Gomez Jose A, Höffner Kai, Barton Paul I
Process Systems Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA.
BMC Bioinformatics. 2014 Dec 18;15(1):409. doi: 10.1186/s12859-014-0409-8.
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.
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'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.
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.
动态通量平衡分析（DFBA）是一种用于生化过程的动态模拟框架。DFBA可以使用不同的方法来执行，如静态优化（SOA）、动态优化（DOA）和直接方法（DA）。现有的模拟器很少能解决非唯一交换通量或不可行线性规划（LP）的理论和实际挑战。这两者都是这些模拟器常见的失败和效率低下的原因。
介绍了DFBAlab，这是一个基于MATLAB的模拟器，它使用LP可行性问题来获得扩展系统，并使用字典序优化来产生唯一的交换通量。DFBAlab能够快速可靠地模拟具有多种物种的复杂动态培养物，包括微分代数方程（DAE）系统。此外，DFBAlab的运行时间与物种模型的数量呈线性比例关系。给出了三个比较COBRA、DyMMM和DFBAlab性能的例子。
字典序优化用于确定定义明确的动态系统所需的唯一交换通量。DFBAlab在数值积分过程中不会因不可行的LP而失败。通过DFBAlab中的LP可行性问题获得的扩展系统提供了一个可用于优化算法的惩罚函数。
