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CellNetAnalyzer specifications

Information


Unique identifier OMICS_05189
Name CellNetAnalyzer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • OptMDFpathway

Versioning


No version available

Documentation


Maintainer


  • person_outline Steffen Klamt

Publications for CellNetAnalyzer

CellNetAnalyzer citations

 (23)
library_books

ATLANTIS Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming

2018
Sci Rep
PMCID: 5824948
PMID: 29476134
DOI: 10.1038/s41598-018-22031-3

[…] s have been developed for construction,, visualization, and analyses, of logical networks. From amongst them, the leading tools for computing attractor states include BoolNet, The Cell Collective and CellNetAnalyzer. However, these tools fail to associate biologically relevant network states with emergent cell fates. It is the lack of this functionality which further impedes cell fate reprogrammin […]

library_books

Unraveling a tumor type specific regulatory core underlying E2F1 mediated epithelial mesenchymal transition to predict receptor protein signatures

2017
Nat Commun
PMCID: 5543083
PMID: 28775339
DOI: 10.1038/s41467-017-00268-2

[…] ificant impact on the disease phenotypes. To identify molecular signatures, the regulatory core is translated into a logic-based model, and steady state analysis is performed using the software tool CellNetAnalyzer.We developed logic-based models of the regulatory cores and carried out in silico perturbation experiments. To this end and upon the selection of the relevant network motifs, we establ […]

library_books

Simulation of the dynamics of primary immunodeficiencies in CD4+ T cells

2017
PLoS One
PMCID: 5407609
PMID: 28448599
DOI: 10.1371/journal.pone.0176500

[…] econstruction of the Boolean equations for the T cell model. Only those nodes that have been demonstrated to play a crucial role in the TCR/CD28-dependent activation of CD4+ T cells were retained.The CellNetAnalyzer version 2016.1 [] was used for identifying feedback loops in the underlying interaction graph of the model. The base R software version 3.2.3 [] and Cytoscape version 3.3.0 [] were use […]

library_books

Identifying model error in metabolic flux analysis – a generalized least squares approach

2016
BMC Syst Biol
PMCID: 5020535
PMID: 27619919
DOI: 10.1186/s12918-016-0335-7

[…] o a level where they can be solved directly from measured extracellular transport rates [, ], continuing the use of traditional overdetermined MFA. The simplification can be aided by software such as CellNetAnalyzer that can deal with both underdetermined COBRA models and overdetermined MFA formulations [, ]. Recent developments have also led to an automation of the model simplification process [] […]

library_books

Designing minimal microbial strains of desired functionality using a genetic algorithm

2015
PMCID: 4687386
PMID: 26697103
DOI: 10.1186/s13015-015-0060-6

[…] number of EFMs are one order of magnitude larger than that used in [].Tools which use EFMs to find intervention strategies include the MHScalculator [, ] and a tool to calculate cMCSs as part of the CellNetAnalyzer, a MATLAB package providing comprehensive structural and functional analysis of biochemical networks []. These methods use EFMs and hence consider the entire metabolic landscape of the […]

library_books

Dynamical modeling of uncertain interaction based genomic networks

2015
BMC Bioinformatics
PMCID: 4596957
PMID: 26423606
DOI: 10.1186/1471-2105-16-S13-S3

[…] for Boolean modeling, the translation is not unique and can be unstable in relation to small interaction alterations. There are also software tools that can be used to run such simulations, including CellNetAnalyzer [], CellNOpt [], BooleanNet [], and CPN tools [].Furthermore, all the existing approaches, differential equations, Boolean, or Petri net, require a complete and exact knowledge of the […]

Citations

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CellNetAnalyzer institution(s)
Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
CellNetAnalyzer funding source(s)
Supported by the German Ministry of Research and Education (HepatoSys), the German Research Society (FOR521), and the Ministry of Education of Saxony-Anhalt (Research Focus Dynamical Systems).

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