Enhancing Elementary Flux Modes analysis using filtering techniques in an integrated environment

Publicado em "Advances in bioinformatics : 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010)", ISBN 978-3-642-13213-1Elementary Flux Modes (EFMs) have been claimed as one of the most promising approaches for pathway analysis. These are a set of vectors that emerge from the stoichiometric matrix of a biochemical network through the use of convex analysis. The computation of all EFMs of a given network is an NP-hard problem and existing algorithms do not scale well. Moreover, the analysis of results is difficult given the thousands or millions of possible modes generated. In this work, we propose a new plugin, running on top of the OptFlux Metabolic Engineering workbench, whose aims are to ease the analysis of these results and explore synergies among EFM analysis, phenotype simulation and strain optimization.The authors wish to thank the financial support of the Portuguese FCT for the Ph.D grant SFRH/BD/61465/2009 and the company Dupont under the scope of the Dupont European University Support Program Award

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

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.The work is partially funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT (Portuguese Foundation for Science and Technology) within project ref. COMPETE FCOMP-01-0124-FEDER-015079. RC's work is funded by a Ph.D. grant from the Portuguese FCT (ref. SFRH/BD/66201/2009).The authors would also like to thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013 and the Projects "BioInd - Biotechnology and Bioengineering for improved Industrial and Agro-Food processes", REF. NORTE-07-0124-FEDER-000028 and "PEM - Metabolic Engineering Platform", project number 23060, both co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER