Improving The Plugin Interface for CellDesigner: Midterm Evaluation Edition
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Transcript of Improving The Plugin Interface for CellDesigner: Midterm Evaluation Edition
![Page 1: Improving The Plugin Interface for CellDesigner: Midterm Evaluation Edition](https://reader034.fdocuments.in/reader034/viewer/2022052622/559626551a28ab905a8b4598/html5/thumbnails/1.jpg)
Student: Ibrahim Vazirabad
Mentors: Dr. Andreas Dräger, Alex Thomas & the JSBML team
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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
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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
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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
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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
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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
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PluginCompartment-CompartmentGlyph Mapping
25 June 2014 Ibrahim Vazirabad
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PluginSpeciesAlias-SpeciesGlyph Mapping
25 June 2014 Ibrahim Vazirabad
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PluginReaction-ReactionGlyph Mapping
25 June 2014 Ibrahim Vazirabad
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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
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SBML Export/Visualization Plugin
25 June 2014 Ibrahim Vazirabad
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SBML Export/Visualization Plugin
25 June 2014 Ibrahim Vazirabad
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JTree: Layout Visualization
25 June 2014 Ibrahim Vazirabad
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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
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Thank you!
25 June 2014 Ibrahim Vazirabad