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

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SURF 2020 project description

Figure 1: Modeling and analysis tools in the synthetic biology pipeline
  • 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. Swaminathan, Anandh, et al. "Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape." (2017). Github link
  3. BioCRNPyler - Biomolecular Chemical Reaction Network Compiler : A Python toolbox to create CRN models in SBML for biomolecular mechanisms. Github link
  4. Sub-SBML : A Python based toolbox to create, edit, combine, and model interactions among multiple Systems Biology Markup Language (SBML) models. Github link