Jdesigner protocols

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Jdesigner specifications

Information


Unique identifier OMICS_14534
Name Jdesigner
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C#, C++, Delphi, Fortran, Java
License BSD 3-clause “New” or “Revised” License
Computer skills Medium
Version 2.9.0
Stability No
Maintained Yes

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Maintainer


  • person_outline Ravishankar Rao Vallabhajosyula <>

Publication for Jdesigner

Jdesigner in pipeline

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

[…] 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 to export […]


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Jdesigner in publications

 (15)
PMCID: 5938413
PMID: 29765315
DOI: 10.3389/fninf.2018.00020

[…] ). in this study, we used the following simulation tools: genesis/kinetikit (wilson et al., ; bower and beeman, ; bhalla and iyengar, ; bhalla, , ), gepasi (mendes, , ; mendes and kell, ), jarnac/jdesigner (sauro, , ), xppaut (ermentrout, ), simtool (aho, ), dizzy (ramsey et al., ), copasi (hoops et al., ), neuron (carnevale and hines, ), systems biology toolbox (schmidt and jirstrand, ), […]

PMCID: 5484552
PMID: 28804243
DOI: 10.1177/1177625017710941

[…] default parameterization of the model was calibrated to be representative of a statin-naïve patient with non–familial hypercholesterolemia (non-fh)., the qsp platform was developed and calibrated in jdesigner (systems biology workbench, inc., claremont, ca, usa ) using published data in accordance with rosa’s model qualification method. the base parameterization of the model, vp0, […]

PMCID: 5026379
PMID: 27636091
DOI: 10.1371/journal.pone.0162428

[…] of pbpk models we have used sbml as the specification language for the pbpk odes. the pbpk model of wambaugh and shah [] was translated into sbml using sbw tools, particularly jarnac [] and jdesigner []. (the systems biology workbench, including jarnac, is available at http://sys-bio.org/.) annotation was carried out using sbmleditor [] […]

PMCID: 4879472
PMID: 27299936
DOI: 10.1002/psp4.12071

[…] work on intracellular signaling, saez–rodriguez et al. developed apps to link cytoscape with mathematical capability in r. other graphical user interface (gui) based diagramming software, including jdesigner, celldesigner, and sbml's qualitative models package, can be integrated with mathematical tools, such as the systems biology workbench or sbml‐compatible modeling software. some biological […]

PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] specific layout and style, which follows many traditional aspects. in order to display and draw similar maps, several programs have been developed, for instance, celldesigner (funahashi et al., ), jdesigner (sauro et al., ), tinkercell (chandran et al., ), vcell (resasco et al., ), or cytoscape (shannon et al., ) with its diverse plug-ins (könig et al., ; gonçalves et al., ). we now discuss […]


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Jdesigner institution(s)
Keck Graduate Institute, Claremont, CA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
Jdesigner funding source(s)
This work was supported from the US DOE GTL Program.

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