*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, up to genome-scale metabolic networks (mass-flow networks) 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

- Computation of graph-theoretical path lengths
- Connectivity histogram
- Detection of (elementary) conservation relations, coupled reactions, blocked and parallel reactions

### Metabolic flux analysis

- Classification of flux scenarios (determinacy and redundancy) and rates (balanceability and calculability)
- Calculation of flux distributions based on given (measured) reaction rates
- Balancing, weighted least-squares solutions and consistency checks in redundant systems
- Sensitivity analysis of calculated rates
- Feasibility check of a given scenario

### Flux balance analysis (FBA; flux optimization)

- Flux optimization (FBA) subject to user-defined linear objective functions
- Parsimonious FBA
- Flux variability analysis
- Yield maximization
- Calculation of yield space plot and phase planes (production envelopes)
- Computing minimal (flux) corrections to make infeasible FBA scenario feasible

### Metabolic pathway analysis / Elementary-modes analysis

- Large-scale calculation of elementary (flux) modes, extreme pathways or convex bases of flux cones (via METATOOL or EFMTOOL)
- Inhomogeneous constraints can now be considered for calculating elementary flux vectors of flux polyhedra (generalization of elementary modes)
- Computed pathways can be displayed in the interactive maps
- Selection of pathways with respect to certain criteria
- Statistical analysis of computed pathway vectors (yield distributions, 2D yield spaces or production envelopes, reaction participation, pathway lengths etc)

### Minimal cut sets

- Finding targets in and analyzing the fragility of biochemical reaction networks
- Calculation of constrained minimal cut sets (cMCS) blocking undesired and preserving desired functionalities - either via elementary modes (GUI, API) or via inequalities (only API)
- Display of minimal cut sets within the interactive maps
- Statistical analysis and assessment of minimal cut sets

### Signal-flow (signaling, regulatory) networks:

### Analysis of interaction graphs

- Basic topological properties
- Large-scale enumeration of positive and negative signaling paths connecting inputs with outputs or of all signaling paths between given sets of start and end nodes; statistical analysis of these paths
- Large-scale enumeration of all positive and negative feedback loops; statistical analysis of these loops
- Computation of minimal cut sets (removing reactions or species) for a given set of paths or/and loops
- Computation of distance (shortest paths) matrices; separately for positive and negative paths
- Large-scale dependency analysis (which species has (positive/negative) influence on which species; identification of activators and inhibitors of a given species enabling predictions on perturbation experiments)
- Detection of inconsistencies between experimental (high-throughput) data and dependency matrix

### Analysis of logical (Boolean) interaction networks

- Arbitrary logical models (constructed with AND,OR and NOT operators) with Boolean or multiple discrete levels can be set-up
- Logical steady state analysis for a given set of inputs/fixed states: useful for studying input-output behavior and signal processing
- Odefy plugin (developed by Fabian Theis' group: Jan Krumsiek, Dominik Wittmann): simulate and export ODE models created from Boolean models
- Computation of (logical) minimal intervention sets (sets of knock-outs/knock-ins) repressing or provoking a certain behavior or function of the network
- Computation of species equivalence classes
- Automated conversion of the logical model into an interaction graph

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

- The API (Application Programming Interface) of CNA allows interested users and developers
- To use functions of CNA (e.g., for FBA, FVA, computation of elementary modes or signaling paths) from command line and without CNA GUI
- To read/write or import/export the network structure of a project
- To read values from text boxes (GUIs), then to perform own calculations and finally to display the results in the interactive network maps
- To integrate own functions as a new menu-entry in CNA's menu - you can thus construct and integrate plugins for CNA
- To change network/project attributes directly from MATLAB's command line (for advanced users)

- Scenarios (e.g. different flux distributions) can be saved and then loaded later again
- Cliboard function: for saving intermediate results; also allows arithmetic combination of different scenarios (+, -, \, *) - useful for comparinge .g. different flux distributions)
- Network composer (see screenshots): for managing and editing the network structure (based on masks as in Fig. 2)
- Element selector: search for species and reactions/interactions using diverse filters and specifications
- For large-scale networks: automatic generation of basic network maps as a starting point to work with the GUI
- Import/Export of models in SBML, ASCII and COBRA (for metabolic networks) format
- Zoom tool (for zooming in and out in large maps)
- Toolbar: quick access for frequent actions