Systems biology researchers study the network of molecular interactions within a biological system and publish the deduced models in a diagram format. Many XML variants were developed to represent diagrams, including SBML and SBGN. However, SBML can represent much more complex models than SBGN. For example, the SBML qual extension package can mechanistically describe events in its models, such as the relationship that A activates C, B activates C, but A and B cannot activate C at the same time. The SBGN Activity Flow language can describe a similar relationship, but the relationship is represented visually only, and therefore is not stored in its model. The incompatibilities between SBML and SBGN prevent direct comparison between the models.

In this project, I will build tools to support bidirectional conversion between SBML and SBGN, which acts as a machinery to map between SBGN-specific and SBML-specific information. SBML Layout package will be used to represent SBML diagrams, and the SBML qual package used to store the logic model.




Haoran Yu


  • Nicolas Rodriguez
  • Sarah Keating