CellNetAnalyzer - A toolbox for analyzing structure and function of metabolic, signaling, and regulatory networks
CellNetAnalyzer (CNA) is a MATLAB toolbox providing various computational methods for analyzing structure and function of metabolic, signaling, and regulatory networks. For metabolic networks, CNA supports a variety of stoichiometric and constraint-based modeling techniques, including flux balance analysis (FBA), metabolic flux analysis, elementary-modes analysis, or computational strain design (e.g., minimal cut set analysis).
Signal transduction and (gene) regulatory networks can be represented as logical networks (Boolean or multivalued logic) and as interaction graphs and be explored through logical steady state analysis (qualitative input-output behavior of signaling networks), minimal intervention sets, discrete simulations, simulation of logic-based ODEs (via ODEfy plugin) as well as analysis of global interdependencies and of feedback loops and signaling paths. Computations can be started within a GUI (interactive network maps) or from command line (via API functions).
Funding: Development and maintenance partially funded by de.NBI.