Dynamic Flux Balance Analysis Models in SBML
Dynamic Flux Balance Analysis Models in SBML
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DOI：
10.1101/245076
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发表时间：
2018-01
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通讯作者：
Leandro H. Watanabe;M. König;C. Myers
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作者：
Leandro H. Watanabe;M. König;C. Myers
系统生物学和系统医学中的计算模型通常使用单一形式进行模拟，例如常微分方程 (ODE)。然而，更复杂的模型需要多种形式的耦合，因为不同的生物现象可以通过不同的方法更好地描述。例如，稳态代谢通常使用通量平衡分析 (FBA) 进行建模，而模型组件的动态变化则可以通过 ODE 更好地描述。 FBA 和 ODE 建模形式的耦合产生了动态 FBA 模型。一个主要的挑战是如何描述这种以标准化方式耦合多种形式的混合模型，以便它们可以在工具之间交换并以可再现的方式一致地进行模拟。本文提出了一种在系统生物学标记语言（SBML）中编码和实现动态 FBA 模型的方案，从而能够在软件工具之间交换多框架计算模型。我们使用各种示例模型证明了该方法的可行性，并表明不同的工具能够模拟混合模型并就结果达成一致。作为这项工作的一部分，已经开发了支持此类模型的动态 FBA 多框架模拟方法的两个独立实现：iBioSim 和 sbmiutils。
Computational models in systems biology and systems medicine are typically simulated using a single formalism such as ordinary differential equations (ODE). However, more complex models require the coupling of multiple formalisms since different biological phenomena are better described by different methods. For example, metabolism in steady state is often modeled using flux-balance analysis (FBA) whereas dynamic changes of model components are better described via ODEs. The coupling of FBA and ODE modeling formalisms results in dynamic FBA models. A major challenge is how to describe such hybrid models that couple multiple formalisms in a standardized way so that they can be exchanged between tools and simulated consistently in a reproducible manner. This paper presents a scheme for encoding and implementation of dynamic FBA models in the Systems Biology Markup Language (SBML), thereby enabling the exchange of multi-framework computational models between software tools. We demonstrate the feasibility of the approach using various example models and show that different tools are able to simulate the hybrid models and agree on the results. As part of this work, two independent implementations of a multi-framework simulation method for dynamic FBA have been developed supporting such models: iBioSim and sbmiutils.