improving the plug-in interface for celldesigner v2.6
DESCRIPTION
Presented on 17/7/2014 for a weekly group meeting with Professor Funahashi, main developer of CellDesigner.TRANSCRIPT
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Improving the Plug-in Interface for CellDesigner
Student: Ibrahim VazirabadMentors: Dr. Andreas Dräger, Alex
Thomas
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Project MotivationWhy improve CellDesigner/JSBML plugin
interface?1. Allows increased debugging capabilities.2. Harness power of CellDesigner.3. CellDesigner can become platform for JSBML
programs
17 July 2014 Ibrahim Vazirabad
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Project OverviewCellDesigner API accesses info that existing plugin
interface does not access. Layout: element position, size.Appearance: Component color, shapes, line
widths/styles, etc.
CellDesigner/JSBML model synchronization.
17 July 2014 Ibrahim Vazirabad
![Page 4: Improving the Plug-in Interface for CellDesigner v2.6](https://reader035.vdocument.in/reader035/viewer/2022081515/556175f8d8b42a171a8b4b9a/html5/thumbnails/4.jpg)
Project GoalsDevelop dual-function CellDesigner plugin.
1. Obtains CellDesigner's plugin structure and copy to JSBML structures.
2. Visualization of SBML network changes via JTree. Synchronize all changes between plugin and CellDesigner
model.
First step: map CellDesigner plugin structure to Layout/Render. PluginCompartment, PluginSpeciesAlias,
PluginReaction
17 July 2014 Ibrahim Vazirabad
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PluginCompartment-JSBML Mapping
17 July 2014 Ibrahim Vazirabad
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PluginSpeciesAlias-JSBML Mapping
17 July 2014 Ibrahim Vazirabad
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PluginReaction-JSBML Mapping
17 July 2014 Ibrahim Vazirabad
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Current Progress: Plugin Development1. Have added CellDesigner Layout data to JSBML
structure. Functions
1. SBML export/visualization2. JTree-based layout visualization
Have started work on synchronizing CellDesigner and JSBML data structures.
17 July 2014 Ibrahim Vazirabad
![Page 9: Improving the Plug-in Interface for CellDesigner v2.6](https://reader035.vdocument.in/reader035/viewer/2022081515/556175f8d8b42a171a8b4b9a/html5/thumbnails/9.jpg)
1. SBML Export/Visualization Plugin
17 July 2014 Ibrahim Vazirabad
![Page 10: Improving the Plug-in Interface for CellDesigner v2.6](https://reader035.vdocument.in/reader035/viewer/2022081515/556175f8d8b42a171a8b4b9a/html5/thumbnails/10.jpg)
1. SBML Export/Visualization Plugin
17 July 2014 Ibrahim Vazirabad
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2. JTree: Layout Visualization
17 July 2014 Ibrahim Vazirabad
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CellDesigner/JSBML Synchronization
17 July 2014 Ibrahim Vazirabad
![Page 13: Improving the Plug-in Interface for CellDesigner v2.6](https://reader035.vdocument.in/reader035/viewer/2022081515/556175f8d8b42a171a8b4b9a/html5/thumbnails/13.jpg)
CellDesigner/JSBML Synchronization
17 July 2014 Ibrahim Vazirabad
![Page 14: Improving the Plug-in Interface for CellDesigner v2.6](https://reader035.vdocument.in/reader035/viewer/2022081515/556175f8d8b42a171a8b4b9a/html5/thumbnails/14.jpg)
Difficulties So Far: Reaction Text
17 July 2014 Ibrahim Vazirabad
How is Reaction text position calculated?
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Difficulties So Far: PluginModel Objects
17 July 2014 Ibrahim Vazirabad
Want to check if two PluginModels are identical. How can it be done?
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Difficulties So Far: Batch File
17 July 2014 Ibrahim Vazirabad
@ECHO OFF MOVE /Y "C:\Users\Yusef-PC\workspace-2\JSBML\modules\celldesigner\lib\jsbml-1.0-
incl-libs.jar" "C:\Program Files (x86)\CellDesigner4.4\lib" MOVE /Y "C:\Users\Yusef-PC\workspace-2\JSBML\modules\celldesigner\dist\jsbml-
celldesigner-1.0\ExamplePlugin.jar" "C:\Program Files (x86)\CellDesigner4.4\plugin"
start "" "C:\Program Files (x86)\CellDesigner4.4\CellDesigner4.4.exe" /I
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Thank you!
17 July 2014 Ibrahim Vazirabad