Thursday, June 26, 2014

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:

* COPASI should support reading layout:

* There are more tools that mention SBML layout support, at"

Things are going well with my project. These are my future plans:

Saturday, June 21, 2014

Preparing for the Second Group Meeting and Project Update

After 4 hours of struggle and toil debugging my code and figuring out why CellDesigner's plugin interface was crashing: the photo below is the result. Without them, I would not have been able to work through the myriad of errors and obstacles that were appearing. Some of these errors had to do with the fact that one null pointer or any oversight caused no observable error message, but simply a dramatic failure, which is analogous to a missing nail collapsing the Empire State Building. Luckily, my mentors and I cobbled together a class that gives lots of debugging information when a plugin crashes.

As one can see from the image, TextGlyphs, ReactionGlyphs, CompartmentGlyphs, and SpeciesGlyphs have now been added to the JSBML Layout Package. This is a great first step to completing my project's aims.

The Second Group Meeting and my second presentation is on Wednesday the 25th. My first presentation went well, and I have plenty to talk about for the second presentation. I will post my presentation here soon.

Sunday, June 15, 2014

At the Cusp of Great Progress

Hello everyone,

I just committed a revision to the JSBML project, most likely the biggest since I began committing JUnit tests in early May. I:

  1. Added two more JUnit Tests to the Render Package
  2. Added UserMessages.xml in the examples/resource folder to the CellDesigner build.xml file
  3. Moved SwingWorker to its' own file
  4. AbstractCellDesignerPlugin now implements PropertyChangeListener
I did run into problems with the Ant Script in regards to adding UserMessages.xml to the CellDesigner build file. I will be asking my mentors about how to fix this issue.

I have also been developing schematics for my main project, the mapping of CellDesigner data structures to JSBML data structures. They are shown below in their (probably) final form.

1. SpeciesGlyph
 2. ReactionGlyph

3. CompartmentGlyph

Current To-Do List
  1. Suggest additions to user guide setting up JSBML development in Eclipse.  
  2. Fix UserMessages.xml problem.
  3. Begin to convert the CellDesigner plugin data structure to  JSBML data structure via a new class called convertModelLayoutPackage (or something analogous)

Monday, June 2, 2014

Render Package JUnit Tests and Schematics

May 28th was our Group Meeting, and Victor and Leandro did excellent work! :)

The Render Package JUnit tests as of June 2nd, 2014

Over the past week, I have been working on extending the coverage of the JUnit tests in the Render Extension Package. There are now 10 completed unit tests out of the 34 Render Classes. 

I am planning on making schematics of each mapping of the CellDesigner plugin interface. The image below is the first schematic of a series. It was first seen during the May 28th Presentation.

I will be making other schematics for classes in the Layout Package ReactionGlyph, TextGlyph, CompartmentGlyph, etc.

I have not been running into any problems that I have not been able to solve this week. 

I will continue my JUnit testing, and I will begin to:

Develop CellDesigner plugin.
1.Obtains CellDesigners's plugin structure and export pure Layout/Render  SBML. 
2.Visualization of SBML network changes via JTree.
Synchronize changes between plugin and CellDesigner.