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.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940746 | PMC |
| http://dx.doi.org/10.1186/s12918-016-0284-1 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Content analysis of psychological first aid training manuals via topic modelling.
Eur J Psychotraumatol
July 2023
Rzeszów University of Technology, Rzeszów, Poland.
Psychological First Aid (PFA) is practiced worldwide. This practice in English is guided through a small collection of training manuals. Despite ubiquitous practice and formal training materials, little is known about what topics are covered and in what depth in these influential manuals.
View Article and Find Full Text PDFPFA toolbox: a MATLAB tool for Metabolic Flux Analysis.
BMC Syst Biol
July 2016
MICElab, IIIA, Universitat de Girona, Campus Montilivi, P4, Girona, 17071, Spain.
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.
View Article and Find Full Text PDFDual-colour fluorescence microscopy using yEmCherry-/GFP-tagging of eisosome components Pil1 and Lsp1 in Candida albicans.
Yeast
April 2011
Carlsberg Laboratory, Yeast Biology, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark.
PCR-based gene targeting technologies have previously been developed for Candida albicans molecular genetic manipulation. Modular marker plasmids for the functional analysis of C. albicans genes have been generated to delete genes, exchange promoters and tag genes with GFP.
View Article and Find Full Text PDFNew pFA-cassettes for PCR-based gene manipulation in Candida albicans.
J Basic Microbiol
November 2006
Growth-Control of Fungal Pathogens, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute and Dept. of Microbiology, Friedrich-Schiller University, Jena.
Several modules for efficient PCR-based gene disruption have recently been introduced in Candida albicans. These are based on auxotrophic marker genes for deficient strains derived from SC5314/CAI4. Commonly used protocols for the transformation C.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!