latest version: 2019.2

CellNetAnalyzer - Detailed Description

CellNetAnalyzer is a MATLAB toolbox for analyzing structure and function of biological networks on the basis of topological, stoichiometric, qualitative and semi-quantitative modeling approaches requiring no or only few parameters. In particular, metabolic networks (mass-flow) can be studied based on stoichiometric and constraint-based modeling approaches whereas signaling and regulatory networks (signal-flow networks) can be explored by qualitative and semi-quantitative modeling approaches (Boolean/logical models, interaction graphs, logic-based ODEs). CNA can be used via a graphical user interface with embedded network visualizations (interactive network maps) or vial command-line based operations (supported by an application programming interface; API).

Here is a (incomplete) list of features and of (GUI and API) functions in CellNetAnalyzer:

Mass-flow (stoichiometric, metabolic) networks:

Analysis of basic topological/structural properties

Metabolic flux analysis

Flux balance analysis (FBA; flux optimization)

Network composer (Fig. 1): for managing and editing the network structure (based on masks as in Fig. 2)

Metabolic pathway analysis / Elementary-modes analysis

Minimal cut sets

Signal-flow (signaling, regulatory) networks:

Analysis of interaction graphs

Analysis of logical (Boolean) interaction networks

General features (for mass-flow and signal-flow networks):

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