Improving the JSBML/CellDesigner Plugin Interface: COMBINE 2014
CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira...
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Transcript of CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira...
![Page 1: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/1.jpg)
CellDesigner Tutorial
Akira FunahashiKitano Symbiotic Systems Project, JST, ERATO-SORST8th Oct. 2006
![Page 2: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/2.jpg)
Overview
Introduction of CellDesignerSBML (Systems Biology Markup Language)SBGN (Graphical Notation)
How to build a model with CellDesignerHow to create CellDesigner plugin
![Page 3: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/3.jpg)
AcknowledgmentSBML * Caltech John Doyle Michael Hucka Ben Bornstein Bruce Shapiro Ben Kovitz * Univ. Hertfordshire Andrew Finney Sarah Keating Maria Schilstra Joanne Matthews * SBI Hiroaki Kitano
SBGN Hiroaki Kitano (SBI) Yukiko Matsuoka (SBI) Michael Hucka (Caltech) Nicolas Le Novere (EBI)
CellDesigner * 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
Models Noriko Hiroi (SBI) Akiya Jouraku (SBI) Yukiko Matsuoka (SBI)
![Page 4: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/4.jpg)
Software InfrastructureModel representation
Database
Software toolsStandard representationmethod of biologicalmodels
CellDesigner
Jarnac Plot Gibson
![Page 5: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/5.jpg)
CellDesigner+ +
CellDesigner=
+
![Page 6: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/6.jpg)
SBMLSBML (Systems Biology Markup Language)A machine-readable format (XML) for representing computational models in systems biology
Compartment Species Reaction
![Page 7: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/7.jpg)
What kind of model can you express in SBML?
Focus: systems of biochemical reactions
Model can also include:CompartmentsRules/ConstraintsEvents
Many phenomena can be expressed in this form
aA+bB f([A],[B],[C],X) cCnC +oD f([C],[D],[E],Y) tE +hF
![Page 8: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/8.jpg)
What does SBML look like?
<?xml version="1.0" encoding="UTF-8"?><sbml xmlns = "http://www.sbml.org/sbml/level1" level = "2" version = "1">
<model name = "ATitle"> <listOfCompartments> </listOfCompartments> <listOfSpecies> </listOfSpecies> <listOfReactions> </listOfReactions> </model></sbml>
![Page 9: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/9.jpg)
Reactions According to SBML
Modifiers: M
Reactants: R
Products: P
‘Kinetic law’:v = f( R, P, M, parameters )
![Page 10: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/10.jpg)
What does SBML look like?
![Page 11: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/11.jpg)
Over 100 software packages support SBMLhttp://sbml.org
Applications Supporting SBML
![Page 12: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/12.jpg)
SBGNGraphical Notation for representing biological interactionsprotein-protein interaction, gene regulatory networks
Kitano, H. et al. "Using process diagrams for the graphical representation of biological networks", Nature Biotechnology 23(8), 961 - 966 (2005)
![Page 13: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/13.jpg)
Notation
![Page 14: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/14.jpg)
Examples: NFkBProcess Diagram
![Page 15: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/15.jpg)
Examples: NFkBBlock Diagram
![Page 16: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/16.jpg)
Examples: NFkBMolecular Interaction Map (Kohn Map)
![Page 17: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/17.jpg)
Examples: NFkBEdinburgh Notation
![Page 18: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/18.jpg)
SBGN communityBioModels Database
BioPAX
BioUML (Russia)
CellDesigner (Japan)
CellML (New Zealand)
COPASI (Germany)
Cytoscape (USA)
Design Suite (USA)
EPE, EPN (UK)
INOH (Japan)
JDesigner (USA)
Narrator (UK)
Panther (USA)
ProMot (Germany)
QBT (USA)
SBML Layout extension
Virtual Cell (USA)And more...
![Page 19: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/19.jpg)
Graphical notation SBMLSpecies type, Reaction type is stored in <annotation> for each species, reactionsLayout information is stored separately (just as same as SBML layout extension)
<sbml> <model> <annotation> layout information </annotation> <listOfSpecies> <species> <annotation>species type</annotation> </species> </model></sbml>
![Page 20: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/20.jpg)
<celldesigner:speciesAlias compartmentAlias="ca3" id="a3" species="s3"> <celldesigner:activity>active</celldesigner:activity> <celldesigner:bounds h="40.0" w="80.0" x="559.0" y="184.0"> </celldesigner:bounds> <celldesigner:singleLine width="1.0"></celldesigner:singleLine> <celldesigner:paint color="ffb3d2ff" scheme="Gradation"> </celldesigner:paint></celldesigner:speciesAlias>
Graphical notation SBML
![Page 21: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/21.jpg)
SBML w/ or w/o notationPure SBML (w/o notation)
w/ notation
![Page 22: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/22.jpg)
CellDesigner+ +
CellDesigner=
+
![Page 23: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/23.jpg)
CellDesigner
http://celldesigner.org
Full SBML supportGraphical 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
![Page 24: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/24.jpg)
CellDesigner 4.0 alphaAuto-layout functionPlugin development frameworkGUI improvement
![Page 25: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/25.jpg)
Auto-layout
uVol
MKKK P MKKK
MKKP
MKKP
P
MKK
MAPKP
MAPKP
P
MAPK
uVol
MKKK
P MKKK
MKK
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uVol
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MKK
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MAPK
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MAPK
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P
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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
![Page 26: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/26.jpg)
Plugin developmentDevelop plugin on EclipseCall plugin from [Plugin] menu on CellDesigner
![Page 27: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/27.jpg)
Download
Please download CellDesigner 4.0 alpha from
http://celldesigner.org/
![Page 28: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/28.jpg)
Installation
![Page 29: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/29.jpg)
DemonstrationCreate new model:
[File] → [New] → input title → [OK]
![Page 30: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/30.jpg)
TipsEnable [Grid Snap] will help you draw your model much easier
![Page 31: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/31.jpg)
Create Reaction
![Page 32: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/32.jpg)
Add Anchor PointAdd 2 anchor points to reactionDrag reaction and anchor point to change its shape
![Page 33: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/33.jpg)
Add Catalysis reaction
Add Protein “C”Add Catalysis reaction from “C” to the reaction
![Page 34: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/34.jpg)
Set Active stateSelect Protein “B”[Component] → [Set Active]
![Page 35: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/35.jpg)
Change ColorRight click on Protein “C”Select [Change Color & Shape...]
![Page 36: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/36.jpg)
CompartmentClick [Compartment] icon
Drag mouse cursor to specify its areaInput name of compartment
![Page 37: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/37.jpg)
Add Residue to ProteinCreate new model (test2)Create Protein “A”Select Protein “A” in [Proteins] TabClick [Edit] button
![Page 38: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/38.jpg)
Add Residue to ProteinClick [add] button on [Protein] dialogInput name for the residue (tst1)Click [Close] buttonClick [Update] Button
![Page 39: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/39.jpg)
Add Residue to ProteinCopy & Past Protein “A” and then draw “State Transition” arrowRight Click on “A” (right side) and select [Change Identity...]Click residue “tst1” in DialogSelect [phosphorylated] in modification
![Page 40: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/40.jpg)
Change position of ResidueSelect Protein “A” in [Proteins] TabClick [Edit] buttonClick residue “tst1” in DialogClick [edit] buttonDrag [angle] slidebar
![Page 41: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/41.jpg)
ComplexCreate new model (test3)Create Proteins “A” and “B”Copy & Paste both “A” and “B”
![Page 42: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/42.jpg)
Complex
Click [Complex] icon and create complex “C”
Drag Protein “A” and “B” into complex CDraw “Association” arrow
![Page 43: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/43.jpg)
Gene & RNACreate new model (test4)Create gene, RNA and ProteinDraw “Transcription” and “Translation”
See “geneRNA.xml” for more examples
![Page 44: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/44.jpg)
Database connectionSearch Database by Name:
SGDDBGETiHOPEntrez GeneGenome Network Platform
![Page 45: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/45.jpg)
Database connectionSearch Database by Notes:
PubMed: PMID: 123456Entrez Gene: GeneID: 4015
![Page 46: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/46.jpg)
Database connectionImport model from BioModels.net
![Page 47: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/47.jpg)
Auto layout[File] → [Open] → samples/MAPK.xml[Layout] → [Orthogonal Layout]
![Page 48: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/48.jpg)
Auto layout
uVol
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P MKKK
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P
MAPK
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Simulation (ex1)Create following biochemical reactionClick [Simulation] → [ControlPanel] and call SBML ODE Solver
d[B]/d[t] = k * [A]
k = 0.3A = 0.1B = 0
![Page 50: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/50.jpg)
Simulation (ex1)Create new model (ex1)Create reactionRight click on the reaction and select [Edit KineticLaw...]
![Page 51: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/51.jpg)
Simulation (ex1)Click [New] button on [Parameters] tab
Input values as follows:id: kname: kvalue: 0.3
d[B]/d[t] = k * [A]
k = 0.3A = 0.1B = 0
![Page 52: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/52.jpg)
Simulation (ex1)Select parameter “k”Click top most text fieldClick [copy] buttonClick [*] buttonSelect Protein “A”Click top most text fieldClick [copy] button
d[B]/d[t] = k * [A]
k = 0.3A = 0.1B = 0
![Page 53: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/53.jpg)
Simulation (ex1)Double click [initialQuantity] column for Protein “A”
Set value as 0.1
d[B]/d[t] = k * [A]
k = 0.3A = 0.1B = 0
![Page 54: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/54.jpg)
Simulation (ex1)
Click [Simulation] → [ControlPanel]Set [End Time] to 20Click [Execute] button
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Simulation (ex2)Create following biochemical reactionsExecute simulation from [ControlPanel]
A = 0.5
B = 0.2
k1 * A * Bk1 = 0.3
C = 0.01 D = 0.02
E = 0
F = 0
k2 * C k3 * Dk3 = 0.6k2 = 0.01
0 < t < 100
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Simulation (ex2)Change parameter k1 to 30.0
A = 0.5
B = 0.2
k1 * A * Bk1 = 0.3
C = 0.01 D = 0.02
E = 0
F = 0
k2 * C k3 * Dk3 = 0.6k2 = 0.01
0 < t < 100
k1 = 30.0
k1 = 0.3 k1 = 30.0
![Page 57: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/57.jpg)
Simulation (ex2)Click [Parameters] tabDouble click [Value] column for k1Change parameter k1 to 30.0
![Page 58: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/58.jpg)
Simulation (ex2)Click [Interactive Simulation] tabClick [Parameter value] radio buttonClick [Define Range] buttonClick [Max] column for k1 and set value as 3.0
Drag sliderbar for k1
![Page 59: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/59.jpg)
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Create following model on CellDesigner
Exercise
re1re2
re3 re4
re6
re10 re9
re8re7
re5
![Page 61: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/61.jpg)
Kinetic LawReaction Rate
re1 V1 * MKKK / ((1 + MAPK_PP / Ki) * (k1 + MKKK))
re2 V2 * MKKK_P / (KK2 + MKKK_P)
re3 k3 * MKKK_P * MKK / (KK3 + MKK)
re4 k4 * MKKK_P * MKK_P / (KK4 + MKK_P)
re5 V5 * MKK_PP / (KK5 + MKK_PP)
re6 V6 * MKK_P / (KK6 + MKK_P)
re7 k7 * MKK_PP * MAPK / (KK7 + MAPK)
re8 k8 * MKK_PP * MAPK_P / (KK8 + MAPK_P)
re9 V9 * MAPK_PP / (KK9 + MAPK_PP)
re10 V10 * MAPK_P / (KK10 + MAPK_P)
![Page 62: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/62.jpg)
Initial amount & parametersSpecies value
MKKK 90
MKKK_P 10
MKK 280
MKK_P 10
MKK_PP 10
MAPK 280
MAPK_P 10
MAPK_PP 10
Parameter valueV1 2.5Ki 9.0k1 10.0V2 0.25KK2 8.0k3 0.025KK3 15.0k4 0.025KK4 15.0V5 0.75KK5 15.0
Parameter valueV6 0.75KK6 15.0k7 0.025KK7 15.0k8 0.025KK8 15.0V9 0.5KK9 15.0V10 0.5KK10 15.0
![Page 63: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/63.jpg)
Simulation resultsEnd Time: 4000
![Page 64: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/64.jpg)
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Plugin development
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Plugin developmentDevelop plugin on EclipseCall plugin from [Plugin] menu on CellDesigner
![Page 67: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/67.jpg)
Development environment
CellDesigner 4.0 alphaJDK 1.5.0 or 1.4.2 (for MacOSX 10.3)Eclipse (tested on 3.2.1)
![Page 68: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/68.jpg)
How to Install PluginsCopy plugin file (.jar file) to CellDesigner’s plugin folder
Windows: C:/Program Files/CellDesigner4.0alpha/pluginMacOSX: /Applications/CellDesigner4.0alpha/plugin
![Page 69: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/69.jpg)
Sample pluginCopy sample_plugin.jar in samples/plugin/jar folder to plugin folderRestart CellDesigner
![Page 70: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/70.jpg)
Sample plugin[File] → [Open] → samples/MAPK.xml[Plugin] → [Sample Plugin1] → [Open Sample Plugin1 dialog]Select MKKK and click [GET]
![Page 71: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/71.jpg)
Sample plugin
Create new modelInput Species Information and click [ADD]
![Page 72: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/72.jpg)
How to build your pluginDownload Eclipse 3.2.1 from
http://www.eclipse.org/Launch Eclipse and specify your workspace (ex. Desktop/workspace)Click [Workbench] icon
![Page 73: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/73.jpg)
Create new project[File] → [New] → [Project]Select “Java Project” and click [Next]Input “Project name” (MyPlugin) and select [Create separate source and output folders]
![Page 74: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/74.jpg)
Import sample sourceClick [+] button next to [MyPlugin] Right click “src” folder and click [Import]Select [File system] and click [Next]
![Page 75: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/75.jpg)
Import source fileClick [Browse] button next to “From directory”Select “C:\Program Files\CellDesigner4.0alpha\samples\plugin\src” and click [OK]Click check box next to “src” folder
![Page 76: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/76.jpg)
Select Java Build PathRight click [MyPlugin] → [Properties]Click [Java Build Path] and click [Libraries] tabClick [Add External JARs] button
![Page 77: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/77.jpg)
Select Java Build PathSelect following .jar files
C:\Program Files\CellDesigner4.0alpha\exec\celldesigner.jarC:\Program Files\CellDesigner4.0alpha\lib\sbmlj.jar
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CompileImported java source files are automatically compiled and java class files are generated in the "bin" directory of your project directory
NG OK
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Generate jar filesRight click [MyPlugin] → [Export]Select [JAR file] and click [Next]
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Generate jar filesCheck your project (MyPlugin)Select [Export generated class files and resources]Specify JAR file
Put jar file to plugin folder
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How to implement pluginWrite your plugin class
extend CellDesignerPlugin classWrite an action class
extend PluginAction classCreate menu and menu item
use PluginMenu, PluginMenuItemRegister PluginMenu to CellDesigner
use addCellDesignerPluginMenu()Implement some methods to receive events from CellDesigner
![Page 82: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/82.jpg)
1. Write your plugin classYour plugin class must extend the CellDesignerPlugin class. CellDesigner will call the constructor of your plugin class to instantiate it.
public class SamplePlugin extends CellDesignerPlugin { // Constructor public SamplePlugin() {
}
}
![Page 83: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/83.jpg)
2. Write action classWrite an action class which extends the PluginAction class for an action event that would be passed when the plugin menu is selected on CellDesigner.
public class SampleAction extends PluginAction {
public SampleAction(SamplePlugin plugin) {// Write your code for constructor
}
public void myActionPerformed(ActionEvent e) {// Write your code for action event
}}
![Page 84: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/84.jpg)
3. Create menu and itemUse PluginMenu class and PluginMenuItem class to create menus on CellDesigner. Register the action class to the PluginMenuItem for CellDesigner to invoke the action.
public class SamplePlugin extends CellDesignerPlugin {// Constructorpublic SamplePlugin() {
PluginMenu menu = new PluginMenu(“Sample”);SampleAction action = new SampleAction(this);PluginMenuItem item = new PluginMenuItem(“Sample1”, action);menu.add(item);addCellDesignerPluginMenu(menu);
} }
![Page 85: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/85.jpg)
4. Register PluginMenuUse following methods to register PluginMenu to CellDesigner
addCellDesignerPluginMenu()Register menu to Plugin menu
addSpeciesPopupMenu()addReactionPopupMenu()addCompartmentPopupMenu()
Register menu to right-clicked pop-up menu
![Page 86: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/86.jpg)
5. Implement methodsImplement following methods to receive events from CellDesigner (required).
public class SamplePlugin extends CellDesignerPlugin {public SamplePlugin() {} // Constructorpublic void addPluginMenu() {} // add PluginMenu
public void SBaseAdded(PluginSBase sbase) {}public void SBaseChanged(PluginSBase sbase) {}public void SBaseDeleted(PluginSBase sbase) {}public void modelOpened(PluginSBase sbase) {}public void modelSelectChanged(PluginSBase sbase) {}public void modelClosed(PluginSBase sbase) {}
}
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Accessible informationPlugin can get following information
Selected model (SBML)PluginModel getSelectedModel()
All opened model (SBML)PluginListOf getAllModels()
Selected node on modelPluginListOf getSelectedAllNode()
All nodes on modelPluginListOf getAllSpeciesNodes()
![Page 88: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/88.jpg)
Notification from PluginYou can implement functions to add, update and delete PluginSBase in CellDesignerPlugin. The Plugin can notify CellDesigner these changes via CellDesignerPlugin interface.
notifySBaseAdded(PluginSBase sbase)notifySBaseChanged(PluginSBase sbase)notifySBaseDeleted(PluginSBase sbase)
![Page 89: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/89.jpg)
RestrictionSome actions trigger sequential actions. You have to implement the sequential actions in your plugin.
S2 S3
Example: delete species S2
S1
S3S1
S3S1
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Example codeGet Species properties from CellDesigner
private void getSelectedSpecies() {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)
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Example pluginGet SpeciesAlias info
Print out SpeciesAlias info (for debug)Change SpeciesAlias property
Change color, size, position of Proteins depend on its name (work with MAPK.xml)
Visualize InitialAmountChange color of Species when its InitialAmount < 20.0
http://celldesigner.org/funasample.zip
![Page 92: CellDesigner Tutorialcelldesigner.org/~funa/CellDesignerTutorial.pdf · CellDesigner Tutorial Akira Funahashi Kitano Symbiotic Systems Project, JST, ERATO-SORST 8th Oct. 2006. ...](https://reader031.fdocuments.in/reader031/viewer/2022030501/5aad3f207f8b9a9c2e8dfa4d/html5/thumbnails/92.jpg)