Improving the Plugin Interface for CellDesigner v2.2

This is the Powerpoint I made for the JSBML group meeting on 28/5/2014.

1. Improving the Plug-in Interface for CellDesigner 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. Supports SBML format. SBML lacked layout/rendering support. CD-specific way developed. CellDesigner model of Yeast M-Phase 28 May 2014 Ibrahim Vazirabad 2

3. SBML Layout and Render Extension 2006: 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 28 May 2014 Ibrahim Vazirabad 3

4. Project Overview CD plugins: Java Plug-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. Obtains CD's plugin structure and export pure Layout/Render SBML.  Visualization of SBML network changes via JTree . Synchronize changes between plug-in and CellDesigner. 28 May 2014 Ibrahim Vazirabad 4 -Adapted from 2011 COMBINE poster

5. Proposed SpeciesAlias - SpeciesGlyph Mapping 28 May 2014 Ibrahim Vazirabad 5

6. 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. 28 May 2014 Ibrahim Vazirabad 6

7. Current Progress: JUnit Tests Created for classes in both Layout and Render Extension Package. Layout package: TextGlyph SpeciesReferenceGlyph Render Package ColorDefinition Curve Ellipse LinearGradient Polygon Rectangle Text Currently working on duplicating libSBML tests in JSBML. 28 May 2014 Ibrahim Vazirabad 7

8. Future Plans Continue development of libSBML-quality unit tests. Implement test plugin as described previously. Document progress and communicate with JSBML team as necessary. 28 May 2014 Ibrahim Vazirabad 8

9. Thank you! 28 May 2014 Ibrahim Vazirabad 9