IsoDesign: A Software for Optimizing the Design of 13C-Metabolic Flux Analysis Experiments
IsoDesign: A Software for Optimizing the Design of 13C-Metabolic Flux Analysis Experiments
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DOI：
10.1002/bit.24997
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发表时间：
2014-01-01
影响因子：
3.8
通讯作者：
Portais, Jean-Charles
中科院分区：
文献类型：
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作者：
Millard, Pierre;Sokol, Serguei;Portais, Jean-Charles
代谢工程和系统生物学领域对C-13代谢通量分析（C-13-MFA）的需求日益增长，这推动了对合理化昂贵且耗时的C-13标记实验的需求。实验设计是提高从一组同位素数据计算通量的数量和通量值的精度的关键步骤。我们提出了IsoDesign，一个软件，使这些参数最大化，通过优化同位素组成的标签输入。它可以应用于C-13-MFA研究，使用广泛的分析工具（MS，MS/MS，H-1 NMR，C-13 NMR等）。单独地或组合地。它包括一个可视化模块，用于根据要解决的生物学问题直观地选择最佳标签输入。IsoDesign的应用程序进行了描述，整个C-13-MFA工作流程的一个例子，从实验设计的通量图，包括重要的实际考虑。IsoDesign使C-13-MFA实验的实验设计更容易为更广泛的生物界所接受。IsoDesign在http://metasys.insa-toulouse.fr/software/isodes/ Biotechnol上以开源许可证发布。Bioeng. 2014;111：202-208. (c)2013 Wiley Periodicals，Inc.
The growing demand for C-13-metabolic flux analysis (C-13-MFA) in the field of metabolic engineering and systems biology is driving the need to rationalize expensive and time-consuming C-13-labeling experiments. Experimental design is a key step in improving both the number of fluxes that can be calculated from a set of isotopic data and the precision of flux values. We present IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to C-13-MFA investigations using a broad panel of analytical tools (MS, MS/MS, H-1 NMR, C-13 NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. Applications of IsoDesign are described, with an example of the entire C-13-MFA workflow from the experimental design to the flux map including important practical considerations. IsoDesign makes the experimental design of C-13-MFA experiments more accessible to a wider biological community. IsoDesign is distributed under an open source license at http://metasys.insa-toulouse.fr/software/isodes/ Biotechnol. Bioeng. 2014;111: 202-208. (c) 2013 Wiley Periodicals, Inc.