PFA Toolbox

A MATLAB toolbox for interval and possibilistic MFA

View the Project on GitHub kikollan/PFA-Toolbox

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

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.


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


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.


About Interval and Possibilistic MFA:

Two examples of applications:

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.

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).