SURF 2021: Modeling tools for design and analysis of synthetic biological circuits

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SURF 2020 project description

  • Mentor: Richard Murray
  • Co-mentor: Ayush Pandey


Research directions for the SURF project include:

  • Modeling of cell-free systems
  • System identification by parts, global sensitivity analysis, model decomposition, reduced models
  • Using extract and tx-tl data

We are interested in both theoretical and computational directions for this project.


  1. Tuza, Zoltan A., et al. "An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system." 52nd IEEE Conference on Decision and Control. IEEE, 2013. Link
  2. Bioscrape
  3. BioCRNpyler
  4. Sub-SBML