FluxExplorer: A general platform for modeling and analyses of metabolic networks based on stoichiometry

Stoichiometry-based analyses of metabolic networks have aroused significant interest of systems biology researchers in recent years. It is necessary to develop a more convenient modeling platform on which users can reconstruct their network models using completely graphical operations, and explore them with powerful analyzing modules to get a better understanding of the properties of metabolic systems. Herein, an in silico platform, FluxExplorer, for metabolic modeling and analyses based on stoichiometry has been developed as a publicly available tool for systems biology research. This platform integrates various analytic approaches, including flux balance analysis, minimization of metabolic adjustment, extreme pathways analysis, shadow prices analysis, and singular value decomposition, providing a thorough characterization of the metabolic system. Using a graphic modeling process, metabolic networks can be reconstructed and modified intuitively and conveniently. The inconsistencies of a model with respect to the FBA principles can be proved automatically. In addition, this platform supports systems biology markup language (SBML). FluxExplorer has been applied to rebuild a metabolic network in mammalian mitochondria, producing meaningful results. Generally, it is a powerful and very convenient tool for metabolic network modeling and analysis.