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Automatic Generation of Genome-scale Flux Balance Models

自动生成基因组规模的通量平衡模型

基本信息

批准号：
7615735
负责人：
Ranjan Srivastava
金额：
$ 7.64万
依托单位：
UNIVERSITY OF CONNECTICUT STORRS
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-05-01 至 2011-04-30
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): Flux balance analysis (FBA) is proving to be a powerful tool for analyzing metabolic networks. With the rapid publication of the genome sequences of a variety of organisms, the potential of FBA is only increasing. Although FBA is predicated on relatively straightforward mathematical principles, the implementation and use of FBA is not trivial. As a result, a significant hurdle is placed in the path of researchers who would like to use this approach, especially if those researchers do not have a strong quantitative background to begin with. The overarching objective of this work is to develop a new research technology which, when given an appropriately annotated genome, will allow any researcher to carry out genome-scale flux balance analysis. Specifically, upon completion of this project, a researcher will be able to use this tool to (1) determine the fluxes for all the metabolic reactions in an organism; (2) generate phenotypic phase plane plots; (3) quantitatively evaluate how probable a given metabolic objective function is relative to other objective functions; and (4) quantitatively evaluate how probable a given metabolic network is relative to other networks. In all cases, it will be possible for the researcher to customize their calculations based on their own or publicly available data. The proposed research technology will have significant biomedical benefits, particularly in regard to the analysis of microbial pathogens. They include the ability to rapidly identify key metabolic pathways in pathogens that are potential drug targets, the ability to elucidate the mechanism of action of new drugs, the ability to carry out in silico screening of new drugs to focus on the experimental development of the most promising ones, and enhance the ability to perform basic fundamental quantitative biological research, particularly for researchers who might lack the appropriate mathematical background to normally carry out such research. Finally this work should significantly enhance the national and international medical informatics and bioinformatics infrastructure.

描述(由申请人提供)：通量平衡分析(FBA)被证明是分析代谢网络的有力工具。随着各种生物基因组序列的迅速公布，FBA的潜力只会越来越大。尽管FBA基于相对简单的数学原理，但FBA的实现和使用并不是微不足道的。因此，想要使用这种方法的研究人员的道路上设置了一个巨大的障碍，特别是如果这些研究人员一开始就没有很强的量化背景。这项工作的首要目标是开发一种新的研究技术，当给予适当注释的基因组时，将允许任何研究人员进行基因组规模的通量平衡分析。具体地说，在这个项目完成后，研究人员将能够使用这个工具来(1)确定生物体中所有代谢反应的通量；(2)生成表型相平面图；(3)定量评估给定的代谢目标函数相对于其他目标函数的可能性；以及(4)定量评估给定的代谢网络相对于其他网络的可能性。在所有情况下，研究人员都可以根据自己或公开获得的数据定制他们的计算。拟议的研究技术将具有显著的生物医学益处，特别是在微生物病原体分析方面。它们包括能够快速识别作为潜在药物靶点的病原体的关键代谢途径，阐明新药作用机制的能力，能够在电子计算机上进行新药筛选，专注于最有前途的新药的实验开发，以及提高进行基础定量生物学研究的能力，特别是对于可能缺乏正常开展此类研究的适当数学背景的研究人员。最后，这项工作将大大加强国内和国际的医学信息学和生物信息学基础设施。