Göksel Mısırlı

The paper presents an ontology-driven approach using LLMs to create software libraries for knowledge graphs in engineering biology, demonstrating it with the SBOL3 Ontology and sbol-script library.

The paper introduces libSBOLj3, a Java library for exchanging synthetic biology designs using the SBOLv3 standard, enabling interoperability between tools.

The paper designs a diffusion-based molecular communication system using synthetic genetic circuits and introduces a tool to optimize communication parameters for efficient cellular signal transmission.

The paper introduces Virtual Parts Repository 2, a resource for model-driven design of genetic regulatory circuits, providing modular and reusable models and a rule-based abstraction for scalable simulations.

The paper demonstrates how the SBOL standard can represent multicellular biological systems, enabling better sharing of complex designs across multiple cells.

The paper introduces the SBOL Visual 2 Ontology to standardize the mapping of genetic elements to visual glyphs, facilitating tool development and integration with biological standards.

The paper introduces SBOL-OWL, an ontology that enables machine-readable semantic representation of synthetic genetic circuits, enhancing computational tools' ability to understand and validate designs.