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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

Flux estimation. Estimations for every flux were obtained with the PFA Toolbox. a Three interval estimates are given, for maximum conditional possibility (box), possibility of 0.8 (black line), and 0.5 (gray line). b Possibility distributions are depicted with solid lines and dashed lines represent measured values
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Fig3: Flux estimation. Estimations for every flux were obtained with the PFA Toolbox. a Three interval estimates are given, for maximum conditional possibility (box), possibility of 0.8 (black line), and 0.5 (gray line). b Possibility distributions are depicted with solid lines and dashed lines represent measured values

Mentions: Finally, we plot the interval estimates using the function plot_intervals. The metabolic network and the main features of the algorithm to solve the problem with the PFA Toolbox are shown in Fig. 2. Figure 3a shows the interval estimations for each dataset. Notice that even if only two measurements are available, the estimation is reliable.Fig. 3


PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

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

Flux estimation. Estimations for every flux were obtained with the PFA Toolbox. a Three interval estimates are given, for maximum conditional possibility (box), possibility of 0.8 (black line), and 0.5 (gray line). b Possibility distributions are depicted with solid lines and dashed lines represent measured values
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Flux estimation. Estimations for every flux were obtained with the PFA Toolbox. a Three interval estimates are given, for maximum conditional possibility (box), possibility of 0.8 (black line), and 0.5 (gray line). b Possibility distributions are depicted with solid lines and dashed lines represent measured values
Mentions: Finally, we plot the interval estimates using the function plot_intervals. The metabolic network and the main features of the algorithm to solve the problem with the PFA Toolbox are shown in Fig. 2. Figure 3a shows the interval estimations for each dataset. Notice that even if only two measurements are available, the estimation is reliable.Fig. 3

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