Capturing the essence of a metabolic network: A flux balance analysis approach

Murabito, Ettore and Simeonidis, Evangelos and Smallbone, Kieran and Swinton, Jonathan (2009) Capturing the essence of a metabolic network: A flux balance analysis approach. Journal of Theoretical Biology, 260 (3). pp. 445-452. ISSN 0022-5193

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As genome-scale metabolic reconstructions emerge, tools to manage their size and complexity will be increasingly important. Flux Balance Analysis (FBA) is a constraint-based approach widely used to study the metabolic capabilities of cellular or subcellular systems. FBA problems are highly underdetermined and many different phenotypes can satisfy any set of constraints through which the metabolic system is represented. Two of the main concerns in FBA are exploring the space of solutions for a given metabolic network and finding a specific phenotype which is representative for a given task such as maximal growth rate. Here we introduce a recursive algorithm suitable for overcoming both of these concerns. The method proposed is able to find the alternate optimal patterns of active reactions of a FBA problem and identify the minimal subnetwork able to perform a specific task as optimally as the whole. Our method represents an alternative to and an extension of other approaches conceived for exploring the space of solutions of an FBA problem. It may also be particularly helpful in defining a scaffold of reactions upon which to build up a dynamic model, when the important pathways of the system have not yet been well-defined.

Item Type: Article
Uncontrolled Keywords: Mixed Integer Linear Programming problem; alternate optimal solutions; alternate optimal patterns; minimal optimal subnetwork; minimal effort principle
Subjects: MSC 2010, the AMS's Mathematics Subject Classification > 92 Biology and other natural sciences
Depositing User: Dr Kieran Smallbone
Date Deposited: 02 Sep 2009
Last Modified: 20 Oct 2017 14:12

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