DAUIN - GR-24 - SMILIES - reSilient coMputer archItectures and LIfE Sci
Expanding our language for synthetic life design
External reference persons Leonardo Giannantoni (email@example.com)
Thesis type APPLIED, APPLIED, EXPERIMENTAL, DESIGN AND SIMULATIONS, EXPERIMENTAL - DESIGN, EXPERIMENTAL AND MODELING
Description Synthetic biology is a biology-based interdisciplinary field of study, that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature, for them to have new useful abilities. Synthetic biology is intertwined with systems biology, that is, the computational analysis and modeling of complex biological systems.
Modeling biological systems requires making different sub-domains work together, by describing them in the same model, and enabling communication between its parts.
However, different languages exist for describing biological models for each specific sub-domain.
Our research group has been working to create a unifying language able to model complex biological systems. Whereas other languages are based on the XML syntax, we chose a much more human-readable format to make the language biologist-friendly. It is designed to completely hide the underlying formalism (Nets-within-Nets), while focusing on accessibility and standardization.
Our language currently supports a limited set of primitives describing cells and some phenomena at the sub-cellular level: transcription, translation, degradation, formation of protein complexes, signaling, and regulation (through inhibition, induction and activation) of said processes.
Our source-to-source compiler (transpiler) translates these primitives into Nets-within-Nets (nested Petri nets) data structures written in python code that can be directly simulated and visualized using our simulator.
The next step now is to systematically extend our language relying on BioModels, the Registry of Standard Biological Parts, and similar repositories offering many types of biological parts and devices, organized in a hierarchy.
To this end, we expect you to expand both the grammar and the transpiler with some categories of interest.
Required skills * Languages and compiler
* Object-oriented programming
Deadline 30/10/2023 PROPONI LA TUA CANDIDATURA