The second week of coding period is completed and I have successfully completed two tasks in this week.

The task for the second week is Validation of the SBML file:

In simple words, successful completion of this task helps us to validate an imported sbml file and gives us the information such as warnings and errors occurred in that particular sbml file. This validation gives us a detailed analysis as to which particular elements in the model are not diagrammed according to the sbml standard.

The task involves adding an Validate button to the main pane of the PathVisio editor. When ever the validate button is pressed, a validate dialog box containing button pane [open and validate file buttons] and output pane is opened. The open button is equipped with the file chooser action, hence when the open button is pressed the file chooser event is invoked which allows us to select the sbml file. Here the file chooser is written such that it even filters the files which can be chosen (here .sbml and .xml ).

The status bar in the dialog box shows which file is chosen. When the “validate the file” button is clicked ,the validate method is invoked and  the output is showed. Currently the output is shown in the console of the eclipse, but it should be shown in the output pane of the dialog box. Refer: ValidatePanel.java

The following figures depicts the functionality:

validation

validateclick selected file outputonconsole

Note: The sbml file is taken from http://www.ebi.ac.uk/biomodels-main/BIOMD0000000002

The next blog post depicts the third task.

 

Cheers,

Sri Harsha.P

One thought on “Validation of SBML File

  1. I am actually satisfied with your way with words-at all as well as with the layout on your web site. Is that this the paid style or did you customize it your self? In any case continue the nice good quality posting, it really is unusual to see a fantastic weblog exactly like it these days.

    Reply

Leave a reply

<a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <s> <strike> <strong> 

required