Extending the IBW Biocompilation Interface with SBOL and SBML Import/Export Capabilities

<p>The Infobiotics Workbench (IBW) is a synthetic biology design tool with three major functionalities: stochastic simulations, which mimic the procession of complex biological pathways; verification of simulation rulesets; and biomatter compilation. Its simulations are driven by designs written in the domain-specific Infobiotics Language (IBL), which contains data that is then sent to the Biocompiler to be built into a Biocompiler Model internal structure.<br> Currently, IBW offers limited support for two standard biological languages, the functionality-based Systems Biology Markup Language (SBML) and the design-based Synthetic Biology Open Language (SBOL), a common medium of exchange for synthetic devices. While SBML is made use of by the simulation aspect of IBW, the design-based SBOL is used by the Biocompiler as a format to write its compiled design into. This project aims to enhance the Biocompiler’s ability to export and import SBOL and SBML. If IBW’s capacity to work with these two biological modelling standards is improved, its accessibility to computational biologists around the world would increase dramatically. Hence, this project will enable this integration.</p>