Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan, R.O.C.
Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.
Genome-scale metabolic network models have become an indispensable part of the increasingly important field of systems biology. Metabolic systems biology studies usually include three major components-network model construction, objective- and experiment-guided model editing and visualization, and simulation studies based mainly on flux balance analyses. Bioinformatics tools are required to facilitate these complicated analyses. Although some of the required functions have been served separately by existing tools, a free software resource that simultaneously serves the needs of the three major components is not yet available.
Here we present a software platform, GEMSiRV (GEnome-scale Metabolic model Simulation, Reconstruction and Visualization), to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies. GEMSiRV comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases and metabolic network maps, all of which can be input into GEMSiRV as the starting materials for network construction or simulation analyses. Furthermore, all of the GEMSiRV-generated metabolic models and analysis results, including projects in progress, can be easily exchanged in the research community. GEMSiRV is a powerful integrative resource that may facilitate the development of systems biology studies.
The software is freely available on the web at http://sb.nhri.org.tw/GEMSiRV.
基因组规模代谢网络模型已成为系统生物学这一日益重要领域不可或缺的一部分。代谢系统生物学研究通常包括三个主要组成部分——网络模型构建、目标和实验指导的模型编辑和可视化，以及主要基于通量平衡分析的模拟研究。需要生物信息学工具来促进这些复杂的分析。尽管一些所需的功能已分别由现有工具提供，但仍缺乏同时满足这三个主要组成部分需求的免费软件资源。
我们在这里介绍了一个软件平台 GEMSiRV（基因组规模代谢模型模拟、重建和可视化），它提供了易于代谢网络起草和编辑的功能、便于实验数据集成的网络可视化功能以及通量平衡分析工具，用于模拟研究。GEMSiRV 附带可下载的、现成的公共领域代谢模型、参考代谢物/反应数据库和代谢网络图，所有这些都可以作为网络构建或模拟分析的起始材料输入到 GEMSiRV 中。此外，GEMSiRV 生成的所有代谢模型和分析结果，包括正在进行的项目，都可以在研究社区中轻松交换。GEMSiRV 是一个功能强大的集成资源，可能有助于系统生物学研究的发展。
该软件可在网络上免费获得，网址为 http://sb.nhri.org.tw/GEMSiRV。
