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PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

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

BMC Systems Biology, 2016, vol. 10, p. 46

BioMed Central

Autor: Morales, Yeimi
Bosque, Gabriel
Vehí, Josep
Picó i Marco, Jesús
Llaneras Estrada, Francisco
Data: 11 juliol 2016
Resum: 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
Format: application/pdf
ISSN: 1752-0509
Accés al document: http://hdl.handle.net/10256/13927
Llenguatge: eng
Editor: BioMed Central
Col·lecció: Reproducció digital del document publicat a: http://dx.doi.org/10.1186/s12918-016-0284-1
Articles publicats (D-EEEiA)
És part de: BMC Systems Biology, 2016, vol. 10, p. 46
Drets: Attribution 4.0 Spain
URI Drets: http://creativecommons.org/licenses/by/4.0/es/
Matèria: Matlab (Programes d’ordinador)
Matlab (Computer programs)
Títol: PFA toolbox: a MATLAB tool for Metabolic Flux Analysis
Tipus: info:eu-repo/semantics/article
Repositori: DUGiDocs

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