Biological Circuit Design

Chapters

• 0. Configuring your computer to use Python for scientific computing
• 1. Introduction to biological circuit design
• 2. Design principles governing the rate of gene expression
• 3. Sticky switches: bistability through positive feedback
• 4. Analysis of feedforward loops
• 5. Incoherent feed-forward loops serve as dosage compensators
• 6. Exact adaptation in the chemotaxis pathway
• 7. Amplification of extracellular signals
• 8. Kinetic proofreading: Multi-step processes reduce error rates in molecular recognition
• 9. Blinking bacteria: The repressilator enables self-sustaining oscillations
• 10. Uses, simplifications, and elaborations of negative feedback oscillators
• 11. Time-based regulation in cells
• 12. Molecular titration generates ultrasensitive responses in biological circuits
• 13. Promiscuous receptor-ligand interactions increase the bandwidth and specificity of cell-cell communication systems
• 14. MultiFate enables expandable and controllable multistability
• 15. The noisy, noisy nature of gene expression: How stochastic fluctuations create variation
• 16. Bursty gene expression
• 17. Cellular bet-hedging
• 18. Excitability enables probabilistic, transient differentiation
• 20. Lateral Inhibition: Spontaneous symmetry breaking to form a spatial pattern of cells
• 21. Turing patterns
• 22. Scaling reaction-diffusion patterns

Technical Appendices

• 2a. Approximate solutions to autorepressive dynamics
• 2b. Numerical solutions to ODEs with SciPy
• 2c. Interactive plotting with Bokeh
• 3a. Nondimensionalization
• 4a. Numerical solution of FFLs
• 9a. Fixed points and composite functions
• 9b. Linear stability analysis
• 9c. Numerical one-dimensional bounded root finding
• 10a. Stability diagrams by numerical computation of eigenvalues
• 10b. The Greshgorin circle theorem
• 10c. Numerical solution of delay differential equations
• 10d. Linear stability analysis of delay differential equations
• 16a. Stochastic (Gillespie) simulation
• 16b. Profiling code for speed and an application of the Gillespie algorithm

Appendices

• Appendix A: Mathematical review
• Appendix B: Introduction to Python
• Appendix C: Numerical solutions of ODES
• Appendix D: Regulatory functions and their derivatives

Package docs

• biocircuits package documentation