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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.
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flexFBA and tFBA source
Source code used in the production of simulations and figures for publication.
Publication
Dec 22, 2013

Released upon publication. IMPORTANT NOTE: It has come to my attention that this file downloads without extension, please add ".zip" and then decompress.Notes  View License

Download Links

Dec 21, 2013
152 KB
Any
Source code
Source code and model flat files used to produce manuscript figures using Python.

PLEASE CITE THESE PAPERS

Birch, E.W., et al., Incorporation of flexible objectives and time-linked simulation with flux balance analysis. J. Theor. Biol. (2013), (2013) View


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flexFBA for MatLab COBRA
A script and example model (iAF1260) in COBRA format for running the flexible FBA method. Output visualized via printing to command window. Thoroughly commented to explain method implementation.
Publication
Nov 27, 2013

Initial release to accompany publication. IMPORTANT NOTE: It has come to my attention that this file downloads without extension, please add ".zip" and then decompress.Notes  View License

Download Links

Dec 21, 2013
268 KB
Any
Source code
Flexible FBA matlab script archive with model for example use.

PLEASE CITE THESE PAPERS

Please cite this article as: Birch, E.W., et al., Incorporation of flexible objectives and time-linked simulation with flux balance analysis. J. Theor. Biol. (2013) (2013) View


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