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Ibrahim Vazirabad
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Project Completion
I am very excited to say that my project for GSoC is complete! :) I spent 5 days in Los Angeles at COMBINE 2014. I presented on August the 20th. Presentation link and video link are below. <iframe src="//www.slideshare.net/slideshow/embed_code/38292434" wid...
Project Completion
Project Completion
jsbmlcelldesigner2014.blogspot.com
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The Final Week is here!
Hello all, I have quite a bit to report on the advancement of my project. My current checklist was as so: 1. Complete synchronization of CellDesigner plugin model and JSBML. 2. maintain map of SBases. 2. Finish Render Extension additions 3. Work on adding c...
The Final Week is here!
The Final Week is here!
jsbmlcelldesigner2014.blogspot.com
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The Final Week is here!
Hello all, I have quite a bit to report on the advancement of my project. My current checklist was as so: 1. Complete synchronization of CellDesigner plugin model and JSBML. 2. maintain map of SBases. 2. Finish Render Extension additions 3. Work on adding c...
The Final Week is here!
The Final Week is here!
jsbmlcelldesigner2014.blogspot.com
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Synchronizing CellDesigner and JSBML
Just a quick update since it is late here, but over the past week, I have been continuing with my synchronization of the JSBML/CellDesigner(CD) model representations. I have added a Map<PluginSBase, Set<SBase>>. The key is the CD object and all JSBML object...
Synchronizing CellDesigner and JSBML
Synchronizing CellDesigner and JSBML
jsbmlcelldesigner2014.blogspot.com
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Aftermath of 17/7 Meeting
I presented the slideshow below to Professor Funahashi (Akira), the main developer of CellDesigner, and my mentors at 15:00 UTC on 17/7/2014. The presentation was a success because Akira was able to provide me with inside information and clarity to my work ...
Aftermath of 17/7 Meeting
Aftermath of 17/7 Meeting
jsbmlcelldesigner2014.blogspot.com
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CellDesigner Reaction positioning and CellDesigner/JSBML synchronization
Over the past week, I have been working on two separate topics: 1. Complete algorithm that use the CellDesigner Plugin API to calculate positioning for ReactionGlyphs and SpeciesReferenceGlyphs. 2. Establish way to synchronize CellDesigner's plugin datastru...
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Calculating ReactionGlyph position in CellDesigner and new Plugin
CellDesigner does not make its Reaction position data available for developers to access. Therefore, we need to figure out how to determine Reaction size and position using our own algorithms. We have two choices: 1. Create a BoundingBox with x,y, height an...
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Midterm Presentation
Here are my slides that I presented today for the midterm evaluation meeting: Dr. Hucka linked me to some Layout Extension links that I should look into further. They are here: "* Frank wrote an online SBML layout viewer:  http://sysbioapps.dyndns.org/ Layo...
Midterm Presentation
Midterm Presentation
jsbmlcelldesigner2014.blogspot.com
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