Journal
BMC SYSTEMS BIOLOGY
Volume 8, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s12918-014-0123-1
Keywords
Constraint-based modeling; Metabolic Flux analysis; Metabolic engineering; Open-source software
Categories
Funding
- ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness)
- National Funds through the FCT (Portuguese Foundation for Science and Technology) [COMPETE FCOMP-01-0124-FEDER-015079]
- Portuguese FCT [SFRH/BD/66201/2009]
- FCT Strategic Project [PEst-OE/EQB/LA0023/2013]
- Project BioInd - Biotechnology and Bioengineering for improved Industrial and Agro-Food processes - Programa Operacional Regional do Norte [NORTE-07-0124-FEDER-000028, ON.2 - O Novo Norte]
- Project PEM - Metabolic Engineering Platform - Programa Operacional Regional do Norte [ON.2 - O Novo Norte, 23060]
- QREN
- FEDER
- Fundação para a Ciência e a Tecnologia [PEst-OE/EQB/LA0023/2013, SFRH/BD/66201/2009] Funding Source: FCT
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Background: Flux analysis methods lie at the core of Metabolic Engineering (ME), providing methods for phenotype simulation that allow the determination of flux distributions under different conditions. Although many constraint-based modeling software tools have been developed and published, none provides a free user-friendly application that makes available the full portfolio of flux analysis methods. Results: This work presents Constraint-based Flux Analysis (CBFA), an open-source software application for flux analysis in metabolic models that implements several methods for phenotype prediction, allowing users to define constraints associated with measured fluxes and/or flux ratios, together with environmental conditions (e. g. media) and reaction/gene knockouts. CBFA identifies the set of applicable methods based on the constraints defined from user inputs, encompassing algebraic and constraint-based simulation methods. The integration of CBFA within the OptFlux framework for ME enables the utilization of different model formats and standards and the integration with complementary methods for phenotype simulation and visualization of results. Conclusions: A general-purpose and flexible application is proposed that is independent of the origin of the constraints defined for a given simulation. The aim is to provide a simple to use software tool focused on the application of several flux prediction methods.
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