Improving the Plug-in Interface for CellDesigner

Student: Ibrahim VazirabadMentors: 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.

Supports SBML format.SBML lacked

layout/rendering support.CD-specific way developed.

CellDesigner model of Yeast M-Phase

28 May 2014 Ibrahim Vazirabad

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SBML Layout and Render Extension2006: Layout and Render

specifications introduced. Layout: graphical representation

of Species and Reactions (position, size).

Render: shapes, colors, line styles, line widths, text fonts, etc.

-from SBML Level 3 Package: Layout specification

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Project OverviewCD plugins: JavaPlug-in interface accesses network

information that the existing JSBML/CD plugin interface cannot import. Network layout: element position, size.Rendering information: Color of network

components, shapes, line widths/styles, etc.Ideal for assimilation via SBML Layout/Render.

Project goals: Develop CD plugin.1. Obtains CD's plugin structure and export pure

Layout/Render SBML. 2. Visualization of SBML network changes via

JTree. Synchronize changes between plug-in and

CellDesigner.28 May 2014 Ibrahim Vazirabad

-Adapted from 2011 COMBINE poster

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Proposed SpeciesAlias-SpeciesGlyph Mapping

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Current Progress: Documentation A model diagram layout extension for SBML. Gauges, R., Rost, U., Sahle, S.

& Wegner, K. CellDesigner: a process diagram editor for gene-regulatory and

biochemical networks. Funahashi, A. et al. CellDesigner Extension Tag Specification Document. Mitsui Knowledge

Industry Co., Ltd. Complementing layout information with render information in SBML

files. Gauges, R., Sahle, S., Wegner, K. JSBML: a flexible Java library for working with SBML. Dräger, A. et al. SBML Level 3 Package: Layout. Bergmann, F., Gauges, R., Sahle, S., Rost, U.,

Wegner, K. Systems Biology Graphical Notation: Activity Flow Language Mi, H. et al. Systems Biology Graphical Notation: Process Description Language.

Moodie, S. et al.

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Current Progress: JUnit TestsCreated for classes in both Layout and Render

Extension Package. Layout package:

1. TextGlyph 2. SpeciesReferenceGlyph

Render Package1. ColorDefinition2. Curve3. Ellipse4. LinearGradient5. Polygon6. Rectangle7. Text

Currently working on duplicating libSBML tests in JSBML.

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Future PlansContinue development of libSBML-quality unit

tests.Implement test plugin as described previously.Document progress and communicate with

JSBML team as necessary.

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Thank you!

28 May 2014 Ibrahim Vazirabad