PFA Toolbox

A MATLAB toolbox to perform Interval MFA and Possibilistic MFA.

Interval and Possibilistic MFA are two variants of Metabolic Flux Analysis (MFA), a widely used procedure to estimate the metabolic fluxes within living cells. These methods overcome some limitations of traditional MFA, particularly in scenarios of uncertainty —where measurements are scarce and imprecise— which are indeed common in research laboratories and industry (see references below).

PFA Toolbox features

• Provides reliable MFA estimations in uncertain (or underdetermined) scenarios, where only a few fluxes can be measured.
• Provides MFA estimations accounting for measurements imprecision.
• Allows to easily plot interval estimates and flux distributions. *Allow describing the measurements with a graphic interface.
• The toolbox is composed of simple MATLAB functions, which are flexible and can be modified by the user.
• It is compatible with the COBRA Toolbox.
• The toolbox is completely free.

If you want a more detailed description of PFA Toolbox, check the User's Manual. There you will find backgrounds, scientific details and several simple examples to illustrate the use of each function.

Download

You can download the PFA Toolbox here by clicking in 'Download ZIP'.

Installation

To install the PFA Toolbox:

1. Unzip PFA-Toolbox zip file.
2. Copy the PFA Toolbox folder where you want it to be installed.
3. Start MATLAB.
4. Navigate to the PFA-toolbox/Toolbox_Code path.
5. Run the following script, 'initPFAtoolbox'.

This action will add the PFA Toolbox directories to your MATLAB path and run the initialization script of YALMIP. The PFA Toolbox require solving linear programming problems, and these are solved using a flexible and efficient external optimizer: YALMIP. A copy of YALMIP is provided with the PFA Toolbox, but details about it can be found in their webpage.

References

About Interval and Possibilistic MFA:

• Llaneras F, Sala A, Picó J (2009). A possibilistic framework for constraint-based metabolic flux analysis. BMC Systems Biology.
• Llaneras F, Picó J (2007). An interval approach for dealing with flux distributions and elementary modes activity patterns. Journal of Theoretical Biology.
• Llaneras F (2011). Interval and possibilistic methods for constraint-based metabolic models. PhD Thesis, Valencia.

Two examples of applications:

• Morales Y, Tortajada M, Picó J, Vehí J, Llaneras F (2014). Validation of an FBA model for Pichia pastoris in chemostat cultures. BMC Systems Biology.
• Tortajada M, Llaneras F, Ramón D, Picó J (2012). Estimation of recombinant protein production in Pichia pastoris based on a constraint-based model. Journal of Process Control.

You can find more references with applications of both Interval and Possibilistic MFA in the User's manual.

The PFA Toolbox has been developed by Francisco Llaneras, Yeimy Morales, Jesús Picó, Josep Vehí and Gabriel Bosque, from two groups at Universitat de Girona and Universidad Politécnica de Valencia.

• MICELab, at UdG.
• CCSG, at UPV.

Acknowledgements:This research has been partially supported by the Spanish Government (cicyt: DPI2011-28112-C04-01), Biopolis S.L. (R.C.055/12), and the University of Girona (BR2012/26).