BioMet Toolbox: genome-wide analysis of metabolism
BioMet Toolbox: genome-wide analysis of metabolism
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DOI：
10.1093/nar/gkq404
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发表时间：
2010-07-01
影响因子：
14.9
通讯作者：
Nielsen, Jens
中科院分区：
文献类型：
--
作者：
Cvijovic, Marija;Olivares-Hernandez, Roberto;Nielsen, Jens
定向遗传修饰的分子生物学工具、精确的定量实验方法、高通量测量以及基因组测序的发展为代谢模型驱动的代谢工程新领域奠定了基础。通过建模和模拟对生物过程进行系统分析，可以识别代谢网络并预测不同条件下的代谢能力。为了促进这种系统的分析，我们已经开发了BioMet的，基于网络的资源化学计量分析和整合的转录组和相互作用组数据，从而利用基因组规模的代谢模型的能力。BioMet ®提供了一种有效的用户友好的方式来执行线性规划模拟，通过检测相关通量，模拟单基因和双基因缺失或检测主要转录变化集中的代谢物，以最大化或最小化生长速率，底物摄取速率和代谢生产速率。这些工具可用于高通量的计算机筛选，并允许完全标准化的模拟。包括各种模式生物（真菌和细菌）的模型文件。总的来说，BioMet是探索这些代谢网络能力的宝贵资源。BioMet Toolbox可在www.sysbio.se/BioMet/上免费获取。
The rapid progress of molecular biology tools for directed genetic modifications, accurate quantitative experimental approaches, high-throughput measurements, together with development of genome sequencing has made the foundation for a new area of metabolic engineering that is driven by metabolic models. Systematic analysis of biological processes by means of modelling and simulations has made the identification of metabolic networks and prediction of metabolic capabilities under different conditions possible. For facilitating such systemic analysis, we have developed the BioMet Toolbox, a web-based resource for stoichiometric analysis and for integration of transcriptome and interactome data, thereby exploiting the capabilities of genome-scale metabolic models. The BioMet Toolbox provides an effective user-friendly way to perform linear programming simulations towards maximized or minimized growth rates, substrate uptake rates and metabolic production rates by detecting relevant fluxes, simulate single and double gene deletions or detect metabolites around which major transcriptional changes are concentrated. These tools can be used for high-throughput in silico screening and allows fully standardized simulations. Model files for various model organisms (fungi and bacteria) are included. Overall, the BioMet Toolbox serves as a valuable resource for exploring the capabilities of these metabolic networks. BioMet Toolbox is freely available at www.sysbio.se/BioMet/.