PathCase-SB: integrating data sources and providing tools for systems biology research
PathCase-SB: integrating data sources and providing tools for systems biology research
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DOI：
10.1186/1752-0509-6-67
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发表时间：
2012-06-14
影响因子：
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通讯作者：
Ozsoyoglu, Zehra Meral
中科院分区：
文献类型：
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作者：
Coskun, Sarp A.;Qi, Xinjian;Ozsoyoglu, Zehra Meral
背景资料：整合代谢途径资源和代谢网络模型，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。结果：PathCase系统生物学（PathCase-SB）构建并发布。本文介绍了PathCase-SB用户界面开发的日期。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的目标是在网络上集成选定生物数据源的系统生物学模型数据和代谢网络数据（目前分别为BioModels Database和KEGG），并通过新的基于网络的综合框架提供更强大和/或新的功能。目前的四个PathCase-SB接口，即浏览器、可视化、查询和模拟接口，与原始数据源相比，具有扩展和新的功能。PathCase-SB已经可以在网上找到，并被地球仪的研究人员使用。
Background: Integration of metabolic pathways resources and 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 of 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.Results: PathCase Systems Biology (PathCase-SB) is built and released. This paper describes PathCase-SB user interfaces developed to date. 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 systems biology models data and metabolic network data of selected biological data sources on the web (currently, BioModels Database and KEGG, respectively), and to provide more powerful and/or new capabilities via the new web-based integrative framework.Conclusions: Each of the current four PathCase-SB interfaces, namely, Browser, Visualization, Querying, and Simulation interfaces, have expanded and new capabilities as compared with the original data sources. PathCase-SB is already available on the web and being used by researchers across the globe.