Visualizing multi-omics data in metabolic networks with the software Omix-A case study
Visualizing multi-omics data in metabolic networks with the software Omix-A case study
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DOI：
10.1016/j.biosystems.2011.04.003
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发表时间：
2011-08-01
期刊：
影响因子：
1.6
通讯作者：
Noeh, Katharina
中科院分区：
文献类型：
--
作者：
Droste, Peter;Miebach, Stephan;Noeh, Katharina
系统生物学是一个多学科的研究领域，目的是了解生物体内复杂过程的功能。这些细胞内过程由生化网络描述。与计算机模拟相结合的实验研究导致与生化网络的不同层联系的数据量不断增加。因此，可视化对于获得与网络组件相关的数据概览是非常重要的。OMix是一款用于可视化生化网络中的任何数据的软件。OMix的独特功能是：该软件可以通过一种称为OMix可视化语言(OVL)的脚本语言进行编程。在OMix中，来自实验或模拟的数据的可视化完全由软件用户用简洁的OVL脚本实现。因此，可视化变得更加灵活和适应用户的需求，并可以适应新的应用领域。我们给出了四个实例，利用OMix和OVL脚本语言在代谢水平上可视化生化网络中的各种数据。这些工作的例子展示了OVL与令人愉快的可视化相结合的力量，这是在更多的实验和更多的理论研究人员之间的界面上成功进行跨学科交流的重要要求。(C)2011爱思唯尔爱尔兰有限公司。保留所有权利。
Systems Biology is a multi-disciplinary research field with the aim of understanding the function of complex processes in living organisms. These intracellular processes are described by biochemical networks. Experimental studies in alliance with computer simulation lead to a continually increasing amount of data in liaison with different layers of biochemical networks. Thus, visualization is very important for getting an overview of data in association with the network components.Omix is a software for the visualization of any data in biochemical networks. The unique feature of Omix is: the software is programmable by a scripting language called Omix Visualization Language (OVL). In Omix, the visualization of data coming from experiment or simulation is completely performed by the software user realized in concise OVL scripts. By this, visualization becomes most flexible and adaptable to the requirements of the user and can be adapted to new application fields.We present four case studies of visualizing data of diverse kind in biochemical networks on metabolic level by using Omix and the OVL scripting language. These worked examples demonstrate the power of OVL in conjunction with pleasing visualization, an important requirement for successful interdisciplinary communication in the interface between more experimental and more theoretical researchers. (C) 2011 Elsevier Ireland Ltd. All rights reserved.