Contract-based design for large-scale design of engineered biological systems

Large-scale design automation has been transformative in the development of modern day electronic devices like our smartphones. Can we apply similar principles to study biological networks that cause diseases like cancer? But, biological systems are unique because of their complexity and context-dependence. So, in this project, we will apply computational principles of formal system design to study biological networks composed of hundreds of interacting biomolecules. Our primary objective is to uncover insights that are experimentally elusive and to computationally investigate a vast array of design possibilities for a chosen biomolecular network.

Current Participants

  1. None

Selected references

  1. Python tool: Pacti
  2. Python tool: BioCRNpyler
  3. Incer, Inigo, et al. "Pacti: Scaling assume-guarantee reasoning for system analysis and design." arXiv preprint arXiv:2303.17751 (2023).
  4. Pandey, Ayush, et al. "From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology." bioRxiv (2022): 2022-04.
  5. Pandey, Ayush. Modeling Frameworks for Modular and Scalable Biological Circuit Design. Chapter 4 of Dissertation California Institute of Technology, 2024.


None to date

Last update: Mar 15, 2024. You can contribute to this page by creating a pull request on GitHub.