Hi everyone!
Summer of Code is finally coming to an end. The official “pencils down” date is the 29th, so a great deal of the work I’ve been doing this past week has been testing my code and creating documentation. You can find my final project at https://github.com/BoyDun/IBW_SBML_SBOL_Export. The Repressilator SBML model produces a nicely oscillating graph when simulated in iBioSim, and you can run it for yourself with the converted file I included in the “Example Conversions” folder. My repository contains every file in IBW that I’ve created or modified, but since Infobiotics Workbench will be open-source pending publication, my code isn’t runnable by itself. However, I’ve included a link to the IBW executable in the README, where you can run the compiled program and look for my feature under File->Export->SBML/SBOL.
The logical next step in a hypothetical extension to this project would be to allow for the import and conversion of SBOL and SBML models into IBL documents, but that would require implementing a function that can convert the Eclipse Modeling Framework IBL model back into a document. Another challenge would be to properly handle missing information from either the SBOL or SBML side since neither standard captures every aspect of IBL.
As for me, I’m hoping to present my work at COMBINE, an annual conference coordinating the development of systems biology standards. Additionally, after discussing with my mentors, I’m happy to say I will be continuing my work with the Infobiotics Workbench, although at a much reduced pace due to academic obligations during the school year.
And I think that about sums up my experience this summer – if you want to reach out for whatever reason, feel free to do so at bodun@stanford.edu. Other than that, see you maybe next summer 🙂
Regards,
Peter