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Transcript of CellDesigner 4.0 alphasbml.org › images › 2 › 21 › AkiraCellDesigner2006.pdf ·...
CellDesigner 4.0 alpha
Akira FunahashiKitano Symbiotic Systems Project, JST, ERATO-SORST8th Oct. 2006
CellDesigner+ +
CellDesigner=
+
CellDesigner
http://celldesigner.org
Import/export SBML using libSBMLGraphical notation (SBGN)Built-in simulator (SBML ODE Solver)Integrate with Analysis tool, other simulators through SBWDatabase connectionExport to PDF, PNG, etc.Freely availableSupported Environment
Windows (2000 or later)Mac OS XLinux
CellDesigner 4.0 alphaAuto-layout functionPlugin development frameworkGUI improvement
Auto-layout
uVol
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Plugin developmentDevelop plugin on EclipseCall plugin from [Plugin] menu on CellDesigner
Development environment
CellDesigner 4.0 alphaJDK 1.5.0 or 1.4.2 (for MacOSX 10.3)Eclipse (tested on 3.2.1)
LibrariesAdd following .jar files to your class path
C:\Program Files\CellDesigner4.0alpha\exec\celldesigner.jarC:\Program Files\CellDesigner4.0alpha\lib\sbmlj.jar
Documents / SamplesDocuments
documents/PluginTutorial40A.pdfdocuments/plugin/ ... Javadoc
Sample codehttp://celldesigner.org/funasample.zipsamples/plugin/src/
Example codeGet Species properties from CellDesigner
private void getSelectedSpeciesProperties() {PluginListOf lof = plugin.getSelectedSpeciesNode();if (lof != null) {
// get PluginSpeciesAliasPluginSpeciesAlias alias = (PluginSpeciesAlias)lof.get(0);
// get positiondouble x = alias.getX();double y = alias.getY();
// get SpeciesPluginSpecies sp = alias.getSpecies();String name = sp.getName();String id = sp.getId();}
}
S1
(100, 150)
Future plan
SBML L2v2 supportExport SBML Layout extensionUpdate with new SOSlib (SBML ODE Solver)Integrate with COPASICheck & support new SBW modulesImport models/kineticLaws from SABIO-RK
AcknowledgmentCellDesigner * SBI Akiya Jouraku Yukiko Matsuoka Hiroaki Kitano * MKI Norihiro Kikuchi Yusuke Tamaru * Mizuho-IR Naoki Tanimura * Univ. Vienna Rainer Machne Christoph Flamm * KGI Frank Bergmann Herbert Sauro * SRI Huaiyu Mi Anushya Muruganujan