PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

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 ind...

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Vydáno v:BMC systems biology Ročník 10; číslo 1; s. 46
Hlavní autoři: Morales, Yeimy, Bosque, Gabriel, Vehí, Josep, Picó, Jesús, Llaneras, Francisco
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 11.07.2016
Témata:
Algorithms
Bioinformatics
Biomass
Biomedical and Life Sciences
Cellular and Medical Topics
Computational Biology - methods
Computational Biology/Bioinformatics
Escherichia coli - growth & development
Escherichia coli - metabolism
Fluctuations
Life Sciences
Matlab (Computer programs)
Matlab (Programes d'ordinador)
Metabolic Flux Analysis
Methods
Physiological
Pichia - metabolism
Simulation and Modeling
Software
software and technology
Systems Biology
User-Computer Interface
Possibilistic MFA
Metabolic Flux Analysis
Interval MFA
Constraint-based modelling
ISSN:1752-0509, 1752-0509
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Shrnutí: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.
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ISSN:1752-0509
1752-0509
DOI:10.1186/s12918-016-0284-1