CellDesigner statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CellDesigner
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Tool usage distribution map

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

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

Versioning


No version available

Publications for CellDesigner

CellDesigner citations

 (93)
library_books

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

2018
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 […]

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

2017
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 […]

library_books

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

2017
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 []. […]

library_books

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

2017
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 ( […]

library_books

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

2017
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. […]

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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

2017
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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