Use of CellNetAnalyzer in biotechnology and metabolic engineering

•Constraint-based modeling (CBM) of metabolic networks: an important tool for biotechnology.•CellNetAnalyzer is a MATLAB toolbox providing various methods for CBM.•Includes powerful methods for computational strain design and metabolic engineering.•Can be used via interactive network maps or via command-line based operations.

Mathematical models of the cellular metabolism have become an essential tool for the optimization of biotechnological processes. They help to obtain a systemic understanding of the metabolic processes in the used microorganisms and to find suitable genetic modifications maximizing the production performance. In particular, methods of stoichiometric and constraint-based modeling are frequently used in the context of metabolic and bioprocess engineering. Since metabolic networks can be complex and comprise hundreds or even thousands of metabolites and reactions, dedicated software tools are required for an efficient analysis. One such software suite is CellNetAnalyzer, a MATLAB package providing, among others, various methods for analyzing stoichiometric and constraint-based metabolic models. CellNetAnalyzer can be used via command-line based operations or via a graphical user interface with embedded network visualizations. Herein we will present key functionalities of CellNetAnalyzer for applications in biotechnology and metabolic engineering and thereby review constraint-based modeling techniques such as metabolic flux analysis, flux balance analysis, flux variability analysis, metabolic pathway analysis (elementary flux modes) and methods for computational strain design.

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