Monday, May 9, 2016

Week 3

Hi everyone!

There were couple of problems, that had to be solved.
Debugging  with Spyder was not as effective, nor comfortable for big project like this, so I set up PyCharm Community Edition, which has very robust debugging tools.
Creating UML diagrams for the SBML and JSBML extensions by hand was not effective and because of that I decided to find programs for the automatic generation of class diagrams and looked through programs such as Umbrello, ArgoUml, SmartUML and others, but in the end I installed ObjectAid for Eclipse, and Oovaide(
Here's the summary what was done during this weekend.

  1. Migrated from Spyder to PyCharm, Spyders' debugging tools are not as powerful as PyCharm.
  2. Eclipse was set up and all JSBML tests were passed.(Fig.1) 
  3. ObjectAid for Eclipse was set up for the automatic creation of  java class diagrams to aid analysis and comparison between SBML and JSBML extensions. (Fig.2)
  4. Oovaide was set up for the automatic creation of  c++ class diagrams, but it's not as powerful as ObjectAid.
    Fig.1. Passed JSBML tests.

Fig.2 ObjectAid created diagram for FBC extension


  1. Great progress, but it would be nice to see the UML diagrams in a higher resolution. Do you think you could export PDF files as well and attach them to your future posts?

    1. Yes, Dr. Bergman, for future posts I will share higher resolution PDF files.