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

James D Brunner and Nicholas Chia

PLOS Computational Biology, 2020, vol. 16, issue 9, 1-20

Abstract: 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 https://github.com/jdbrunner/surfin_fba.Author summary: The standard methods in the field for dynamic flux balance analysis (FBA) carry a prohibitively high computational cost because it requires solving a linear optimization problem at each time-step. We have developed a novel method for producing solutions to this dynamical system which greatly reduces the number of optimization problems that must be solved. We prove mathematically that we can solve the optimization problem once and simulate the system forward as an ordinary differential equation (ODE) for some time interval, and solutions to this ODE provide solutions to the optimization problem. Eventually, the system reaches an easily check-able condition which implies that another optimization problem must be solved. We compare our method against typically used methods for dynamic FBA to validate that it provides equivalent solutions while requiring fewer linear-program solutions.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1007786

DOI: 10.1371/journal.pcbi.1007786

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