Websites, Software, and Other Products Generated by Our Research Group

• TBNExplorer2: Python framework and CLI tools for computing concentrations of Thermodynamic Binding Networks (TBNs).
• COFFEE: Convex Optimization For Free Energy Equilibria online tool. Efficient determination of chemical equilibrium of monomer-polymer systems given concentrations of monomers and free-energies of polymers [command line tool].
• Concentrat.io: online tool for computing free energies and concentrations of domain-level DNA designs.
• StableGen: online tool for answering questions about stable configurations of a Thermodynamic Binding Network [related paper, command line tool].
  For large problem instances, we recommended using David Haley's command line tool.
  (Legacy: a restricted set of functionalities is available as the TBNSolver Mathematica package.)
• Many Worlds Intervention: project to test how the belief in parallel universes can affect you psychologically.
  YouTube video on the Many Worlds Interpretation of Quantum Mechanics.
  Also a simple Universe Splitter.
• CRNSimulator: Mathematica package for deterministic and stochastic simulation of Chemical Reaction Networks.