This is the Powerpoint I made for the JSBML group meeting on 25/6/2014.

1. Student: Ibrahim Vazirabad
Mentors: Dr. Andreas Dräger, Alex
Thomas & the JSBML team

2. What is CellDesigner?
 CellDesigner (CD) is a process
diagram editor for biochemical
networks.
 Since its release, supports SBML
format.
 SBML lacked layout/rendering
support.
 CD developers created own way.
CellDesigner model of Yeast M-Phase
25 June 2014 Ibrahim Vazirabad

3. SBML Layout and Render Extension
 2006: Layout and Render packages
proposed.
 Layout: position, size of network
components
 Render: appearance, shapes, colors, line
styles, text fonts, etc.
-from SBML Level 3 Package: Layout
specification
25 June 2014 Ibrahim Vazirabad

4. Testing JSBML Extension Packages
 Layout package:
1. TextGlyph
2. SpeciesReferenceGlyph
 Render Package
1. ColorDefinition
2. Curve
3. Ellipse
4. GraphicalPrimitive1D
5. GraphicalPrimitive2D
6. LinearGradient
7. Polygon
8. Rectangle
9. RenderCubicBezier
10. Text
25 June 2014 Ibrahim Vazirabad

5. Project Overview
 CD functions extended by plugins.
 Plugin interface accesses info that existing JSBML/CD
plugin interface cannot import.
 Layout: element position, size.
 Appearance: Component color, shapes, line widths/styles, etc.
 Ideal for addition via SBML Layout/Render.
25 June 2014 Ibrahim Vazirabad

6. Project Goals
 Develop dual-function CD plugin.
1. Obtains CD'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 CD plugin structure to Layout/Render.
 PluginCompartment, PluginSpeciesAlias, PluginReaction
25 June 2014 Ibrahim Vazirabad

7. PluginCompartment-CompartmentGlyph Mapping
25 June 2014 Ibrahim Vazirabad

8. PluginSpeciesAlias-SpeciesGlyph Mapping
25 June 2014 Ibrahim Vazirabad

9. PluginReaction-ReactionGlyph Mapping
25 June 2014 Ibrahim Vazirabad

10. Current Progress: Plugin Development
 Have cloned CD’s plugin structure and added Layout
data to JSBML structure.
 Functions
1. SBML export/visualization
2. JTree-based layout visualization
25 June 2014 Ibrahim Vazirabad

11. SBML Export/Visualization Plugin
25 June 2014 Ibrahim Vazirabad

12. SBML Export/Visualization Plugin
25 June 2014 Ibrahim Vazirabad

13. JTree: Layout Visualization
25 June 2014 Ibrahim Vazirabad

14. Future Plans
 Implement Render Extension Package cloning as described
previously.
 Synchronize CD model/SBML struct; Visualize real-time
network changes in JTree.
 Document progress and communicate with JSBML team as
necessary.
25 June 2014 Ibrahim Vazirabad

15. Thank you!
25 June 2014 Ibrahim Vazirabad