Hi all,

I am very happy to present the SBML Layout. I have implemented the Prefuse algorithms to complete the SBML layout. My friend Christ Leemans has implemented the algorithm for the gpml and I have written the extension for the sbml. Previously the algorithm was unable to recognize the process node, hence it failed to execute the sbml layout. Now I made some changes which made the algorithm work with the process nodes too. Refer commit: link

The following screenshots depicts the functionality of the sbml layout:


Figure1: Before Layout.

rsz_2         Figure2: After clicking on Force directed Layout button.


Figure3: Further clicking on the same button.

rsz_4         Figure4: Demo with different file[before layout]


Figure5: After clicking on Force Directed Layout Button.



Sri Harsha.P

Hi all,

I am overjoyed to present the SBML export feature in this project. Now one can export the gpml file as sbml. Here is a brief summary about the import and export. When ever the SBML file is imported into the Pathvisio editor. It is internally converted into gpml by using SBGN PD as a bridge. Then, while exporting the gpml file should be converted back into the sbml through SBGN PD.

The following screen shots delineate the functionality of the SBML Export:


Figure 1: Importing an SBML file.


Figure 2: After importing the sbml file into the editor and clicking on export button from the file menu.


Figure 3: Saving it in a preferred location. Note:  Should select the sbml extension from the drop down.


Figure 4: Saved SBML file on the disk.



Figure 5: The output file after exporting with all the details like species,reactions,list of reactants, list of species and species references.


Sri Harsha.P