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

MKKK P MKKK

MKKP

MKKP

P

MKK

MAPKP

MAPKP

P

MAPK

uVol

MKKK

P MKKK

MKK

P

MKK

P

P

MKK

MAPK

P

MAPK

P

P

MAPK

uVol

MKKK

P MKKK

MKK

P

MKK

P

P

MKK

MAPK

P

MAPK

P

P

MAPK

uVol

MKKK P MKKK

MKK

P

MKK

P

P

MKK

MAPK

P

MAPK

P

P

MAPK

uVol

MKKKP MKKK

MKKP

MKK

P

P

MKK

MAPKP

MAPK

P

P

MAPK

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