据库支持的框架和基于网络的计算工具，以促进生物系统动力学模型的发展。PathCase-SB旨在整合网络上选定的生物数据源（目前为BioModels数据库和KEGG）的数据，并通过新的基于网络的整合框架提供更强大和/或新的功能。本文描述了PathCase-SB设计和实现中遇到的体系结构和数据库设计问题，并介绍了PathCase-SB体系结构和数据库的当前设计。结论：PathCase-SB体系结构和数据库提供了一个高度可扩展和可扩展的环境，可以轻松快速（实时）访问数据库中的数据。PathCase-SB本身已经被世界各地的研究人员使用。
Background: Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks.Description: PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database.Conclusions: PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world.