This document discusses a project to improve the interface between the Java library JSBML and the biochemical network modeling software CellDesigner. The goals are to 1) import CellDesigner's layout and rendering information into JSBML using SBML extensions, 2) complete synchronization between model changes in CellDesigner and JSBML, and 3) develop plugins to visualize the new capabilities. Progress includes exporting CellDesigner layouts to JSBML and visualizing them, as well as updating JSBML models based on events from CellDesigner. Future work involves implementing additional rendering features and improving reaction positioning.

1. Ibrahim Vazirabad
20-8-2014

2. What is JSBML?
 Java library to read/write/manipulate
SBML files.
 Offers full platform independence.
 CellDesigner plugin interface.
20 August 2014 Ibrahim Vazirabad
CellDesigner model and JSBML plugin
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3. What is CellDesigner?
 CellDesigner is a process diagram
editor for biochemical networks.
 One of most frequently used tools
in systems biology.
 Accesses many SBML model
databases: BioModels, PANTHER.
 Function augmentation: plugins
 Essential for project.
20 August 2014 Ibrahim Vazirabad
-CellDesigner sample file: M_phase.xml
-PANTHER logo: http://www.pantherdb.org/
-BioModels logo: http://www.ebi.ac.uk/biomodels-main/
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4. SBML Layout and Render Extension
 Pre-L3 SBML, no way to specify network
layout or appearance.
 2006: Layout and Render packages proposed.
1. Layout: element position, size.
2. Render: colors, shapes, line widths, etc.
 CellDesigner has own specification.
 Would like to connect both SBML’s and
CellDesigner’s specifications.
-from SBML Level 3 Package: Layout
specification
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5. Project Motivation
 Why improve CellDesigner/JSBML plugin interface?
1. JSBML users: harness model layout power of CellDesigner.
2. CellDesigner users: access diverse suite of JSBML tools.
3. Plugin developers: Interface can ease plugin development.
 Looking to improve a good thing.
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6. Project Overview
1. CellDesigner provides non-accessed layout/render
information.
 Want to import these attributes via Layout/Render.
2. CellDesigner/JSBML model synchronization was incomplete.
1. JSBML notified CellDesigner of core Model changes.
2. CellDesigner  JSBML unimplemented.
 When CellDesigner sends events, need to update JSBML Model.
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7. Project Goal
 Develop small collection of CellDesigner plugins.
1. Visualize Layout/Render data additions from CellDesigner.
2. Visualize synchronization from CellDesigner to JSBML.
 1st step: map CellDesigner plugin interface to Layout/ Render.
 PluginCompartment, PluginSpeciesAlias, PluginReaction
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8. PluginCompartment-JSBML Mapping
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9. PluginSpeciesAlias-JSBML Mapping
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10. PluginReaction-JSBML Mapping
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11. CellDesigner Plugin Creation
 To create plugin, implementation of only two abstract classes required.
 Once implemented, link formed between JSBML and CellDesigner.
 Easily make JSBML application into CellDesigner plugin.
AbstractCellDesigner
Plugin
CellDesigner
Loads
on start
Declares
Invokes
Calls
-Schematic: Dräger 2014
AbstractCellDesigner
PluginAction
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12. Project Progress
1. Imported CellDesigner Layout data into JSBML.
1. SBML file export plugin.
2. Tree-based Layout visualization plugin.
2. CellDesignerJSBML synchronization completed.
 Tree-based SBML visualization plugin.
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13. SBML File Export Plugin
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-CellDesigner sample file: MAPK.xml
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14. Layout Visualization: MAPK Pathway
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-CellDesigner sample file: MAPK.xml
Visualized by SBML Layout Viewer
URL: sysbioapps.dyndns.org/Layout
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15. Layout Visualization: De novo nucleotide biosynthesis
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-PANTHER Model: De novo pyrimidine deoxyribonucleotide biosynthesis
Visualized by SBML Layout Viewer
URL: sysbioapps.dyndns.org/Layout
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16. Layout Visualization: E. coli TCA Cycle
20 August 2014 Ibrahim Vazirabad
BioModels Model #: BIOMD0000000222
Visualized by SBML Layout Viewer
URL: sysbioapps.dyndns.org/Layout
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Layout information has been translated to JSBML.

17. CellDesigner/JSBML Synchronization
20 August 2014 Ibrahim Vazirabad
 CellDesigner plugins sends notifications when:
1. SBaseAdded()
2. SBaseChanged()
3. SBaseDeleted()
4. modelOpened()
5. modelSelectChanged()
6. modelClosed()
 To understand further, created plugin that receives/prints
events.
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18. CellDesigner/JSBML Synchronization
20 August 2014 Ibrahim Vazirabad
-CellDesigner sample file: MAPK.xml
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Four reactions, one species.
J6, J7 changed, J3, J4
deleted in addition.
One user action, many events sent.
Update JSBML Model accordingly.

19. CellDesigner/JSBML Synchronization
20 August 2014 Ibrahim Vazirabad
-CellDesigner sample file: MAPK.xml
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Synchrony maintained between CellDesigner and JSBML.

20. Next Steps/Further Work
1. Render Extension additions are not implemented.
a) JSBML bug prevented Render Extension from being implemented.
b) Good news: bug fixed!
2. Reaction positioning algorithm issues:
1. Guesswork involved in finding the process node.
2. Updated CellDesigner plugin interface released on Sunday.
3. Synchronize Layout Extension changes from JSBML to
CellDesigner.
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21. Project Discussion
 Once completed, hope that it will make the interface
between CellDesigner and JSBML very fluid.
 Will provide a way to communicate between generic
functionality of JSBML and visualization function of
CellDesigner.
 With improvements, it will be a polished addition to
current JSBML-CellDesigner bridge.
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22. Acknowledgements
Mentors:
Dr. Andreas Dräger
Alex Thomas
Dr. Akira Funahashi
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Funding: Thank you!
Questions?