An insight to flux-balance analysis for biochemical networks

ABSTRACT

Systems biology is one of the integrated ways to study biological systems and is more favourable than the earlier used approaches. It includes metabolic pathway analysis, modelling, and regulatory as well as signal transduction for getting insights into cellular behaviour. Among the various techniques of modelling, simulation, analysis of networks and pathways, flux-based analysis (FBA) has been recognised because of its extensibility as well as simplicity. It is widely accepted because it is not like a mechanistic simulation which depends on accurate kinetic data. The study of fluxes through the network is informative and can give insights even in the absence of kinetic data. FBA is one of the widely used tools to study biochemical networks and needs information of reaction stoichiometry, growth requirements, specific measurement parameters of the biological system, in particular the reconstruction of the metabolic network for the genome-scale, many of which have already been built previously. It defines the boundaries of flux distributions which are possible and achievable with a defined set of genes. This review article gives an insight into FBA, from the extension of flux balancing to mathematical representation followed by a discussion about the formulation of flux-balance analysis problems, defining constraints for the stoichiometry of the pathways and the tools that can be used in FBA such as FASIMA, COBRA toolbox, and OptFlux. It also includes broader areas in terms of applications which can be covered by FBA as well as the queries which can be addressed through FBA.

KEYWORDS:

• Flux-balance analysis (FBA)
• metabolic pathway
• system biology
• cellular metabolism

Acknowledgments

The authors are thankful to TEQIP-III for financial support and Birla Institute of Technology Mesra, Ranchi, Jharkhand.

Disclosure statement

No, potential conflict of interest was reported by the author(s).

Additional information

Notes on contributors

Shreya Anand

Shreya Anand is a PhD Scholar in the Department of Bioengineering, Birla Institute of Technology, Mesra, Ranchi, India. She is doing research on the production of a polyol as her PhD work. Her subject of research interest is Bioprocess Engineering and Bioinformatics.

Koel Mukherjee

Koel Mukherjee is an Assistant Professor in the Department of Bioengineering, Birla Institute of Technology, Mesra, Ranchi, India. She has valuable research experiences and has an interest in Computational Biology, Drug Designing & delivery system, MD simulation, DNA-Protein interaction study and Nanobiotechnology.

Padmini Padmanabhan

Padmini Padmanabhan is a Professor and Dean (Academic Programme) in the Department of Bioengineering, Birla Institute of Technology, Mesra, Ranchi, India. She has adequate research experience and has an interest in Industrial Bioprocess engineering, Nano Biotechnology and Renewable energy.