CellDesigner protocols

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CellDesigner specifications

Information


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

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Publications for CellDesigner

CellDesigner in pipeline

2006
PMCID: 1665465
PMID: 17109765
DOI: 10.1186/1471-2105-7-506

[…] hand, of both the graph and text, can be a cumbersome and error-prone task. there are many tools available to set up models describing signaling networks as a biochemical reaction network, such as celldesigner, jdesigner, and promot [-]. however, to the best of our knowledge, there is currently no tool available that allows the visual setup of large logical networks, and has the ability […]


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CellDesigner in publications

 (132)
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, […]

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 […]

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 […]

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 […]

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 […]


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

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