title: Structural and functional analysis of cellular networks with CellNetAnalyzer.
abstract: BACKGROUND
  Mathematical modelling of cellular networks is an integral part of Systems Biology and requires appropriate software tools. An important class of methods in Systems Biology deals with structural or topological (parameter-free) analysis of cellular networks. So far, software tools providing such methods for both mass-flow (metabolic) as well as signal-flow (signalling and regulatory) networks are lacking.
  
  
  RESULTS
  Herein we introduce CellNetAnalyzer, a toolbox for MATLAB facilitating, in an interactive and visual manner, a comprehensive structural analysis of metabolic, signalling and regulatory networks. The particular strengths of CellNetAnalyzer are methods for functional network analysis, i.e. for characterising functional states, for detecting functional dependencies, for identifying intervention strategies, or for giving qualitative predictions on the effects of perturbations. CellNetAnalyzer extends its predecessor FluxAnalyzer (originally developed for metabolic network and pathway analysis) by a new modelling framework for examining signal-flow networks. Two of the novel methods implemented in CellNetAnalyzer are discussed in more detail regarding algorithmic issues and applications: the computation and analysis (i) of shortest positive and shortest negative paths and circuits in interaction graphs and (ii) of minimal intervention sets in logical networks.
  
  
  CONCLUSIONS
  CellNetAnalyzer provides a single suite to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks in a user-friendly environment. It provides a large toolbox with various, partially unique, functions and algorithms for functional network analysis. CellNetAnalyzer is freely available for academic use.
authors.affiliation: Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany. klamt@mpi-magdeburg.mpg.de
authors.forename: Steffen
authors.initials: S
authors.lastname: Klamt
authors.forename: Julio
authors.initials: J
authors.lastname: Saez-Rodriguez
authors.forename: Ernst D
authors.initials: ED
authors.lastname: Gilles
mesh_terms: D003198:Computer Simulation; D004926:Escherichia coli / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012984:Software; D049490:Systems Biology / Q000379:methods*; D013601:T-Lymphocytes / Q000378:metabolism