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PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

Morales Y, Bosque G, Vehí J, Picó J, Llaneras F - BMC Syst Biol (2016)

Bottom Line: The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format.In addition, the PFA Toolbox includes a User's Guide with a thorough description of its functions and several examples.The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations.

View Article: PubMed Central - PubMed

Affiliation: MICElab, IIIA, Universitat de Girona, Campus Montilivi, P4, Girona, 17071, Spain. yeimy.morales@udg.edu.

ABSTRACT

Background: Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, particularly when measurements are scarce and imprecise. This is very common in industrial environments. The PFA Toolbox can be used to face those scenarios.

Results: Here we present the PFA (Possibilistic Flux Analysis) Toolbox for MATLAB, which simplifies the use of Interval and Possibilistic Metabolic Flux Analysis. The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format. In addition, the PFA Toolbox includes a User's Guide with a thorough description of its functions and several examples.

Conclusions: The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations.

No MeSH data available.


Related in: MedlinePlus

Protocol to use the PFA Toolbox. A step by step to use the PFA Toolbox. Protocol is the same to solve the MFA problems with Interval and possibilistic MFA. Possibilistic has two additional steps, which are optional, a Graphical User Interface (GUI) to represent graphically the measures in possibilistic terms and a function to check if the measures and their uncertainties are well-defined
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Fig1: Protocol to use the PFA Toolbox. A step by step to use the PFA Toolbox. Protocol is the same to solve the MFA problems with Interval and possibilistic MFA. Possibilistic has two additional steps, which are optional, a Graphical User Interface (GUI) to represent graphically the measures in possibilistic terms and a function to check if the measures and their uncertainties are well-defined

Mentions: » It is composed of simple, free and open functions.


PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

Morales Y, Bosque G, Vehí J, Picó J, Llaneras F - BMC Syst Biol (2016)

Protocol to use the PFA Toolbox. A step by step to use the PFA Toolbox. Protocol is the same to solve the MFA problems with Interval and possibilistic MFA. Possibilistic has two additional steps, which are optional, a Graphical User Interface (GUI) to represent graphically the measures in possibilistic terms and a function to check if the measures and their uncertainties are well-defined
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4940746&req=5

Fig1: Protocol to use the PFA Toolbox. A step by step to use the PFA Toolbox. Protocol is the same to solve the MFA problems with Interval and possibilistic MFA. Possibilistic has two additional steps, which are optional, a Graphical User Interface (GUI) to represent graphically the measures in possibilistic terms and a function to check if the measures and their uncertainties are well-defined
Mentions: » It is composed of simple, free and open functions.

Bottom Line: The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format.In addition, the PFA Toolbox includes a User's Guide with a thorough description of its functions and several examples.The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations.

View Article: PubMed Central - PubMed

Affiliation: MICElab, IIIA, Universitat de Girona, Campus Montilivi, P4, Girona, 17071, Spain. yeimy.morales@udg.edu.

ABSTRACT

Background: Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, particularly when measurements are scarce and imprecise. This is very common in industrial environments. The PFA Toolbox can be used to face those scenarios.

Results: Here we present the PFA (Possibilistic Flux Analysis) Toolbox for MATLAB, which simplifies the use of Interval and Possibilistic Metabolic Flux Analysis. The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format. In addition, the PFA Toolbox includes a User's Guide with a thorough description of its functions and several examples.

Conclusions: The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations.

No MeSH data available.


Related in: MedlinePlus