Systematic integration of experimental data and models in systems biology.
Systematic integration of experimental data and models in systems biology.
复制标题
实验数据和系统生物学模型的系统整合。
DOI：
10.1186/1471-2105-11-582
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发表时间：
2010-11-29
影响因子：
3
通讯作者：
Paton NW
中科院分区：
文献类型：
--
作者：
Li P;Dada JO;Jameson D;Spasic I;Swainston N;Carroll K;Dunn W;Khan F;Malys N;Messiha HL;Simeonidis E;Weichart D;Winder C;Wishart J;Broomhead DS;Goble CA;Gaskell SJ;Kell DB;Westerhoff HV;Mendes P;Paton NW
生物系统的行为可以从它们的数学模型中推导出来。然而，在构建模型时需要多种形式的数据源，以便定义其组分及其生化反应和相应的参数。系统生物学模型的自动组装和使用依赖于涉及数据和分析资源互操作的数据集成过程。Taverna工作流程已开发用于在系统生物学标记语言（SBML）中自动组装定量参数化代谢网络。SBML模型通过工作流程以系统的方式构建，该工作流程从使用来自符合MIRIAM的酵母代谢基因组规模模型的数据构建定性网络开始。其次是参数化的SBML模型与实验数据从两个仓库，SABIO-RK酶动力学数据库和定量实验结果的数据库。然后在调用COPASIWS的工作流程中对模型进行校准和模拟，COPASIWS是COPASI软件应用程序的Web服务接口，用于分析生化网络。评价了这些系统生物学工作流程构建酵母糖酵解参数化模型的能力。关于已被描述为MIRIAM标准的代谢反应的分布式信息使得能够基于用户定义的标准自动组装代谢网络的定量系统生物学模型。这样的数据集成过程可以作为Taverna工作流来实现，以提供生化系统内的组件及其关系的快速概览。
The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.
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影响因子：
46.9
作者：
Le Novère, N;Finney, A;Wanner, BL
通讯作者：
Wanner, BL
影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
影响因子：
5.8
作者：
Bornstein, Benjamin J.;Keating, Sarah M.;Hucka, Michael
通讯作者：
Hucka, Michael
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
5.8
作者：
Li, Peter;Oinn, Tom;Kell, Douglas B.
通讯作者：
Kell, Douglas B.