CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data

BMC Systems Biology

Miguel Rocha²  Isabel Rocha²  Jean-François Tomb³  Marcellinus Pont³  Paulo Vilaça¹  Paulo Maia¹  Pedro Evangelista¹  Rafael Carreira¹ 

[1] SilicoLife, Lda, Rua do Canastreiro 15, Braga, Portugal;Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal;E.I. DuPont De Nemours & Co., Inc, Wilmington, DE, USA

关键词: Open-source software;    Metabolic engineering;    Metabolic Flux analysis;    Constraint-based modeling;   

Others  :  1091410
DOI  :  10.1186/s12918-014-0123-1

 received in 2014-06-30, accepted in 2014-10-16,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Carreira et al.; licensee BioMed Central Ltd.

【 图 表 】

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