Student: Ibrahim Vazirabad

Mentors: Dr. Andreas Dräger, Alex Thomas & the JSBML team

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

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

Testing JSBML Extension Packages Layout package:

1. TextGlyph

2. SpeciesReferenceGlyph

Render Package1. ColorDefinition

2. Curve

3. Ellipse

4. GraphicalPrimitive1D

5. GraphicalPrimitive2D

6. LinearGradient

7. Polygon

8. Rectangle

9. RenderCubicBezier

10. Text

25 June 2014 Ibrahim Vazirabad

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

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

PluginCompartment-CompartmentGlyph Mapping

25 June 2014 Ibrahim Vazirabad

PluginSpeciesAlias-SpeciesGlyph Mapping

25 June 2014 Ibrahim Vazirabad

PluginReaction-ReactionGlyph Mapping

25 June 2014 Ibrahim Vazirabad

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

SBML Export/Visualization Plugin

25 June 2014 Ibrahim Vazirabad

SBML Export/Visualization Plugin

25 June 2014 Ibrahim Vazirabad

JTree: Layout Visualization

25 June 2014 Ibrahim Vazirabad

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

Thank you!

25 June 2014 Ibrahim Vazirabad