Structural and functional analysis of cellular networks with CellNetAnalyzer

By Steffen Klamt, J. Sáez-Rodríguez, Ernst Dieter Gilles. BMC Systems Biology, 2007

378 citations recorded by the source corpus.

BackgroundMathematical 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.ResultsHerein 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.ConclusionCellNetAnalyzer 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/239b5397105f4994d7b32dbd0d80576a45d315f5

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Citations in the corpus

Analysis of global control of Escherichia coli carbohydrate uptake (2007, positive): “For example, networks are used to study functional enrichment [1], to analyze the structure of cellular networks [2], to model biological signalling or regulatory networks [1,3], to reconstruct metabolic networks [4], and to study the dynamic behavior of gene regulatory networks [5].”
Logic-Based Models for the Analysis of Cell Signaling Networks (2010, positive): “and network properties analysis logic steady state (41, 50)”
A Logical Model Provides Insights into T Cell Receptor Signaling (2007, positive): “MISs satisfying a given intervention goal can be computed by systematically testing sets of permanently activated or/and deactivated nodes [13,31].”
OptFlux: an open-source software platform for in silico metabolic engineering (2010, neutral): “From all the surveyed software tools, the CellNetAnalyzer [13], the COBRA toolbox [14] and the Systems Biology Research Tool (SBRT) [15] are the most similar to OptFlux , in terms of the available features.”
Reconstruction of Biochemical Networks in Microbial Organisms (2008, neutral): “Various computational platforms have been developed that apply constraint-based methods to metabolic GEM”
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction (2009, neutral): “Computer routines to perform simulations (in particular, to compute logical steady states that are generated by a certain combination of stimuli and inhibitors) are original to this work or are adapted from CellNetAnalyzer (Klamt et al , 2007).”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, neutral): “In addition, modules dedicated to constraint-based modeling have been developed for MATLAB : FLUXANALYZER (Klamt et al ., 2007), the COBRA TOOLBOX (Becker et al ., 2007), or METATOOL (von Kamp & Schuster, 2006) for elementary mode analysis are good representatives.”