OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.
OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.
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DOI：
10.1155/2014/627014
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发表时间：
2014
影响因子：
--
通讯作者：
Shimizu H
中科院分区：
文献类型：
--
作者：
Kajihata S;Furusawa C;Matsuda F;Shimizu H
基于13c代谢通量分析（13C-MFA）的体内代谢通量测量为细胞生理学提供了有价值的信息。利用13c标记碳源的示踪同位素标记实验结果，已经开发出生物信息学工具来估计代谢通量分布。代谢通量是由代谢模型非线性拟合到质谱测量的细胞内代谢物的同位素标记富集来确定的。虽然13C- mfa通常是在同位素恒定条件下进行的，但同位素非稳态13C代谢通量分析（INST-13C-MFA）最近被开发用于具有光合活性的细胞和处于准稳定代谢状态的细胞（例如，固定期的原代细胞或微生物）的通量分析。本文报道了在Windows平台上开发一种新的INST-13C-MFA开源软件。OpenMebius（用于代谢通量分析的开源软件）提供了自动生成代谢模型的功能，用于从用户定义的配置工作表模拟同位素标记富集。通过模拟数据分析，证明了OpenMebius对INST-13C-MFA的适用性。INST-13C-MFA测定的置信区间小于常规方法测定的置信区间，表明INST-13C-MFA用于精确代谢通量分析的潜力。OpenMebius是INST-13C-MFA通用应用的开源软件。
The in vivo measurement of metabolic flux by 13C-based metabolic flux analysis (13C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a 13C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas 13C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary 13C metabolic flux analysis (INST-13C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-13C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-13C-MFA. Confidence intervals determined by INST-13C-MFA were less than those determined by conventional methods, indicating the potential of INST-13C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-13C-MFA.
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影响因子：
2.9
作者：
Toya, Yoshihiro;Ishii, Nobuyoshi;Shimizu, Kazuyuki
通讯作者：
Shimizu, Kazuyuki
影响因子：
3.2
作者：
Costenoble, Roeland;Mueller, Dirk;Heijnen, Joseph J.
通讯作者：
Heijnen, Joseph J.
影响因子：
14.9
作者：
Cvijovic, Marija;Olivares-Hernandez, Roberto;Nielsen, Jens
通讯作者：
Nielsen, Jens
DOI：
10.1093/bioinformatics/bts646
发表时间：
2013-01-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Weitzel M;Nöh K;Dalman T;Niedenführ S;Stute B;Wiechert W
通讯作者：
Wiechert W
影响因子：
3.8
作者：
Shastri, Avantika A.;Morgan, John A.
通讯作者：
Morgan, John A.