论文标题

最小化优化的数量,以进行有效的社区动态通量平衡分析

Minimizing the number of optimizations for efficient community dynamic flux balance analysis

论文作者

Brunner, James D., Chia, Nicholas

论文摘要

动态通量平衡分析使用准稳态态假设,使用众所周知的通量平衡分析技术,在动态模拟的每个时间步中计算生物体的代谢活性。对于微生物群落,此计算特别昂贵,涉及在每个时间步骤为每个社区的每个成员解决线性约束优化问题。但是,这是不必要且效率低下的,因为可以使用先前的解决方案来告知未来的时间步骤。在这里,我们表明,可以为社区中的每个微生物选择内部通量的基础,并且可以在大多数时间步骤中通过求解相对便宜的线性方程式系统来模拟向前模拟。只要所得的代谢活动保留在优化问题的约束范围内(即,对方程线的线性系统对线性程序仍然是可行的),我们就可以使用该解决方案。随着解决方案变得不可行,它首先成为可行但退化的解决方案,解决了优化问题,我们可以解决一个不同但相关的优化问题,以选择适当的基础以继续前进模拟。我们通过与四个物种社区的当前使用方法进行比较来证明我们方法的效率和鲁棒性,并表明我们的方法需要至少$ 91 \%$ $ $ $ $ $ $ $ $。为了重现性,我们使用Python进行了原型。源代码可在\ verb | https://github.com/jdbrunner/surfin_fba |可用。

Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities, this calculation is especially costly and involves solving a linear constrained optimization problem for each member of the community at each time step. However, this is unnecessary and inefficient, as prior solutions can be used to inform future time steps. Here, we show that a basis for the space of internal fluxes can be chosen for each microbe in a community and this basis can be used to simulate forward by solving a relatively inexpensive system of linear equations at most time steps. We can use this solution as long as the resulting metabolic activity remains within the optimization problem's constraints (i.e. the solution to the linear system of equations remains a feasible to the linear program). As the solution becomes infeasible, it first becomes a feasible but degenerate solution to the optimization problem, and we can solve a different but related optimization problem to choose an appropriate basis to continue forward simulation. We demonstrate the efficiency and robustness of our method by comparing with currently used methods on a four species community, and show that our method requires at least $91\%$ fewer optimizations to be solved. For reproducibility, we prototyped the method using Python. Source code is available at \verb|https://github.com/jdbrunner/surfin_fba|.

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