Dynamic Flux Balance Analysis Using DFBAlab

Methods Mol Biol. 2018;1716:353-370. doi: 10.1007/978-1-4939-7528-0_16.

Abstract

Bioprocesses are of critical importance in several industries such as the food and pharmaceutical industries. Despite their importance and widespread application, bioprocess models remain rather simplistic and based on unstructured models. These simple models have limitations, making it very difficult to model complex bioprocesses. With dynamic flux balance analysis (DFBA) more comprehensive bioprocess models can be obtained. DFBA simulations are difficult to carry out because they result in dynamic systems with linear programs embedded. Therefore, the use of DFBA as a modeling tool has been limited. With DFBAlab, a MATLAB code that performs efficient and reliable DFBA simulations, the use of DFBA as a modeling tool has become more accessible. Here, we illustrate with an example how to implement bioprocess models in DFBAlab.

Keywords: Bioprocess modeling; Dynamic flux balance analysis; Dynamic systems; Flux balance analysis; Linear programming.

MeSH terms

  • Algorithms
  • Computer Simulation
  • Metabolic Flux Analysis / methods*
  • Metabolic Networks and Pathways
  • Models, Biological
  • Programming, Linear
  • Systems Biology / methods*