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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

PFA Toolbox methodology to solve example of flux estimation under data scarcity. a Upper panel present a simple metabolic network. Metabolites are in capital letters, each vj represent a flux and the double arrows indicate a reversible reaction. b The step-by-step procedure follow to solve the MFA problem where only two measures are known. c Right panel shows the MATLAB code used to perform the computations
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Fig2: PFA Toolbox methodology to solve example of flux estimation under data scarcity. a Upper panel present a simple metabolic network. Metabolites are in capital letters, each vj represent a flux and the double arrows indicate a reversible reaction. b The step-by-step procedure follow to solve the MFA problem where only two measures are known. c Right panel shows the MATLAB code used to perform the computations

Mentions: We use a toy metabolic network to illustrate how to use the PFA Toolbox in scenarios of data scarcity. The first step is to formulate the problem. Consider the metabolic network shown in Fig. 2a. The network has six fluxes and three balanced metabolites. One of the fluxes is reversible. Additionally, the fluxes v4 and v6 have been measured, with values w4 = 9.5 mmol/h, and w6 = 10.5 mmol/h.Fig. 2


PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

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

PFA Toolbox methodology to solve example of flux estimation under data scarcity. a Upper panel present a simple metabolic network. Metabolites are in capital letters, each vj represent a flux and the double arrows indicate a reversible reaction. b The step-by-step procedure follow to solve the MFA problem where only two measures are known. c Right panel shows the MATLAB code used to perform the computations
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: PFA Toolbox methodology to solve example of flux estimation under data scarcity. a Upper panel present a simple metabolic network. Metabolites are in capital letters, each vj represent a flux and the double arrows indicate a reversible reaction. b The step-by-step procedure follow to solve the MFA problem where only two measures are known. c Right panel shows the MATLAB code used to perform the computations
Mentions: We use a toy metabolic network to illustrate how to use the PFA Toolbox in scenarios of data scarcity. The first step is to formulate the problem. Consider the metabolic network shown in Fig. 2a. The network has six fluxes and three balanced metabolites. One of the fluxes is reversible. Additionally, the fluxes v4 and v6 have been measured, with values w4 = 9.5 mmol/h, and w6 = 10.5 mmol/h.Fig. 2

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