latest version: 2018.1.

CellNetAnalyzer - Detailed Description

CellNetAnalyzer runs under MATLAB and is thus independent of your operating system. It directly benefits from MATLAB's built-in functions and the rich functionalities for building graphical user interfaces. Basically, CellNetAnalyzer consists of (i) user-defined network projects and (ii) a toolbox with various functions for structural network analysis:

(i) Network projects are created and designed by the user. A network project is of type Mass-flow (modeling material flows as in metabolic or other stoichiometric reaction networks) or of type Signal-flow (modeling information or signal flows as in signal transduction networks or regulatory networks). Each network project comprises an abstract (symbolic) network representation as well as one or several network graphics visualizing the network under investigation. The abstract network model is composed by declaring network elements such as reactions or compounds (see Fig. 1 and Fig. 2), whereas the network graphics have to be imported and thus created by other programs (e.g. CellDesigner, xfig, CorelDraw etc.; for signal-flow networks, ProMoT provides an elegant solution to construct network map AND network model (in CellNetAnalyzer format) in one step). Network model and graphical network representation can then be linked with the help of user interfaces (text boxes) leading to interactive network maps. Examples are shown in Fig. 3 (stoichiometric network) and Fig.4 (signal-flow network). Interactive network maps are the central components of network projects. The text boxes facilitate input and output (e.g. of reaction rates) directly within the network visualization.

(ii) The toolbox of CellNetAnalyzer provides functions and procedures which, depending on the network type, facilitate stoichiometric (metabolic) network analysis or the analysis of signal-flow networks (see list below). These functions can be started conveniently from a pull-down menu in the network maps and the user has not to be aware of mathematical details. Some algorithms use the MEX interface of MATLAB to call precompiled C files, others make use of external solvers (e.g. CPLEX, glpk). Computed results are displayed in the interactive maps; different coloration of the text boxes allows highlighting certain results. For example, the screen shot in Fig. 3 shows a scenario of metabolic flux analysis and Fig. 4 a logical steady state resulting from an external stimulation in a signaling network.

CellNetAnalyzer provides also API (Applications Programming Interface) functionalities enabling the exchange of data/variables/models between CellNetAnalyzer and external applications. Furthermore, many functionalities (e.g. calculation of elementary modes or of feedback loops) can also be called from MATLAB command line without the need to first build a CellNetAnalyzer project with interactive maps. User functions can also be embedded in the CNA menu.

Here is an incomplete list of functions for network analysis provided in CellNetAnalyzer:

Mass-flow (stoichiometric, metabolic) networks:

Analysis of basic topological/structural properties

Metabolic flux analysis

Flux balance analysis (FBA; flux optimization)

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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