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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

[…] 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, […]


Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation

PLoS Comput Biol
PMCID: 5813898
PMID: 29447151
DOI: 10.1371/journal.pcbi.1005740

[…] er are therefore useful to avoid combinatorial explosions resulting from multicomponent complexes and molecules with multiple states., sbgn is supported by a range of visualisation tools, including celldesigner [], sbgn-editor (sbgn-ed) [], pathvisio [] and sbgnviz []. sbgn diagrams are published in open repositories such as biomodels [] (for computational models) and reactome [] (for pathway […]


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

[…] 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 […]


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

[…] 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 []., we mainly used stochastic simulation, which is based […]


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

[…] 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., primary myoblasts from adult (6 months old) and old (24 months old) mice were prepared from edl muscles via collagenase and dispase […]


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

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

[…] or the embl-ebi search engine psicquic and the text mining tool ihop to search for more interactions described in the literature., the e2f1 interaction map was built with the process diagram editor celldesigner (v4.3) and visualized as a sbgn (systems biology graphical notation) compliant diagram. we created different regulatory and functional compartments based on the role of molecules […]

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

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