CellDesigner statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CellDesigner

Tool usage distribution map

This map represents all the scientific publications referring to CellDesigner per scientific context
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Associated diseases

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CellDesigner specifications


Unique identifier OMICS_07302
Name CellDesigner
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 4.4
Stability Stable
Maintained Yes


No version available

Publications for CellDesigner

CellDesigner citations


Multifactorial Modes of Action of Arsenic Trioxide in Cancer Cells as Analyzed by Classical and Network Pharmacology

Front Pharmacol
PMCID: 5835320
PMID: 29535630
DOI: 10.3389/fphar.2018.00143

[…] refore, a number of software programs have been developed to address this problem, including programs developed at academia such as network molecular interaction maps (MIMs) (, ; ,; ), Cytoscape, (), CellDesigner (), TranscriptomeBrowser (; ), PathVisio-Validator (), Systems Biology Graphical Notation () as well as commercial products, e.g., Biocarta, Ingenuity Pathway analysis, Pathway Studio, Me […]


Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica

Sci Rep
PMCID: 5711873
PMID: 29196636
DOI: 10.1038/s41598-017-16884-3
call_split See protocol

[…] GN) for building of biological networks to express adequate information in a clearly visible and precise way was used (Fig. ). The Metabolic map of Jasmonic acid signalling pathway was constructed by CellDesigner4.4 and stored in Systems Biology Markup Language (SBML), a machine-readable format for representation of the biological network–. CellDesigner is a process diagram editor tool for represe […]


Computer simulation models as a tool to investigate the role of microRNAs in osteoarthritis

PLoS One
PMCID: 5695613
PMID: 29095952
DOI: 10.1371/journal.pone.0187568

[…] nge of freely available software tools. The models were simulated using COPASI 4.18 [] and tools developed at Newcastle University [] (further details below). The network diagrams were constructed in CellDesigner [], which uses the Systems Biology Graphical Notation []. The model output was analysed in R and plotted with ggplot2 []. […]


SABIO RK: an updated resource for manually curated biochemical reaction kinetics

Nucleic Acids Res
PMCID: 5753344
PMID: 29092055
DOI: 10.1093/nar/gkx1065

[…] terface, SABIO-RK web services can be used to access the database automatically which is also used for retrieval of kinetics data by third-party software tools and data workflows. These tools include CellDesigner (), VirtualCell (), Sycamore (), SBMLsqueezer (), cy3sabiork (http://apps.cytoscape.org/apps/cy3sabiork), Path2Models (), LigDig (), FAIRDOMHub (). Currently SABIO-RK is accessed mostly ( […]


Using computer simulation models to investigate the most promising microRNAs to improve muscle regeneration during ageing

Sci Rep
PMCID: 5614911
PMID: 28951568
DOI: 10.1038/s41598-017-12538-6

[…] rithm. This software is encoded in the C programming language and is available on request. Simulation data were analysed and plotted in R using ggplot2. Network diagrams of the models were created in CellDesigner which used the Systems Biology Graphical Notation. […]


In Silico Model driven Assessment of the Effects of Brain derived Neurotrophic Factor Deficiency on Glutamate and Gamma Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology

PMCID: 5426484
PMID: 28449558
DOI: 10.9758/cpn.2017.15.2.115
call_split See protocol

[…] Representation of the network was built which aids in interpretation and analysing biological networks. Model was structured using System Biology Markup Language (SBML, a XML based language) in CellDesigner software (http://www.celldesigner.org/). SBML is a machine readable format for representing bio-models which can be simulated and analysed. CellDesigner supports all SBML versions and pro […]

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CellDesigner institution(s)
The Systems Biology Institute, Minato-ku, Tokyo, Japan

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