Improving the Plug-in Interface for CellDesigner

Student: Ibrahim VazirabadMentors: Dr. Andreas Dräger, Alex

Thomas

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

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

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

PluginCompartment-JSBML Mapping

17 July 2014 Ibrahim Vazirabad

PluginSpeciesAlias-JSBML Mapping

17 July 2014 Ibrahim Vazirabad

PluginReaction-JSBML Mapping

17 July 2014 Ibrahim Vazirabad

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

1. SBML Export/Visualization Plugin

17 July 2014 Ibrahim Vazirabad

1. SBML Export/Visualization Plugin

17 July 2014 Ibrahim Vazirabad

2. JTree: Layout Visualization

17 July 2014 Ibrahim Vazirabad

CellDesigner/JSBML Synchronization

17 July 2014 Ibrahim Vazirabad

CellDesigner/JSBML Synchronization

17 July 2014 Ibrahim Vazirabad

Difficulties So Far: Reaction Text

17 July 2014 Ibrahim Vazirabad

How is Reaction text position calculated?

Difficulties So Far: PluginModel Objects

17 July 2014 Ibrahim Vazirabad

Want to check if two PluginModels are identical. How can it be done?

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

Thank you!

17 July 2014 Ibrahim Vazirabad