Two sets of models and scripts are provided here: 1) Those which reproduce publication materials, and 2) a simple example for the purpose of explaining the flexFBA method implementation and troubleshooting metabolic models. The example MatLab COBRA script is recommended for almost all users. For any Flux Balance Analysis implementation the vast majority of code is involved in parsing model formats or setting bounds, with comparatively little accomplishing the linear programming problem setup and solver call. Because the example MatLab script takes advantage of COBRA functionality for those setup tasks, it is clearer what pertains specifically to the flexFBA method. Keep in mind that there are a variety of valid ways to set up the matrices to solve the flexFBA optimization problem, and this is just one. The example MatLab script does not include tFBA implementation in part because it would require more fundamental alterations of the COBRA problem setup and the information it contains. Furthermore, tFBA simulation is accomplished with setting of flux bounds based on information from the previous time-step and any integrated models, so it is likely that the most convenient format of its implementation will be customized to specific applications. The Python source code for publication simulation and figure reproduction depends on a number of packages, not all of which are easy to install compatibly depending on platform (Linux is recommended). A virtual machine may eventually be available here to facilitate its evaluation.