DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
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DOI：
10.1186/s12859-014-0409-8
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发表时间：
2014-12-18
影响因子：
3
通讯作者：
Barton, Paul I.
中科院分区：
文献类型：
--
作者：
Gomez, Jose A.;Hoffner, Kai;Barton, Paul I.
背景：动态通量平衡分析（DFBA）是一种生化过程的动态模拟框架。DFBA可以使用不同的方法来执行，例如静态优化（SOA）、动态优化（DOA）和直接方法（DA）。很少有现有的模拟器解决非唯一的交换通量或不可行的线性规划（LP）的理论和实践挑战。两者都是常见的故障和低效率的来源，这些simulators.Results：DFBAlab，基于MATLAB的模拟器，使用LP的可行性问题，以获得一个扩展的系统和字典优化，以产生独特的交换通量，提出。DFBAlab能够快速、可靠地模拟包含多个物种的复杂动态培养物，包括微分代数方程（DAE）系统。此外，DFBAlab装箱时间s的运行时间与物种模型的数量呈线性关系。COBRA，DyMMM和DFBAlab.Conclusions的性能进行了比较的三个例子：字典式优化是用来确定独特的交换通量，这是必要的一个明确的动态系统。DFBAlab在数值积分过程中不会因LP不可行而失败。通过DFBAlab中的LP可行性问题获得的扩展系统提供了可用于优化算法的惩罚函数。
Background: Dynamic Flux Balance Analysis (DFBA) is a dynamic simulation framework for biochemical processes. DFBA can be performed using different approaches such as static optimization (SOA), dynamic optimization (DOA), and direct approaches (DA). Few existing simulators address the theoretical and practical challenges of nonunique exchange fluxes or infeasible linear programs (LPs). Both are common sources of failure and inefficiencies for these simulators.Results: DFBAlab, a MATLAB-based simulator that uses the LP feasibility problem to obtain an extended system and lexicographic optimization to yield unique exchange fluxes, is presented. DFBAlab is able to simulate complex dynamic cultures with multiple species rapidly and reliably, including differential-algebraic equation (DAE) systems. In addition, DFBAlab boxed times s running time scales linearly with the number of species models. Three examples are presented where the performance of COBRA, DyMMM and DFBAlab are compared.Conclusions: Lexicographic optimization is used to determine unique exchange fluxes which are necessary for a well-defined dynamic system. DFBAlab does not fail during numerical integration due to infeasible LPs. The extended system obtained through the LP feasibility problem in DFBAlab provides a penalty function that can be used in optimization algorithms.