GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization
复制标题
DOI：
10.1093/bioinformatics/bts267
复制
发表时间：
2012-07-01
期刊：
影响因子：
5.8
通讯作者：
Hsiung, Chao A.
中科院分区：
文献类型：
--
作者：
Liao, Yu-Chieh;Tsai, Ming-Hsin;Hsiung, Chao A.
动机：基因组尺度的代谢网络模型已经成为系统生物学日益重要的领域中不可或缺的一部分。代谢系统生物学的研究通常包括网络模型构建、以客观和实验为指导的模型编辑和可视化以及以通量平衡分析为主要基础的仿真研究三个主要部分。需要生物信息学工具来促进这些复杂的分析。尽管一些必需的功能已经由现有的工具单独提供，但是同时满足这三个主要组件需求的自由软件资源还没有出现。结果：本文提出了一个名为GEMSiRV （GEnome-scale Metabolic model Simulation, Reconstruction and Visualization）的软件平台，该平台提供了简单的代谢网络绘制和编辑功能，可用于实验数据集成的网络可视化功能，以及用于模拟研究的通量平衡分析工具。GEMSiRV附带了可下载的、随时可用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GEMSiRV。此外，所有gemsirv生成的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是一个强大的综合资源，可以促进系统生物学研究的发展。
Motivation: 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.Results: 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.