Final Infobiotics Workbench implementation of SBOL and SBML conversion functionality, UI updates, and sequence fetching. The Infobotics Workbench is available under the open source GNU GPL v3 license at http://infobiotics.org/download/download.html#source-code. Peter's contributions over the entire GSoC project are captured in this GitHub repo: h…
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Example Conversions
Biocompiler.xtend
BypassGUI.xtend
LICENSE
README.md
SBMLExportInterface.java
SBMLExportWizard.java
SBMLExportWizardPage.java
SBML_Export.java
SBOLExportInterface.java
SBOLExportWizard.java
SBOLExportWizardPage.java
SBOL_Export.java

README.md

SBML and SBOL Model Export from the Infobiotics Workbench

NOTE: The commit history only reflects the most recent changes. Most of my work was done offline since Infobiotics Workbench isn't available on Github.

The Infobiotics Workbench (IBW) is a modeling tool that provides stochastic simulations that mimic the procession of complex biological pathways, verification of simulation rulesets, and biomatter compilation. More specifically, the process of biomatter compilation (biocompilation) includes arranging biological parts, fetching their DNA sequences, inserting cloning sites, and calculating optimal ribosome-binding sites based on user constraints of positioning. Simulations and biocompilation are driven by designs written in the domain-specific Infobiotics Language (IBL).

My Work

To enhance its compatibility with biological modeling standards, I present two functions that are able to parse an Eclipse Modeling Framework model built from IBL into either a SBOL or SBML document. The SBOL model accurately captures high-level interactions and sequence and structural information, while the SBML model maintains functional components including amounts and kinetic laws. A combination of the two comprehensively captures every aspect of an IBL model. The EMF model to be converted can also be preprocessed via biocompilation or flattening, both of which I account for during conversion. The logical step forward is to implement an import functionality that will allow for the generation of IBL models from external SBOL and SBML documents.

  • Biocompiler.xtend - The original, bare-bones SBOL export code was removed from this file and the rest of the file was updated to run on the SBOL v2 library. I also implemented sequence fetching from the SynBioHub SBOL repository.
  • BypassGUI.xtend - This file now runs on the SBOL v2 library instead of v1.
  • SBMLExportInterface.java - This file interfaces between the UI and the actual SBML conversion function. It fetches the correct model resource to convert and either converts a flattened or hierarchical EMF model depending on the user's choice.
  • SBMLExportWizard.java - This file was copied from the SBOLExportWizard.java file that Laurentiu created and encodes the underlying framework for the SBML Export Wizard. I made some minor edits to the names to reference SBML instead of SBOL.
  • SBMLExportWizardPage.java - This file specifies the relevant input fields the user needs to fill in order to convert an EMF model into SBML. Laurentiu created the method headers.
  • SBML_Export.java - This file converts an EMF model into a SBML model.
  • SBOLExportInterface.java - This file interfaces between the UI and the actual SBOL conversion function. It fetches the correct model resource to convert and optionally biocompiles the EMF model before conversion.
  • SBOLExportWizard.java - Written entirely by Laurentiu Mierla. This file encodes the underlying framework for the SBOL Export Wizard.
  • SBOLExportWizardPage.java - This file specifies the relevant input fields the user needs to fill in order to convert an EMF model into SBOL. Laurentiu created the method headers.
  • SBOL_Export.java - This file converts an EMF model into a SBOL model.

Next Steps

Next steps include implementing SBOL/SBML import into IBL, but that requires creating an additional function that can convert the Eclipse Modeling Framework IBL model back into a document. Another challenge is to properly handle missing information from either the SBOL or SBML side since neither standard captures every aspect of IBL.

Running the Code

These files won't be runnable until Infobiotics Workbench is made open-source pending publication. However, you can currently access the executable software in order to use my conversion functionality. Just navigate to File->Export->SBOL/SBML.

Examples

You can access example IBL documents in the "Example Conversions" directory. Simply open one in the IBW executable and follow the previous steps to convert it into an SBML or SBOL model. The subdirectories in "Example Conversions" contain the converted versions of the IBL example documents.

Built With

Author

Read my GSoC blog, where I documented my weekly progress on this project. Feel free to reach out with any questions, comments, suggestions, bug reports, etc.

License

This project is licensed under the MIT License - see the LICENSE file for more details.

Acknowledgments

  • Harold Fellermann and Chris Myers, my mentors who advised me through the entire GSoC process
  • Laurentiu Mierla, for creating the export UI skeleton